[xls]media.nature.com · web view16p13.3-p13.13 xeroderma pigmentosum (f) ercc5 excision repair...

Supplementary Data 2: Manually annotated single-nucleotide polymorphisms (SNPs) and structural variants (SVs)

6-11. SVs in the different cell lines

Lists of SNPs and SVs that were manually verified for their potential presence and effect in the 293 genomes. For the SNPs, we filtered the variants obtained by the CG SNP caller based on their presence in dbSNP, and annotated whether they were present in segmentally duplicated genome regions (UCSC Genome Browser). Additionally, SNPs located in the protein coding region were analyzed with SIFT to predict the impact of the non-synonymous sequence changes on protein function. For the SVs, only the new SVs (subtracted from SVs previously reported in human genome sequences) and those not present in the 293 line (except for the list of SVs in 293) were considered. Here also, we specifically verified genes that often undergo structural rearrangements in cancer (via COSMIC). This resulted in a set of lists with the following content:

1. Novel common homozygous: homozygous SNPs, found in coding regions of genes, that are present in all 6 sequenced HEK293 cell lines and are not present in dbSNP (and therefore novel).

2. Known common homozygous: homozygous SNPs, found in coding regions of genes, that are present in all 6 sequenced HEK293 cell lines and can be found in dbSNP.

3. Novel + known unique homozygous: homozygous SNPs, found in coding regions of genes, unique for that particular cell line. These include SNPs from dbSNP as well as novel SNPs.

4. SNPs in cancer genes: all SNPs, heterozygous and homozygous, found in coding sequences of genes often involved in cancer (according to COSMIC), in any of the 6 cell lines. Evidence of CNV involving these genes is also added if present.

5. SNPs in DNA repair/cell cycle genes: all SNPs, heterozygous and homozygous, found in coding sequences of genes involved in DNA replication and repair (KEGG pathways hsa03030, hsa03410, hsa03430, has 03450) or the cell cycle (KEGG pathway hsa04110), in any of the 6 cell lines.

12. SVs in cancer genes: SVs involving genes that have been correlated with mutations in cancer.

# Gene of lower interest (white)# Gene of high interest (orange)Gene symbol Splice variant mRNA acc SNP numb Type of SNP Specifics Notes chr start end protein Pos 0 means novel

1 CC2D2A 1 1038934 deletion of codon del of Glu 4 15122111 15122114 228 2

2 HSP90B1 - NM_003299.1 3003072 deletion of codon del of Glu 12 102865326 102865329 790 2

3 FAM38A - 3614389 deletion of codon del of Lys prob 16 87315112 87315115 1917 2

4 LDLR all NM_000527.2 3885508 del of Ser 19 11101334 11101337 845 0

NM_001080522.1

-polyE region of exon 9, removes one E in string of 4+4 Es, impact probably low. Function: role in cilia formation, expressed widely in CNS, null mice have randomized left-right axis and various cilia defects. Mutations in this gene correlated with Joubert syndrome type 9 and Meckel syndrome type 6.

-heterozygous in file but probably homozygous because of string of Es (4, in exon 17) and mismapping. ER-residing chaperone of the Hsp90 family.

XM_001714598.1

-heterozygous for T, A and Flp according to file and homo for the rest, but could be a mapping error. Again in region with string of charged AA, here KKRRR where middle K is deleted in exon 39. Probably also not novel, just small mapping difference. Is mechanosensitive ion channel, so one would expect the charged residues to be important, but structure is unknown.

-heterozygous in A and Flp, homo in the rest (pretty clear). In any case deletion of Ser. Anyhow, it is in exon 17, almost completely at the end of the CDS.

5 GPR112 in most NM_153834.3 4313238 deletion of codon del of Asp X 135302110 135302113 2656 0

6 ALPK2 all NM_052947.3 3822073 deletion + change 18 54355371 54355390 1002 18

7 1 28781173 73

8 GBP5 all NM_052942.2 132753 deletion del of C 1 89502154 89502155 404 0

9 CCR5 all 788917 deletion del of 32 bases 3 46389950 46389982 184 31

10 CLDN16 - NM_006580.2 1001121 substitution GG became C 3 191588766 191588768 54 1

-Clearly homozygous in all, and probably NOT novel because its a DD motif, and the reported SNP was the deletion of the second D (here mapped to first D). GPCR of neuroendocrine cells.

del of 15 bases, change of 3

-Most probable change in exon 5 (biggest exon present in both splice variants): RETEDTS to RL, but does coincide with known SNP causing frameshift with EDTSTV to V. Is a kinase recognizing P-sites but weirdly no function known, no disease corr, no GO annotation, only mentioned in large-scale cDNA sequencing projects, though conserved in other mammals.

LOC10013287

completely unannotated gene locus, no info anywhere.- Heterozygous in all lines, deletion causes frameshift in exon 9 of 11 and premature stop of gene. IFN-inducible member of guanylate cyclase family.

NM_001100168.1

-deletion heterozygous in all, and present in dbSNP, removes about 100 AA from end of protein in both splice variants.-hetero in all lines and not novel

11

12 C11orf40 - NM_144663.1 2629788 insertion AG 11 4549286 4549286 199 0

13 OR8I2 - 2720016 deletion of T 11 55617855 55617856 165 0

14 OR8I2 - 2720018 deletion of A 11 55617882 55617883 174 0

15 OR8I2 - - SNP G iso A 11 55617873 171 0

16 OR5M10 - 2721454 deletion del of 8 bases 11 56101421 56101429 115 7

Lots of loci with gene symbol "LOCxxxxxx", but cannot find any annotation for it in any database, unexistent in refseq.

-heterozygous in all, not novel since present in dbSNP, end of last exon (number 4), causes frameshift in last 20 aa

NM_001003750.1

-single exon olfactory receptor of GPCR family. NOVEL, causes frameshift and premature stop.

NM_001003750.1

-NOVEL, causes SECOND frameshift and only 9 AA downstream of first one, also heterozygous in all lines. Expect a third inactivating one? Are those both on 1 allele or not?

NM_001003750.1

`-heterozygous in all lines, in between the two deletions.

NM_001004741.1

-heterozygous in all lines, NOVEL, causes frameshift and premature stop, so 200 AA downstream (of the 315 total). Gene is olfactory receptor family, one exon, present in the intron of another OR gene (OR8U8) in other orientation.

17 TRPC6 - NM_004621.4 2789327 insertion TG 11 100880546 100880546 122 0

18 MRO all 4 NM_031939.2 3809936 deletion AG 18 46585611 46585613 113 0

19 IFI27 all 2 NM_005532.3 3340301 insertion 14 93651886 93651886 42 0

20 TMEM37 - NM_183240.2 524766 insertion 2 119911121 119911121 69 0

21 AGRN - NM_198576.2 679 SNP 1 970730 970731 833 0

22 TAS1R - NM_152232.2 30818 SNP 1 19056661 19056662 77 0

23 HSPG2 - NM_005529.5 35620 SNP 1 22049229 22049230 2445 0

-heterozygous in all lines, causes frameshift, NOVEL SNP, causes frameshift and stop (exon 2 of 13, of about 900 aa). Receptor-activated Ca2+ channel in PM. Defects in this gene are a cause of focal segmental glomerulsclerosis.

-Maestro gene is only transcribed in maels before and after testis differentiation, so prob not imp here. Homozygous in all except A and T. Prob causes frameshift from the middle of the protein till end.

of 6 bp or AMA aa

-Insertion of 3 AA at the beginning of exon 4, of both splice variants. Supp homozygous in all lines, is gene involved in IFN-induced apoptosis, promoting cell death.

of 6 bp so T changes to SVP

-heterozygous in all lines in exon 2. Calcium-channel, neuronal.

A iso G, missense R to Q

-heterozygous in all, neuronal aggregating factor crucial for neuromuscular junciton.

A isoG, missense A to T

-putative taste receptor, but again heterozygous in all lines, novel though.

A iso G, missense S to L

- heterozygous in all. Novel SNP. component of glomerular basement membrane, attachment substrate, cross-links many cell-surface molecules.

24 SEPN1 all 2 NM_206926.1 42857 SNP 1 26007847 26007848 208 0

25 ZNF643 - NM_023070.1 62487 SNP 1 40701555 40701556 335 0

26 KIAA0467 - NM_015284.2 66916 SNP 1 43672651 43672652 1038 0

27 USP1 all 3 91054 SNP 1 62688877 62688878 665 0

28 KIAA0460 - NM_015203.2 189680 SNP 1 148683386 148683387 164 0

29 ZNF687 - NM_020832.1 191043 SNP 1 149525736 149525737 115 0

30 SELP NM_003005.3 219562 SNP 1 167838917 167838918 558 0

31 PCNXL2 - NM_014801.3 318895 SNP 1 231342215 231342216 1175 0

32 KCNK1 - NM_002245.2 319997 SNP 1 231869119 231869120 170 0

33 FLJ34931 - 395637 SNP 2 29148568 29148569 687 0

34 TTC27 - NM_017735.3 401292 SNP 2 32891167 32891168 763 0

35 TMEM166 all 2 NM_032181.1 470728 SNP 2 75574144 75574145 61 0

T iso C , missense P to L

-heterozygous in all lines, changes a P of a poly-P region (4 Pro) in L. Selenoprotein with selenocysteine in active site, related to congenital muscular dystrophies.

G iso A, missense Q to R

-heterozygous in all lines, novel, putative TF

C iso T, missense I to T

-heterozygous in all lines, novel, stimulates SOD activity in dorsal root ganglia

NM_001017416.1

G iso A, missense I to V

-heterozygous in all lines, novel, is a deubiquitylating enzyme in cytoplasm

T iso C, missense R to C

-heterozygous in all lines, novel, unknown function, but brainrelated prob

A iso G, missense G to R

-heterozygous in all lines, novel, unknown TF function

A iso G, missense R to T

-heterozygous in all lines, novel, leukocyote adhesion to endothelium, binds, sialylated Lewis epitopes

A iso G, missense H to Y

-heterozygous in all lines, novel, unknown role, may play role in tumorigenesis of colorectal carcinoma's with high microsatellite instability

A iso G, missense R to H

-heterozygous in all lines, novel, weak K-channel with no activity on its own

NM_001029883.1

T iso C, missense C to Y

-heterozygous in all lines, novel, highly expressed protein in photoreceptor cells, and missense and nonsens mutations of this gene have been associated with retinitis pigmentosa.

A iso G, missense A to T

-heterozygous in all lines, novel, unknown role, but tetratricorepeat domain

T iso C, missense D to Y

-heterozygous in all lines, novel, role in autophagy and apoptosis

36 POLR1A - NM_015425.3 485539 SNP 2 86170522 86170523 157 0

37 KCNIP3 all 2 NM_013434.4 493318 SNP 2 95411914 95411915 206 0

38 TANC1 all 2 NM_033394.1 584287 SNP 2 159736938 159736939 470 0

39 COL6A3 in 5 variants NM_057164.2 701951 SNP 2 237954718 237954719 491 0

40 COL6A3 all 5 NM_057164.2 701952 SNP 2 237954722 237954723 490 0

41 LRRN1 - NM_020873.5 720447 SNP 3 3861664 3861665 113 0

42 EXOG all 2 NM_005107.2 777379 SNP 3 38523412 38523413 198 0

43 SLC9A10 - NM_183061.1 886534 SNP 3 113370819 113370820 988 0

44 CCDC52 - NM_144718.2 888973 SNP 3 114655237 114655238 635 0

45 RYK all 2 919601 SNP 3 135377160 135377161 521 0

G iso C, missense R to P

-heterozygous in all lines, novel, catalytic core SU of RNA polI for ribosomal transcription

T iso C, missense R to W

-heterozygous in all lines but uncalled in EndoT, novel, K-channel regulating neuronal excitability

G iso T, missense S to R

-heterozygous in all lines, no call in RicR, novel, tetratricorepeat protein, poss role in postsynaptic density

C iso G, missense T to S

-heterozygous in all lines, novel, part of alpha chain of collagen type 6

G iso C, missense D to H

-HET in all lines, novel, part of alpha chain of collagen type 6

G iso A, missense G to R

-heterozygous in all lines, novel, Negatively regulates 4-1BB signaling, which results is NFkB and JNK activation. A role in T cell actrivation.

T iso G, missense L to V

-heterozygous in all lines, novel, Endonuclease G-like 1, mitochondrial endo/exonuclease involved in apoptosis and in normal proliferation.

A iso G, missense C to R

-heterozygous in all lines, novel, Sperm specific sodium Hydrogen exchanger needed for sperm mobility.

T iso G, missense Q to P

-heterozygous in all lines, novel, Regulator required for centriole duplication for proper bipolar spindle formation and congression in mitosis.

NM_001005861.2

G iso C, missense F to L

-heterozygous in all lines, novel, May be coreceptor (with FZD8) of Wnt proteins. Involved in neuron differentiation, axon guidance,…

46 TXNDC6 - NM_178130.2 925468 SNP 3 139505121 139505122 220 0

47 GPR149 - 950315 SNP 3 155629756 155629757 113 0

48 HERC6 all 2 NM_017912.3 1124367 SNP 4 89557713 89557714 557 0

49 SPRY1 all 2 NM_199327.1 1162619 SNP 4 124542281 124542282 28 0

50 PCDH18 - NM_019035.3 1178173 SNP 4 138670255 138670256 812 0

51 DCHS2 1 out of 2 NM_017639.2 1195981 SNP 4 155377539 155377540 2116 0

52 ODZ2 - 1493980 SNP 5 167621700 167621701 2305 0

53 LOC643201 - XM_932161.3 1506627 SNP 5 175542885 175542886 20 0

54 ICA1 all 3 NM_022307.2 1811572 SNP 7 8224512 8224513 175 0

C iso T, missense R to Q

-heterozygous in all lines no call in SG, novel, Low level presence in lung, brain and testis. Microtubule associated, may be a regulator of microtubule physiology.

NM_001038705.1

G iso C, missense C to W

-heterozygous in all lines, novel, GPCR 149. Orphan GPCR (?) from family 1.

A iso G, missense N to S

-homozygous in all lines, novel, putative E3 ubiquitin protein ligase.

A iso G, missense Y to C

-homozygous in all lines, novel, May function as an antagonist of fibroblast growth factor (FGF) pathway

C iso T, missense V to M

-homozygous in all lines, novel, Protocadherin 18. Potential calcium-dependent cell-adhesion protein.

A iso C, missense S to A

-homozygous in all lines, novel, Protocadherin 23. Calcium-dependent cell-adhesion protein expressed in cerebral cortex and testis.

NM_001080428.2

A iso G, missense I to V

-HOM in A and Flp, others HET, novel, Teneurin 2. May function as a cellular signal transducer. Tissue specific expression.


-Not annotated, Hypothetical protein inferred from electronical annotation

C iso T, missense V to M

-HOM in T, others HET, novel, Islet autoantigen 1. May play a role in neurotransmitter secretion.

55 NACAD - XM_166571.6 1875182 SNP 7 45091992 45091993 226 0

56 PILRA all 3 NM_013439.2 1952589 SNP 7 99809670 99809671 44 0

57 EXOC4 1 out of 2 NM_021807.3 1997987 SNP 7 133152750 133152751 549 0

58 SORBS3 all 2 NM_005775.4 2100902 SNP 8 22482725 22482726 475 0

59 RAB11FIP1 all 2 2123694 SNP 8 37851382 37851383 476 0

G iso A, missense A to V

-HOM in T, HET in others, no call in A, novel. NAC-alpha-domain containing protein. May prevent inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum. May bind to nascent polypeptide chains as they emerge from the ribosome and block their interaction with the signal recognition particle, which normally targets nascent secretory peptides to the ER. May also reduce the inherent affinity of ribosomes for protein translocation sites in the ER membrane. BUT, normally this function is also performed by NACA1 and 2

A iso G, missense M to V

-HOM in T, HET in all others, novel. Paire IgG-like type 2 receptor alpha. Immune regulation function.

G iso A, missense G to R

-HOM in T, HET in all others, novel. Exocyst complex component 4. Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane. Related to Testis development?

C iso T, missense R to C

-heterozygous in all lines, novel, Vinexin. Role in cytoskeleton.

NM_001002814.1

G iso A, missense S to L

-heterozygous in all lines, novel, Rab 11 family interacting protein. Rab 11 effector involved in phagocytosis and endosomal recycling.

60 STK3 - NM_006281.2 2202267 SNP 8 99848763 99848764 39 0

61 VPS13B NM_017890.3 2202795 SNP 8 100860333 100860334 2584 0

62 SPAG1 all 2 NM_172218.1 2203061 SNP 8 101314891 101314892 688 0

63 TG NM_003235.4 2247531 SNP 8 133992912 133992913 1370 0

64 GOLM1 all 2 NM_016548.2 2372882 SNP 9 87840197 87840198 306 0

65 BAAT all 2 NM_001701.2 2394336 SNP 9 103173098 103173099 136 0

66 MKX - NM_173576.1 2494652 SNP 10 28063693 28063694 178 0

C iso T, missense S to N

-heterozygous in all lines no call in SG, novel, Serin or Threonin protein kinase 3. Stress-activated, pro-apoptotic kinase which, following caspase-cleavage, enters the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation.

2 out of 5, long isoforms

G iso A, missense E to K

-heterozygous in all lines, novel, Vacuolar protein-sorting associated protein 13B. May be involved in protein sorting in post Golgi membrane traffic. Widely expressed.

G iso A, missense G to E

-heterozygous in all lines, novel, Sperm associated antigen 1. GTPase that plays a role in fertility.

1 out of 4, long isoform

G iso A, missense R to Q

-HOM in S, SG and SGendoT, HET in others, novel. Thyroglobulin, Thyroxine and triiodothyronin precursor.

G iso A, missense S to L

-HOM in Flp, HET in all others, no call in A, novel. Golgi membrane protein 1. Unknown function. Cellular response protein to viral infection, widely expressed and upregulated by adenoviral infection.

C iso T, missense V to I

-HOM in Flp, T and A, HET in S, SG, SGendoT, novel, Bile acid-CoA:amino acid N-acyltransferase. Involved in bile acid metabolism.

C iso T, missense E to K

-HOM in all, novel, Homeobox protein Mohawk. Putative morphogenetic regulator of cell adhesion

67 NOC3L - NM_022451.9 2569537 SNP 10 96111494 96111495 44 0

68 ZDHHC16 all 5 NM_032327.2 2572398 SNP 10 99201642 99201643 73 0

69 ZNF143 - NM_003442.4 2641745 SNP 11 9490678 9490679 494 0

70 MICALCL - NM_032867.2 2646884 SNP 11 12272605 12272606 350 0

71 PIK3C2A - NM_002645.2 2654368 SNP 11 17147296 17147297 189 0

72 CCDC34 1 out of 2 NM_030771.1 2675593 SNP 11 27318832 27318833 297 0

73 DGKZ all 4 NM_201532.1 2704562 SNP 11 46353159 46353160 582 0

74 OR5D14 - 2718388 SNP 11 55320414 55320415 269 0

75 CAPN1 - NM_005186.2 2733999 SNP 11 64730857 64730858 532 0

T iso C, missense E to G

-HOM in all, novel, Nucleolar complex protein 3. May be required for adipogenesis.

A iso T, missense N to I

-HOM in all, not really novel, lies inside a large 7.7 kb known deletion, Probable palmitoytransferase. May be involved in apoptosis.

G iso A, missense S to N

-HET in all, novel. Zinc Finger Protein 143. Transcriptional activator. RNApol3 TF, activates selenocysteine tRNA genes.

G iso A, missense R to Q

-HET in all, novel.Involved in spermatid maturation.

G iso C, missense P to A

-HET in all, novel, Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit alpha. Broad metabolic function in insulin signaling.

T iso C, missenseN to S

-HET in all, novel, Coiled-coil domain-containing protein 34.

A iso G, missense M to V

-HET in all, novel, Diacylglycerol Kinase Zeta.

NM_001004735.1

C iso T, missense R to W

-HET in all, no call in SGendoT, novel, Olfactory receptor 5D14

C iso T, missense P to S

-HET in all, novel, Calcium activated neutral proteinase 1. Calcium-regulated non-lysosomal thiol-protease which catalyze limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction

76 PITPNM1 all 2 NM_004910.1 2736508 SNP 11 67018986 67018987 882 0

77 ARHGEF17 - NM_014786.2 2746143 SNP 11 72752011 72752012 1703 0

78 C2CD3 - NM_015531.4 2747303 SNP 11 73528484 73528485 173 0

79 PCF11 - NM_015885.3 2760048 SNP 11 82557152 82557153 709 0

80 PRSS23 - NM_007173.4 2764814 SNP 11 86196828 86196829 165 0

81 BCO2 all 2 NM_031938.4 2807159 SNP 11 111590746 111590747 461 0

82 OR8G2 - 2826465 SNP 11 123601288 123601289 227 0

83 ADAMTS15 - NM_139055.1 2836004 SNP 11 129848515 129848516 814 0


-HET in all, no calls in S and SG, novel, Membrane-associated phosphatidylinositol transfer protein 1. Necessary for normal cytokinesis, necessary for maintaining golgi and ER structure and golgi DAG levels.

G iso A, missense G to S

-HET in all, novel, Rho guanine nucleotide exchange factor 17. GEF for RhoA GTPases. Predominant expression in heart.

C iso T, missense D to N

-HET in all, novel, C2 domain-containing protein 3. Unknown function.

C iso G, missense R to G

-HET in all, novel, Pre-mRNA cleavage complex 2 protein. Involved of 3' end processing of pre-mRNA's.

G iso T, missense A to S

-HET in all, novel, Serin protease 23, secreted protease. Unknown function.

G iso A, missense G to D

-HET in all, no call in A, novel, Beta,beta-carotene 9',10'-oxygenase. Products of enzyme may be precursors of retinoic acid sytnthesis.

NM_001007249.1

C iso T, missense L to F

-HET in all, novel, Olfactory receptor 8G2

C iso T, missense P to S

-HET in all, novel, A disintegrin and metalloproteinase with thrombospondin motifs 15. Member of a multimember family of Zn dependent metalloproteinases. No specific function for this one, may play a role in arthritis and cancer.

84 ANKS1B 1 out of 3 NM_152788.3 2997016 SNP 12 98361700 98361701 485 0

85 RIC8B NM_018157.2 3007528 SNP 12 105733048 105733049 192 0

86 GCN1L1 - NM_006836.1 3025375 SNP 12 119077572 119077573 1161 0

87 OASL all 2 NM_003733.2 3026930 SNP 12 119955727 119955728 133 0

88 DNAH10 - 3031578 SNP 12 122883715 122883716 1431 0

89 DZIP1 all 2 NM_198968.2 3190172 snp 13 95040572 95040573 601 0

90 TMEM55B all 2 NM_144568.2 3227230 snp 14 19998786 19998787 66 0

C iso T, missense A to T

-HET in all, novel, Ankyrin repeat and sterile alpha motif domain-containing protein 1B. Several isoforms with several functions. Nuclear expression in neuronal tissues.

overlapping with MIR548H2

C iso T, missense T to M

-HET in all, novel, Guanine nucleotide exchange factor (GEF) with a putative role in odorant receptor signaling.

G iso A, missense S to F

-HET in all, novel, Translational activator GCN1. Regulates GCN2 protein kinase function and has ths a role in translation.


-HET in all, no call in SG, novel, 59 kDa 2'-5'-oligoadenylate synthase-like protein, interacts with Methyl CpG-binding protein 1. Further function unknown.

NM_001083900.1


-HET in all, novel, Dynein heavy chain 10, axonemal. Force generating protein of respiratory cilia and involved in sperm

C iso T, missense V to I

Hetero: All, DAZ interacting protein 1, regulates Hedgehog

G iso C, missense P to R in region known insertion/deletion variation of named repetitive element (4534bp insertion): rs71780613

Homo: A (no call CG, homo RTG), S, SG, SGendoT Hetero: Flp, T ; transmembrane protein 55B; TMEM55B catalyzes the degradation of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2) by removing the 4-phosphate

91 NEK9 - NM_033116.3 3309664 snp 14 74627915 74627916 750 0

92 RNF111 - NM_017610.6 3412932 snp 15 57111156 57111157 281 0

93 ADAMTSL3 - NM_207517.2 3448914 snp 15 82442060 82442061 892 0

94 CRAMP1L - NM_020825.2 3483640 snp 16 1646574 1646575 401 0

95 FLJ39639 XM_370932.4 3486137 snp 16 3254234 3254235 169 0

96 IQCK NM_153208.1 3519377 snp 16 19682903 19682904 191 0

G iso A, missense P to L

Homo: S, SG, SGendoT Hetero: A, Flp, T; NIMA (never in mitosis gene a)- related kinase 9; prometaphase, replication in, G1 phase, S phase, segregation, formation - regulated by cdc2 - binds the Ran GTPase and regulates mitotic progression - regulates chromosome alignment and segregation in mitosis

A iso C, missense S to R

Homo: All; ring finger protein 111; E3 ubiquitin-protein ligase, acts in the NODAL pathway of mesoderm patterning during embryonic development, enhances the transcriptional activity of TGF-beta and BMP


Hetero: CG: All (except Flp: no call); Homo: RTG: Flp (others hetero except SG: no call)


Homo: All; cramped-like (Drosophila) or Hematological and neurological expressed 1-like protein; function not known.

A iso T, missense R to S

Homo: S, SG, SGendoT Hetero: A, Flp, T; hypothetical protein FLJ39639; function not known

A iso C, missense I to L

Homo: S, SG, SGendoT Hetero: A, Flp, T; IQ motif containing K; function not known.

97 ACSM5 NM_017888.2 3520194 snp 16 20350094 20350095 419 0

98 3546090 snp 16 51302127 51302128 308 0

99 C17orf49 NM_174893.1 3631497 snp 17 6860665 6860666 115 0

100 DNAH9 NM_001372.3 3640490 snp 17 11781543 11781544 4213 0

101 SEZ6 NM_178860.4 3661407 snp 17 24333096 24333097 47 0

C iso T, missense A to V

Homo: S, SG, SGendoT Hetero: A, Flp, T; acyl-CoA synthetase medium-chain family member 5 ; Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro).

LOC100132440

XM_001719251.1


Homo: S, SG, SGendoT Hetero: A, Flp, T; hypothetical protein, Ref seq status withdrawn; function not known

C iso T, missense P to L

Hetero: All; chromatin complexes subunit BAP18 / MLL1/MLL complex subunit C17orf49; Component of chromatin complexes such as the MLL1/MLL and NURF (nucleosome-remodeling factor) complexes

G iso T, missense G to C

Hetero: All; dynein, axonemal, heavy chain 9 ; Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP

G iso T, missense P to T

Hetero: All; seizure related 6 homolog (mouse); May play a role in cell-cell recognition and in neuronal membrane signaling.

102 CRYBA1 NM_005208.3 3661697 snp 17 24600327 24600328 24 0

103 CBX2 NM_005189.1 3734040 snp 17 75372685 75372686 282 0

104 PCSK4 NM_017573.3 3867701 snp 19 1438201 1438202 264 0

105 MOBKL2A NM_130807.2 3868736 snp 19 2027973 2027974 153 0


Hetero: All; crystallin, beta A1; Crystallins are the dominant structural components of the vertebrate eye lens

G iso T, missense K to N

Hetero: All; chromobox homolog 2; Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development

C iso T, missense G to S

Homo: All except Flp is Hetero; proprotein convertase subtilisin/kexin type 4 ; calcium-dependent serine protease. Involved in the processing of hormone and other protein precursors at sites comprised of pairs of basic amino acid residues. Plays a role in transcriptional coactivation. May be involved in stabilizing the multiprotein transcription complex.

T iso G, missense K to Q

Homo: S, SG, SGendoT, T Hetero: A, Flp; MOB1, Mps One Binder kinase activator-like 2A (yeast); May regulate the activity of kinases (By similarity)

106 TSPAN16 NM_012466.2 3885852 snp 19 11269950 11269951 67 0

107 SIPA1L3 NM_015073.1 3927733 snp 19 43264907 43264908 287 0

108 SIRPG NM_080816.2 3967428 snp 20 1577966 1577967 53 0

109 TGM6 NM_198994.2 3968925 snp 20 2345882 2345883 447 0

110 BTBD3 NM_181443.1 3985203 snp 20 11848441 11848442 103 0


Homo: All except A is Hetero; tetraspanin 16; The tetraspanin family proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein might couple to signal transduction pathways and possibly modulate cellular activation and adhesion in haemopoietic and neural tissue.


Homo: S, SG, SGendoT, T Hetero: A, Flp; signal-induced proliferation-associated 1 like 3; GTPase activation

G iso A, missense T to I

Hetero: All; signal-regulatory protein gamma; Probable immunoglobulin-like cell surface receptor. On binding with CD47, mediates cell-cell adhesion.

C iso T, missense R to W

Hetero: All; transglutaminase 6 ; Catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins (By similarity)

G iso A, missense R to H

Hetero: All; BTB (POZ) domain containing 3 ; function not known

111 SEL1L2 NM_025229.1 3988555 snp 20 13817130 13817131 192 0

112 RIN2 NM_018993.2 3998519 snp 20 19885311 19885312 70 0

113 CHD6 NM_032221.3 4018505 snp 20 39483433 39483434 1751 0

114 RBPJL NM_014276.2 4023884 snp 20 43375560 43375561 219 0

T iso C, missense I to V

Hetero: All; sel-1 suppressor of lin-12-like 2 (C. elegans); SEL-1 may be a component of a cell survival pathway induced when unfolded proteins accumulate in the ER

G iso A, missense C to Y

Hetero: All; Ras and Rab interactor 2 ; small GTPase involved in membrane trafficking in the early endocytic pathway. Mutations in this gene cause macrocephaly alopecia cutis laxa and scoliosis (MACS) syndrome, an elastic tissue disorder, as well as the related connective tissue disorder, RIN2 syndrome.

G iso A, missense A to V

Hetero: All; chromodomain helicase DNA binding protein 6 ; probably a core member of a multisubunit protein complex that remodels the chromatin to allow patterns of cell type-specific gene expression

G iso A, missense R to H

Hetero: All; recombination signal binding protein for immunoglobulin kappa J region-like ; Putative transcription factor, which cooperates with EBNA2 (Epstein-Barr virus nuclear antigen-2) to activate transcription

115 CYP24A1 NM_000782.3 4038336 snp 20 52214506 52214507 244 0

116 OGFR NM_007346.2 4053851 snp 20 60914688 60914689 425 0

117 LRP5L NM_182492.1 4140397 snp 22 24080655 24080656 187 0

118 TTC28 XM_929318.3 4145270 snp 22 27355742 27355743 59 0

119 NAGA NM_000262.1 4167058 snp 22 40787001 40787002 324 0

C iso T, missense M to I

Hetero: All; cytochrome P450, family 24, subfamily A, polypeptide 1; this enzyme plays a role in calcium homeostasis and the vitamin D endocrine system


Hetero: All; opioid growth factor receptor; OGF is a negative regulator of cell proliferation and tissue organization in a variety of processes

G iso A, missense R to W

Hetero: All except T is Homo; low density lipoprotein receptor-related protein 5-like; function not known


Hetero: All except T is Homo; tetratricopeptide repeat domain 28 ; function not known


Hetero: All except T is Homo; N-acetylgalactosaminidase, alpha; Removes terminal alpha-N-acetylgalactosamine residues from glycolipids and glycopeptides. Required for the breakdown of glycolipids.

120 P2RY8 NM_178129.3 4190407 snp X 1545078 1545079 124 0

121 EBP NM_006579.1 4235301 snp X 48267179 48267180 25 0

Known SNP: rs28578016 : C iso T, missense V to I

Homo: All; purinergic receptor P2Y, G-protein coupled, 8; P2Y receptors are G-protein-coupled receptors that respond to extracellular purine and pyrimidine, They have diverse physiological roles including regulation of platelet aggregation, muscle traction, neurotransmission, and epithelial cell communication and migration.

G iso T, missense R to L

Hetero: All except Flp is Homo; emopamil binding protein (sterol isomerase); integral membrane protein of the endoplasmic reticulum. It is a high affinity binding protein for the antiischemic phenylalkylamine Ca2+ antagonist (3H)emopamil and the photoaffinity label (3H)azidopamil. Suggested to be involved in the drug transport by the P-glycoprotein. Mutations in this gene cause Chondrodysplasia punctata 2

122 HUWE1 NM_031407.3 4238218 snp X 53619370 53619371 1995 0

123 TFDP3 NM_016521.2 4310964 snp X 132179526 132179527 82 0

124 4329357 snp X 150428175 150428176 17 0

125 LOC389904 4331496 snp X 152397938 152397939 286 0

C iso T, missense R to H

Hetero: All (RTG: S: homo); HECT, UBA and WWE domain containing 1 ; E3 ubiquitin-protein ligase, Regulates apoptosis by catalyzing the polyubiquitination and degradation of MCL1. Mediates monoubiquitination of DNA polymerase beta, thereby playing a role in base-excision repair. Also ubiquitinates the p53/TP53 tumor suppressor and core histones. Regulates neural differentiation and proliferation. May regulate abundance of CDC6 after DNA damage

C iso T, missense A to T

Hetero: All; transcription factor Dp family, member 3; Competitive inhibitor of E2F-mediated transactivation activity. Impairs E2F-mediated cell-cycle progression from G(1) to S phase

LOC100129236

XM_001716550.1


Hetero: All; hypothetical protein, Ref seq status withdrawn; function not known

XM_001716796.1


Hetero: All (RTG: S, Flp, T: homo); hypothetical protein, Ref seq status withdrawn; function not known

126 H6PD NM_004285.3 14788 del del CCCAGGCA 1 9227573 9227581 7

127 SLC38A3 NM_006841.4 792849 ins 3 50226839 50226839 34 0

128 ZNF595 NM_182524.2 1016141 ins 4 77313 77313 639 1

129 PCDHB9 NM_019119.3 1455883 ins 5 140548218 140548218 380 0

Hetero: All (misses first 3 or 8 aa: MWN/MLIVA); hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase); Oxidizes glucose-6-phosphate and glucose, as well as other hexose-6-

Known SNP: rs66535451: ins G ; V(GTC) to G (GGT) VEDPARSCMEGKSFLQKSPSKEPHFTDSTOP -> GRGPCTELYGGQELPTEKSQQGATLHstop

Homo: All; solute carrier family 38, member 3; Sodium-dependent amino acid/proton antiporter. Mediates electrogenic cotransport of glutamine and sodium ions in exchange for protons. May play a role in nitrogen metabolism and synaptic transmission.

Known SNP: rs60154095: ins A; D (GAT) to E (GAA) + last 7 aa are changed, DSYWQGTstop -> EFILARNIVEstop

CG: Homo: A, S, SGendoT, T No call: G en Flp RTG: no data; zinc finger protein 595; May be involved in transcriptional regulation

Known SNP: rs57843788 has become rs33974901: ins A; frameshift (Refseq misannotated)

Homo: All; protocadherin beta 9; Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

130 ZAN NM_173059.1 1952812 ins ins G; frameshift 7 100209412 100209412 1922 0

131 EMID2 NM_133457.2 1955016 ins 7 100987391 100987391 393 0

132 CREB3L1 NM_052854.2 2704543 ins 11 46298837 46298837 508 0

133 SARM1 NM_015077.2 3660808 sub 17 23732426 23732431 182 4

134 MAP3K14 NM_003954.2 3683126 ins 17 40720077 40720077 218 0

Hetero: All, except T is homo; zonadhesin ; Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling

Known SNP: rs67335052: ins G; frameshift (Refseq misannotated)

Homo: All; EMI domain containing 2/Collagen alpha-1(XXVI) chain; function not known

Known SNP: rs67964961: ins G; frameshift

Homo: All; cAMP responsive element binding protein 3-like 1 ; Transcription factor that acts during endoplasmic reticulum stress by activating unfolded protein response target genes.

Known SNPs: rs71373645 (T/C), rs71373646 (G/T), rs71373647 (T/G): TGGGT changed into CGTGG; SGS (agTgGgTca) ->

Homo: All; sterile alpha and TIR motif containing 1; Involved in innate immnune response. Negative regulator of NF-kappa-B and IRF activation.

Known SNP: rs56405343: ins G, frameshift

Homo: All; mitogen-activated protein kinase kinase kinase 14; Lymphotoxin beta-activated kinase which seems to be exclusively involved in the activation of NF-kappa-B and its transcriptional activity.

135 RETNLB NM_032579.2 880049 ins 3 109958693 109958693 13 0

136 XG NM_175569.1 4193622 snp X 2680372 2680373 19 0

137 SRD5A3 NM_024592.2 1082104 del 4 55931008 55931013 316 0

ins GGATTAGG; Similar to known SNP: rs67406203, same insertion one nucleotide downstream; stop after first 11 amino acids

Homo: All; resistin like beta; Probable hormone

C iso T, R to stop; CGA -> TGA (stop after 19 amino acids)

Hetero: All; Xg blood group; This gene encodes the XG blood group antigen

del GTTTT; LFstop -> Lsstop

Homo: All except A is no call; steroid 5 alpha-reductase 3; Probable polyprenol reductase. Plays a key role in early steps of protein N-linked glycosylation by being required for the conversion of polyprenol into dolichol.

xRef dbSNP id mRNA acc ref alt chr start end impact

CDC2L2 all 6 NM_033529.2 1379 snp A G R* R* 1 1575459 75

NADK - rs4751 65220 NM_023018.3 1715 snp G T N K 1 1675899 261

PANK4 - 55229 NM_018216.1 3000 snp G A A V 1 2434273 546

- 9731 NM_014704.2 5015 snp A T L I 1 3742995 413

AJAP1 all 2 rs242056 55966 6871 snp G A G R 1 4672576 262

RNF207 - rs846111 NM_207396.2 9850 snp G C G A 1 6201956 602

Gene symbol

Splice variant

GeneID

SNP number (fannot_id)

Type of SNP

GenomeRefSequence

sampleSequence

Notes (more info on mutation and on gene function)

dbsnp.116:rs7531938

rs7531938

728642

according to Refseq annotation SNP is in intron in all 6 isoforms, so no effect is expected

NONSENSE

dbsnp.52:rs4751

NAD kinase, NADK catalyzes the transfer of a phosphate group from ATP to NAD to generate NADP, which in its reduced form acts as an electron donor for biosynthetic reactions

MISSENSE

dbsnp.116:rs7535528

rs7535528

pantothenate kinase 4, Plays a role in the physiological regulation of the intracellular Coenzyme A concentration (By similarity) MISSEN

SE

KIAA0562

dbsnp.100:rs2275824

rs2275824

centrosomal protein 104kDa, unknown function, glycine-, glutamate-, thienylcyclohexylpiperidine-binding protein-like

MISSENSE

dbsnp.79:rs242056

NM_001042478.1

adherens junctions associated protein 1 , plays a role in cell adhesion and cell migration. Targets to cadherin-mediated junctions in polarized epithelial cells, influences cell invasion and interacts with invasion-promoting protein CD147. MISSEN

SE

dbsnp.86:rs846111

388591

ring finger protein 207, unknown function. Genetic variation in RNF207 may influence the duration of QT interval, a mesure of cardiac repolarization that depends on multiple environmental and genetic contributors. Prolonged or shortened QT intervals predisposes to ventricular arrhythmias and are a risk factor for sudden cardiac death

MISSENSE

PER3 - rs228696 8863 NM_016831.1 12435 snp T C L P 1 7810079 826

CA6 - 765 NM_001215.2 14161 snp C T T M 1 8931992 54

CA6 - 765 NM_001215.2 14185 snp A G S G 1 8939790 89

MASP2 - 10747 NM_006610.2 17069 snp C A D Y 1 11013502 370

PTCHD2 - 57540 NM_020780.1 17826 snp G A G S 1 11484179 181

PTCHD2 - 57540 NM_020780.1 17849 snp G A A T 1 11502056 649

dbsnp.79:rs228696

period homolog 3 (Drosophila), Cell growth-inhibiting gene 13 protein, Component of the circadian clock mechanism which is essential for generating circadian rhythms. Function unknown. Deregulated in chronic myeloid leukemia and breast cancers.

MISSENSE

dbsnp.100:rs2274327

rs2274327

carbonic anhydrase VI, The protein encoded by this gene is one of several isozymes of carbonic anhydrase. This protein is found only in salivary glands and saliva and protein may play a role in the reversible hydratation of carbon dioxide though its function in saliva is unknown.

MISSENSE

dbsnp.100:rs2274333

rs2274333

carbonic anhydrase VI, The protein encoded by this gene is one of several isozymes of carbonic anhydrase. This protein is found only in salivary glands and saliva and protein may play a role in the reversible hydratation of carbon dioxide though its function in saliva is unknown.

MISSENSE

dbsnp.121:rs12711521

rs12711521

mannan-binding lectin serine peptidase 2, Serum protease that plays an important role in the activation of the complement system (essential for the operation of the innate and adaptive immune defense) via mannose-binding lectin. After activation by auto-catalytic cleavage it cleaves C2 and C4, leading to their activation and to the formation of C3 convertase.

MISSENSE

dbsnp.100:rs2817580

rs2817580

patched domain containing 2 , unknown function, a multispan transmembrane protein with sterol-sensing domain.

MISSENSE

dbsnp.96:rs2072994

rs2072994

patched domain containing 2 , unknown function, a multispan transmembrane protein with sterol-sensing domain.

MISSENSE

C1orf167 XM_209234.7 18344 snp C T R C 1 11759268 76

C1orf167 XM_209234.7 18357 snp T C W R 1 11762584 231

IIP45 60672 NM_021933.2 18744 snp A G K E 1 12005512 166

TNFRSF8 - 943 NM_001243.3 18850 snp C T R C 1 12098315 296

NA (not in Refseq)

dbsnp.116:rs7538516

rs7538516

284498

chromosome 1 open reading frame 167, uncharacterized protein, evidence on transcript level, NOT in Refseq!

MISSENSE

NA (not in Refseq)

dbsnp.111:rs4846044

rs4846044

284498

chromosome 1 open reading frame 167, uncharacterized protein, evidence on transcript level, NOT in Refseq!

MISSENSE

- (in literature splice variant known linked to gliomas, pubmed ID:15867349, not linked to this SNP)

dbsnp.100:rs2295283

rs2295283

migration and invasion inhibitory protein. Inhibits glioma cells invasion and down-regulates adhesion- and motility-associated genes such as NFKB2 and ICAM1. Exhibits opposing effects to IGFBP2 on cell invasion. MISSEN

SE

dbsnp.89:rs1763642

rs1763642

tumor necrosis factor receptor superfamily, member 8. Receptor for TNFSF8/CD30L. May play a role in the regulation of cellular growth and transformation of activated lymphoblasts. Regulates gene expression through activation of NF-kappa-B. MISSEN

SE

19290 snp A T M L 1 12698930 0

PDPN all 4 10630 NM_198389.2 20142 snp C G A G 1 13813450 222

FBLIM1 all 3 54751 NM_017556.2 23982 snp C T S F 1 15969520 190

AADACL3

only effect on isoform 2, not on isoform 1.

dbsnp.101:rs3000859

rs3000859

126767

NM_001103169.1

arylacetamide deacetylase-like 3. Function unknown, 'GDXG' lipolytic enzyme family.

MISSTART

dbsnp.100:rs2486188

rs2486188

podoplanin. May be involved in cell migration and/or actin cytoskeleton organization.When expressed in keratinocytes,induces changes in cell morphology with transfected cells showing an elongated shape, numerous membrane protrusions, major reorganization of the actin cytoskeleton, increased motility and decreased cell adhesion. Required for normal lung cell proliferation and alveolus formation at birth. Platelet aggregation-inducing factor expressed in colorectal tumors (PUBmed ID: 14522983). Low podoplanin expression showed a significant correlation with lymphatic invasion (P < 0.0001) and nodal metastasis (P = 0.0058) in cervix carcinoma (Pubmed ID:16528371).

MISSENSE

dbsnp.120:rs10927851

rs10927851

filamin binding LIM protein 1, This protein localizes at cell junctions and may link cell adhesion structures to the actin cytoskeleton. This protein may be involved in the assembly and stabilization of actin-filaments and likely plays a role in modulating cell adhesion, cell morphology and cell motility. This protein also localizes to the nucleus and may affect cardiomyocyte differentiation after binding with the CSX/NKX2-5 transcription factor.

MISSENSE

- NM_152375.2 30113 snp C G P R 1 18680483 140

- NM_152375.2 30114 snp C A R S 1 18680539 159

- NM_152375.2 30115 snp C A H N 1 18680878 272

- NM_152375.2 30117 snp A C T P 1 18681112 350

TAS1R2 - 80834 NM_152232.2 30820 snp G C S C 1 19058715 8

ECE1 all 4 1889 NM_001397.1 34264 snp G A T I 1 21446441 340

HSPG2 - rs897471 3339 NM_005529.5 35649 snp G A A V 1 22064040 1502

KLHDC7A

dbsnp.101:rs2992755

rs2992755

127707

kelch domain containing 7A, function unknown, potential single-pass membrane protein

MISSENSE

KLHDC7A

dbsnp.120:rs11261022

rs11261022

127707


MISSENSE

KLHDC7A

dbsnp.101:rs2992753

rs2992753

127707


MISSENSE

KLHDC7A

dbsnp.101:rs2992752

rs2992752

127707


MISSENSE

dbsnp.119:rs9701796

rs9701796

taste receptor, type 1, member 2, recognizes diverse natural and synthetic sweeteners MISSEN

SE

dbsnp.86:rs1076669

rs1076669

endothelin converting enzyme 1, The protein encoded by this gene is involved in proteolytic processing of endothelin precursors to biologically active peptides. Mutations in this gene are associated with Hirschsprung disease, cardiac defects and autonomic dysfunction. MISSEN

SE

dbsnp.86:rs897471

heparan sulfate proteoglycan 2, Integral component of basement membranes. Component of the glomerular basement membrane (GBM), responsible for the fixed negative electrostatic membrane charge, and which provides a barrier which is both size- and charge-selective. It serves as an attachment substrate for cells. Plays essential roles in vascularization. Critical for normal heart development and for regulating the vascular response to injury. Also required for avascular cartilage development.

MISSENSE

HSPG2 - rs989994 3339 NM_005529.5 35688 snp T C N S 1 22079235 764

HSPG2 3339 NM_005529.5 35690 snp T C M V 1 22079821 637

ZBTB40 all 2 rs209729 9923 NM_014870.3 37140 snp A G Y C 1 22708263 594

ZBTB40 all 2 rs209720 9923 NM_014870.3 37157 snp G A V M 1 22719295 996

dbsnp.86:rs989994


MISSENSE

dbsnp.92:rs1874792

rs1874792


MISSENSE

dbsnp.79:rs209729

zinc finger and BTB domain containing 40. May be involved in transcriptional regulation, Phosphorylated upon DNA damage, probably by ATM or ATR, Pubmed ID:17525332. MISSEN

SE

dbsnp.79:rs209720

zinc finger and BTB domain containing 40. May be involved in transcriptional regulation, Phosphorylated upon DNA damage, probably by ATM or ATR, Pubmed ID:17525332. MISSEN

SE

EPHA8 rs606002 2046 37308 snp T C S P 1 22788339 456

E2F2 - 1870 NM_004091.2 38736 snp C A Q H 1 23720050 225

IL22RA1 - 58985 NM_021258.2 39917 snp C T V I 1 24327274 204


dbsnp.83:rs606002

NM_001006943.1

EPH receptor A8, functions as a receptor for ephrin A2, A3 and A5 and plays a role in short-range contact-mediated axonal guidance during development of the mammalian nervous system

MISSENSE

dbsnp.96:rs2075995

rs2075995

E2F transcription factor 2. Transcription activator that binds DNA cooperatively with differentiation regulated transcription factor proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-2 binds specifically to RB1 protein, in a cell-cycle dependent manner.

MISSENSE

dbsnp.123:rs16829204

rs16829204

leukin 22 receptor, alpha 1, Component of the receptor for IL20, IL22 and IL24. Component of IL22 receptor formed by IL22RA1 and IL10RB enabling IL22 signaling via JAK/STAT pathways. IL22 also induces activation of MAPK1/MAPK3 and Akt kinases pathways. Component of one of the receptor for IL20 and IL24 formed by IL22RA1 and IL20RB also signaling through STATs activation. Mediates IL24 antiangiogenic activity as well as IL24 inhibitory effect on endothelial cell tube formation and differentiation MISSEN

SE

SEPN1 all 2 57190 NM_206926.1 42872 snp C A N K 1 26013159 467

UBXD5 all 3 91544 43548 snp A C L R 1 26483477 191

dbsnp.100:rs2294228

rs2294228

selenoprotein N, 1 ; This gene encodes a selenoprotein, which contains a selenocysteine (Sec) residue at its active site. The selenocysteine is encoded by the UGA codon that normally signals translation termination. The 3' UTR of selenoprotein genes have a common stem-loop structure, the sec insertion sequence (SECIS), that is necessary for the recognition of UGA as a Sec codon rather than as a stop signal. Mutations in this gene cause the classical phenotype of multiminicore disease and congenital muscular dystrophy with spinal rigidity and restrictive respiratory syndrome.

MISSENSE

dbsnp.111:rs4332350

rs4332350

NM_001077262.1

UBX domain protein 11. May be involved in the reorganization of actin cytoskeleton mediated by RND1, RND2 AND RND3. Promotes RHOAactivation mediated by GNA12 and GNA13 (By similarity). This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways.

MISSENSE

SYTL1 - 84958 NM_032872.1 44583 snp A G Q R 1 27552383 443

AHDC1 - 27245 44675 snp C T A T 1 27748410 934

SFRS4 - 6429 NM_005626.3 46780 snp C G G A 1 29347980 337

MECR all 2 51102 46847 snp A G F L 1 29415223 19

HCRTR1 - 3061 NM_001525.1 51565 snp A G I V 1 31865111 407

ZBTB8 - rs704886 52380 snp G C G A 1 32838533 417

ZMYM1 - 79830 NM_024772.3 55834 snp G A V M 1 35335551 72

dbsnp.107:rs3813795

rs3813795

synaptotagmin-like 1, May play a role in vesicle trafficking (By similarity). Binds phosphatidylinositol 3,4,5-triphosphate. Acts as a RAB27A effector protein and may play a role in cytotoxic granule exocytosis in lymphocytes (By similarity) MISSEN

SE

dbsnp.111:rs4908364

rs4908364

NM_001029882.2

AT hook, DNA binding motif, containing 1. Function unknown. Phosphorylated upon DNA damage, probably by ATM or ATR.

MISSENSE

dbsnp.98:rs2230677

rs2230677

Serine/arginine-rich splicing factor 4. This gene encodes a member of the arginine/serine-rich splicing factor family. The encoded protein likely functions in mRNA processing.

MISSENSE

dbsnp.86:rs1128400

rs1128400

NM_001024732.1

mitochondrial trans-2-enoyl-CoA reductase. Catalyzes the reduction of trans-2-enoyl-CoA to acyl-CoA with chain length from C6 to C16 in an NADPH-dependent manner with preference to medium chain length substrate. May have a role in the mitochondrial synthesis of fatty acids.

MISSENSE

dbsnp.100:rs2271933

rs2271933

hypocretin (orexin) receptor 1. The protein encoded by this gene is a G-protein coupled receptor involved in the regulation of feeding behavior. The encoded protein selectively binds the hypothalamic neuropeptide orexin A.

MISSENSE

dbsnp.86:rs704886

653121

NM_001040441.1

zinc finger and BTB domain containing 8A. May be involved in transcriptional regulation MISSEN

SE

dbsnp.101:rs2971408

rs2971408

zinc finger, MYM-type 1. Function unknown.

MISSENSE

C1orf102 NM_145047.3 56904 snp C T G R 1 36658703 316

C1orf102 all 2 NM_145047.3 56915 snp T C T A 1 36670653 140

HIVEP3 all 2 59269 NM_024503.2 64015 snp T C T A 1 41748914 2338


dbsnp.100:rs2275477

rs2275477

127700

organic solute carrier partner 1. May be involved in drug clearance in the placenta MISSEN

SE

dbsnp.126:rs34409118

rs34409118

127700

organic solute carrier partner 1. May be involved in drug clearance in the placenta MISSEN

SE

dbsnp.119:rs9439043

rs9439043

human immunodeficiency virus type I enhancer binding protein 3. Plays a role of transcription factor; binds to recognition signal sequences (Rss heptamer) for somatic recombination of immunoglobulin and T-cell receptor gene segments. Binds also to the kappa-B motif of gene such as S100A4, involved in cell progression and differentiation. its down-regulation promotes cell cycle progression with ultimate formation of multinucleated giant cells. Strongly inhibits TNF-alpha-induced NF-kappa-B activation. Essential regulator of adult bone formation. MISSEN

SE

HIVEP3 all 2 59269 NM_024503.2 64021 snp C G A P 1 41751411 2022

FOXJ3 - rs343376 22887 NM_014947.3 65123 snp A G V A Forkhead box J3. Unknown function. 1 42466183 161

STIL all 2 6491 NM_003035.2 71540 snp T C H R 1 47498673 983

dbsnp.100:rs2483689

rs2483689

human immunodeficiency virus type I enhancer binding protein 3. Plays a role of transcription factor; binds to recognition signal sequences (Rss heptamer) for somatic recombination of immunoglobulin and T-cell receptor gene segments. Binds also to the kappa-B motif of gene such as S100A4, involved in cell progression and differentiation. its down-regulation promotes cell cycle progression with ultimate formation of multinucleated giant cells. Strongly inhibits TNF-alpha-induced NF-kappa-B activation. Essential regulator of adult bone formation. MISSEN

SEdbsnp.79:rs343376

MISSENSE

dbsnp.121:rs13376679

rs13376679

SCL/TAL1 interrupting locus. Immediate-early gene. Plays an important role in embryonic development as well as in cellular growth and proliferation; its long-term silencing affects cell survival and cell cycle distribution as well as decreases CDK1 activity correlated with reduced phosphorylation of CDK1. Play a role as a positive regulator of the sonic hedgehog pathway, acting downstream of PTCH1. proposed to regulate Cdc2 kinase activity during spindle checkpoint arrest. Chromosomal deletions that fuse this gene and the adjacent locus commonly occur in T cell leukemias. MISSEN

SE

STIL all 2 6491 NM_003035.2 71617 snp G A A V 1 47540500 85

C1orf175 all 2 78913 snp T G Y D 1 54892102 305

C1orf175 all 2 rs570218 78963 snp A G H R 1 54912328 617

C8B - 732 NM_000066.2 83103 snp C T G R 1 57195071 116

C1orf87 - rs626251 NM_152377.1 87228 snp T C K E 1 60239401 402

INADL - 10207 NM_176877.2 89892 snp G A G S 1 62152885 1177

dbsnp.103:rs3125630

rs3125630

SCL/TAL1 interrupting locus. Immediate-early gene. Plays an important role in embryonic development as well as in cellular growth and proliferation; its long-term silencing affects cell survival and cell cycle distribution as well as decreases CDK1 activity correlated with reduced phosphorylation of CDK1. Play a role as a positive regulator of the sonic hedgehog pathway, acting downstream of PTCH1. proposed to regulate Cdc2 kinase activity during spindle checkpoint arrest. Chromosomal deletions that fuse this gene and the adjacent locus commonly occur in T cell leukemias. MISSEN

SEdbsnp.89:rs1655519

rs1655519

374977

NM_001039464.1

HEAT repeat containing 8. Function unknown.

MISSENSE

dbsnp.83:rs570218

374977

NM_001039464.1

HEAT repeat containing 8. Function unknown.

MISSENSE

dbsnp.86:rs1013579

rs1013579

complement component 8, beta polypeptide. Constituent of the membrane attack complex (MAC) that plays a key role in the innate and adaptive immune response by forming pores in the plasma membrane of target cells. MISSEN

SEdbsnp.83:rs626251

127795

chromosome 1 open reading frame 87. Function unknown.

MISSENSE

dbsnp.86:rs1056513

rs1056513

InaD-like (Drosophila). Scaffolding protein that may bring different proteins into adjacent positions at the cell membrane. May regulate protein targeting, cell polarity and integrity of tight junctions. May regulate the surface expression and/or function of ASIC3 in sensory neurons MISSEN

SE

INADL - 10207 NM_176877.2 90039 snp G A R H 1 62228601 1281

L1TD1 all 2 54596 NM_019079.3 90504 snp T C V A 1 62445624 245

- NM_181712.4 90672 snp C G V L 1 62485811 934

INSL5 - rs549148 10022 NM_005478.3 97390 snp T A Q L 1 67039343 49

C1orf141 - 97821 snp C T V I 1 67333543 188

IL23R - NM_144701.2 97988 snp G T Q H 1 67406399 2

dbsnp.86:rs1134767

rs1134767

InaD-like (Drosophila). Scaffolding protein that may bring different proteins into adjacent positions at the cell membrane. May regulate protein targeting, cell polarity and integrity of tight junctions. May regulate the surface expression and/or function of ASIC3 in sensory neurons MISSEN

SE

dbsnp.116:rs7542665

rs7542665

LINE-1 type transposase domain containing 1, unknown function

MISSENSE

ANKRD38

dbsnp.101:rs2941679

rs2941679

163782

KN motif and ankyrin repeat domains 4 , function unknown

MISSENSE

dbsnp.83:rs549148

insulin-like 5, May have a role in gut contractility or in thymic development and regulation. Activates RXFP4 with high potency and appears to be the endogenous ligand for this receptor MISSEN

SE

dbsnp.120:rs11208997

rs11208997

400757

NM_001013674.1

chromosome 1 open reading frame 141 . Function unknown

MISSENSE

dbsnp.92:rs1884444

rs1884444

149233

interleukin 23 receptor. Associates with IL12RB1 to form the interleukin-23 receptor. Binds IL23 and mediates T-cells, NK cells and possibly certain macrophage/myeloid cells stimulation probably through activation of the Jak-Stat signaling cascade. IL23 functions in innate and adaptive immunity and may participate in acute response to infection in peripheral tissues. IL23 may be responsible for autoimmune inflammatory diseases and be important for tumorigenesis MISSEN

SE

IL23R - NM_144701.2 98070 snp T C L P 1 67457974 309

NM_152996.1 113173 snp C A L I 1 76865767 222

BXDC5 - 80135 NM_025065.6 125464 snp A G S G 1 84717576 8

SYDE2 - rs709786 84144 NM_032184.1 126570 snp C T V I 1 85397136 1156

SYDE2 - rs817443 84144 NM_032184.1 126581 snp C T V I 1 85421207 568

dbsnp.116:rs7530511

rs7530511

149233

interleukin 23 receptor. Associates with IL12RB1 to form the interleukin-23 receptor. Binds IL23 and mediates T-cells, NK cells and possibly certain macrophage/myeloid cells stimulation probably through activation of the Jak-Stat signaling cascade. IL23 functions in innate and adaptive immunity and may participate in acute response to infection in peripheral tissues. IL23 may be responsible for autoimmune inflammatory diseases and be important for tumorigenesis MISSEN

SE

ST6GALNAC3


dbsnp.87:rs1184626

rs1184626

256435

ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3. Involved in the biosynthesis of ganglioside GD1A from GM1B

MISSENSE

dbsnp.100:rs2292191

rs2292191

ribosome production factor 1 homolog (S. cerevisiae). May be required for ribosome biogenesis. MISSEN

SE

dbsnp.86:rs709786

synapse defective 1, Rho GTPase, homolog 2 (C. elegans). GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state (By similarity) MISSEN

SE

dbsnp.86:rs817443

synapse defective 1, Rho GTPase, homolog 2 (C. elegans). GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state (By similarity) MISSEN

SE

GBP3 - 2635 NM_018284.2 132364 snp G A R C 1 89251455 289

GBP2 - 2634 NM_004120.3 132565 snp T C S G 1 89352528 302

GBP2 - 2634 NM_004120.3 132573 snp G C P A 1 89355277 284

GBP7 - rs676913 NM_207398.2 132655 snp G A T I 1 89410165 13

guanylate binding protein 3, first nt exon 6. NO SNP in SNP130! GBPs specifically bind guanine nucleotides (GMP, GDP, and GTP) and contain two of the three consensus motifs found in typical GTP-binding proteins. The encoded protein interacts with a member of the germinal center kinase family

MISSENSE

dbsnp.98:rs2230338

rs2230338

guanylate binding protein 2, interferon-inducible. Interferons are cytokines that have antiviral effects and inhibit tumor cell proliferation. They induce a large number of genes in their target cells, including those coding for the guanylate-binding proteins (GBPs). GBPs are characterized by their ability to specifically bind guanine nucleotides (GMP, GDP, and GTP). The protein encoded by this gene is a GTPase that converts GTP to GDP and GMP

MISSENSE

dbsnp.89:rs1803632

rs1803632

guanylate binding protein 2, interferon-inducible. Interferons are cytokines that have antiviral effects and inhibit tumor cell proliferation. They induce a large number of genes in their target cells, including those coding for the guanylate-binding proteins (GBPs). GBPs are characterized by their ability to specifically bind guanine nucleotides (GMP, GDP, and GTP). The protein encoded by this gene is a GTPase that converts GTP to GDP and GMP

MISSENSE

dbsnp.83:rs676913

388646

guanylate binding protein 7, Guanylate-binding proteins, such as GBP7, are induced by interferon and hydrolyze GTP to both GDP and GMP

MISSENSE

BRDT all 2 676 NM_207189.1 136980 snp C A Q K 1 92201082 61

EVI5 - 7813 NM_005665.4 137951 snp T C I V 1 92933489 335

DNTTIP2 - 30836 NM_014597.3 139712 snp C A E D 1 94115151 308

- 9411 NM_004815.3 140196 snp C T G D 1 94412034 1254

RWDD3 all 2 25950 NM_015485.4 142054 snp T G N K 1 95482526 85

dbsnp.120:rs10783071

rs10783071

bromodomain, testis-specific. May play a role in the transcriptional regulation of spermatogenesis. Seems to have a structural ATP-independent role in the reorganization of acetylated chromatin MISSEN

SE

dbsnp.100:rs2391199

rs2391199

ecotropic viral integration site 5. Functions as a regulator of cell cycle progression by stabilizing the FBXO5 protein and promoting cyclin-A accumulation during interphase. May play a role in cytokinesis. MISSEN

SE

dbsnp.107:rs3747965

rs3747965

deoxynucleotidyltransferase, terminal, interacting protein 2. This gene is thought to be involved in chromatin remodeling and gene transcription. The encoded nuclear protein binds to and enhances the transcriptional activity of the estrogen receptor alpha, and also interacts with terminal deoxynucleotidyltransferase. The expression profile of this gene is a potential biomarker for chronic obstructive pulmonary disease

MISSENSE

ARHGAP29

dbsnp.92:rs1999272

rs1999272

Rho GTPase activating protein 29. GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has strong activity toward RHOA, and weaker activity toward RAC1 and CDC42. May act as a specific effector of RAP2A to regulate Rho MISSEN

SE

dbsnp.100:rs2296308

rs2296308

RWD domain containing 3. Enhances the sumoylation of a number of proteins including HIF1A, PIAS and I-kappa-B, through direct interaction with UBC9. Has no effect on ubiquitination. MISSEN

SE

VAV3 10451 NM_006113.4 163087 snp T A T S 1 108109249 297

C1orf62 NM_152763.3 164515 snp C T S N 1 109196627 60

57535 NM_020775.2 165089 snp T C L P 1 109547140 1008

CHIA 27159 NM_021797.2 168421 snp A G I V 1 111663363 230

CHIA 27159 NM_021797.2 168422 snp T C F S 1 111663496 245

PPM1J NM_005167.5 170662 snp C T V I 1 113056911 235

PTPN22 26191 NM_015967.3 172317 snp A G W R 1 114179090 619


dbsnp.116:rs7528153

rs7528153

vav 3 guanine nucleotide exchange factor. Exchange factor for GTP-binding proteins RhoA, RhoG and, to a lesser extent, Rac1. Binds physically to the nucleotide-free states of those GTPases. Plays an important role in angiogenesis. Its recruitement by phosphorylated EPHA2 is critical for EFNA1-induced RAC1 GTPase activation and vascular endothelial cell migration and assembly (By similarity) MISSEN


rs1277207

254268

AKNA domain containing 1, function unknown.

MISSENSE

KIAA1324

dbsnp.86:rs1052878

rs1052878

Estrogen-induced gene 121 protein, May play a role as a marker of hyperestrogenic state and estrogen-related type I endometrial carcinoma. MISSEN

SE

dbsnp.100:rs2275253

rs2275253

chitinase, acidic. Degrades chitin and chitotriose. May participate in the defense against nematodes, fungi and other pathogens. MISSEN

SE

dbsnp.100:rs2275254

rs2275254

chitinase, acidic. Degrades chitin and chitotriose. May participate in the defense against nematodes, fungi and other pathogens. MISSEN

SE

dbsnp.120:rs10857971

rs10857971

333926

protein phosphatase, Mg2+/Mn2+ dependent, 1J. Serine/threonine protein phosphatase. Function unknown.

MISSENSE

dbsnp.100:rs2476601

rs2476601

protein tyrosine phosphatase, non-receptor type 22 (lymphoid). Seems to act on Cbl. May play a role in regulating the function of Cbl and its associated protein kinases. Acts as negative regulator of T cell receptor (TCR) signaling. Dephosphorylates and inactivates the SRC family kinases MISSEN

SE

BCL2L15 172398 snp C T D N BCL2-like 15. Function unknown. 1 114226123 89

TSHB 7252 NM_000549.3 173721 snp A G T A 1 115377545 13

TBX15 6913 NM_152380.2 179340 snp A C M R 1 119228989 459

HSD3B1 3283 NM_000862.2 179888 snp C A T N 1 119858768 366

CHD1L - 9557 NM_004284.3 185987 snp G T A S 1 145233772 884

ACP6 51205 NM_016361.3 186756 snp C T V M 1 145588600 315

dbsnp.87:rs1217381

rs1217381

440603

NM_001010922.2

MISSENSE

dbsnp.120:rs10776792

rs10776792

thyroid stimulating hormone, beta. Indispensable for the control of thyroid structure and metabolism MISSEN

SE

T-box 15. Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head. Acts by controlling the number of mesenchymal precursor cells and chondrocytes (By similarity) MISSEN

SE

{dbsnp.86:rs1047303; dbsnp.127:rs45609334}

rs1047303; rs45609334

hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1. bifunctional enzyme, that catalyzes the oxidative conversion of Delta(5)-ene-3-beta-hydroxy steroid, and the oxidative conversion of ketosteroids. The 3-beta-HSD enzymatic system plays a crucial role in the biosynthesis of all classes of hormonal steroids

MISSENSE

dbsnp.111:rs4950394

rs4950394

chromodomain helicase DNA binding protein 1-like. DNA helicase which plays a role in chromatin-remodeling following DNA damage. Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair. Able to catalyze nucleosome sliding in an ATP-dependent manner. Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding. Of note, aa seq after SNP is QSSSSSS, so stretch of 6 serines after SNP with Q in between. MISSEN

SE

dbsnp.116:rs6593795

rs6593795

acid phosphatase 6, lysophosphatidic. Hydrolyzes lysophosphatidic acid to monoacylglycerol. MISSEN

SE

THEM5 NM_182578.1 191818 snp T C D G 1 150086947 196

TCHH 7062 NM_007113.2 192273 snp A C L R 1 150352128 62

TDRD10 - NM_182499.3 195632 snp G A R Q 1 152783100 180

ASH1L - 55870 NM_018489.2 196814 snp T C T A 1 153675258 1770

RXFP4 NM_181885.2 197377 snp T C L S 1 154179109 328

NES 10763 NM_006617.1 198138 snp G A P L 1 154907301 1100

dbsnp.116:rs6587625

rs6587625

284486

Thioesterase superfamily member 5 . Function unknown.

MISSENSE

dbsnp.100:rs2515663

rs2515663

Trichohyalin. Trichohyalin confers mechanical strength to the hair follicle inner root sheath and to other toughened epithelial tissues, such as the hard palate and filiform ridges of the tongue, by forming multiple complex crosslinks with itself and with other structural proteins

MISSENSE

dbsnp.121:rs12750774

rs12750774

126668

tudor domain containing 10. Function unknown

MISSENSE

dbsnp.111:rs4971053

rs4971053

ash1 (absent, small, or homeotic)-like (Drosophila). Histone methyltransferase. Probably methylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation (By similarity). It is a member of the trithorax group of transcriptional activators. It is localized to many small speckles in the nucleus, and also to cell-cell tight junctions. MISSEN


rs2152051

339403

relaxin/insulin-like family peptide receptor 4

MISSENSE

dbsnp.101:rs2886443

rs2886443

nestin. Required for brain and eye development. Promotes the disassembly of phosphorylated vimentin intermediate filaments (IF) during mitosis and may play a role in the trafficking and distribution of IF proteins and other cellular factors to daughter cells during progenitor cell division. Required for survival, renewal and mitogen-stimulated proliferation of neural progenitor cells (By similarity) MISSEN

SE

PEAR1 198541 snp T C S P 1 155144080 233

rs868188 9826 NM_014784.2 198578 snp T C S G 1 155173738 1415

FCRL5 83416 NM_031281.2 199776 snp C T G D 1 155775648 417

FCRL5 83416 NM_031281.2 199786 snp A G Y H 1 155780720 266

dbsnp.92:rs1952294

rs1952294

375033

NM_001080471.1

platelet endothelial aggregation receptor 1; is a platelet receptor that signals upon the formation of platelet-platelet contacts independent of platelet. When overexpressed, reduces the number of both early and late non-adherent myeloid progenitor cells (By similarity).

activation and secondary to platelet aggregation.

MISSENSE

ARHGEF11

dbsnp.86:rs868188

Rho guanine nucleotide exchange factor (GEF) 11. The encoded protein may form a complex with G proteins and stimulate Rho-dependent signals. A similar protein in rat interacts with glutamate transporter EAAT4 and modulates its glutamate transport activity. Expression of the rat protein induces the reorganization of the actin cytoskeleton and its overexpression induces the formation of membrane ruffling and filopodia.

MISSENSE

dbsnp.92:rs2012199

rs2012199

Fc receptor-like 5. May be involved in B-cell development and differentiation in peripheral lymphoid organs and may be useful markers of B-cell stages. May have an immunoregulatory role in marginal zone B-cells. MISSEN

SE

dbsnp.116:rs6679793

rs6679793

Fc receptor-like 5. May be involved in B-cell development and differentiation in peripheral lymphoid organs and may be useful markers of B-cell stages. May have an immunoregulatory role in marginal zone B-cells. MISSEN

SE

SPTA1 6708 NM_003126.2 201902 snp A C S A 1 156886351 1162

OR6N1 rs857825 202123 snp T C Q R 1 157002314 260

OR6N1 rs857826 202124 snp A G F L 1 157002363 244

ATP1A4 480 NM_144699.3 204178 snp G A G D 1 158391498 82

PVRL4 - 81607 NM_030916.1 205569 snp G T P T 1 159316132 103

dbsnp.100:rs2482965

rs2482965

spectrin, alpha, erythrocytic 1 (elliptocytosis 2). Spectrin is the major constituent of the cytoskeletal network underlying the erythrocyte plasma membrane. It associates with band 4.1 and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. MISSEN

SEdbsnp.86:rs857825

128372

NM_001005185.1

olfactory receptor, family 6, subfamily N, member 1

MISSENSE

dbsnp.86:rs857826

128372

NM_001005185.1

olfactory receptor, family 6, subfamily N, member 1

MISSENSE

dbsnp.116:rs6427504

rs6427504

ATPase, Na+/K+ transporting, alpha 4 polypeptide. creates the electrochemical gradient of sodium and potassium ions, providing the energy for active transport of various nutrients. Plays a role in sperm motility. MISSEN

SE

dbsnp.126:rs35434391

rs35434391

poliovirus receptor-related 4 . It is involved in cell adhesion through trans-homophilic and -heterophilic interactions. It is a single-pass type I membrane protein. The soluble form is produced by proteolytic cleavage at the cell surface by the metalloproteinase ADAM17/TACE. The secreted form is found in both breast tumor cell lines and breast tumor patients. Mutations in this gene are the cause of ectodermal dysplasia-syndactyly syndrome type 1, an autosomal recessive disorder. Predominantly expressed in placenta. Not detected in normal breast epithelium but expressed inbreast carcinoma. MISSEN

SE

9507 NM_005099.4 205700 snp T C Q R 1 159429660 625

25903 NM_015441.1 207020 snp A G W R 1 160234304 469

C1orf114 57821 NM_021179.1 219274 snp A T F I 1 167657580 237

C1orf114 57821 NM_021179.1 219275 snp A G F S 1 167657777 171

SELP rs6127 6403 NM_003005.3 219538 snp C T D N 1 167832936 602

BAT2D1 rs760644 23215 NM_015172.3 223427 snp G A A T 1 169775950 905

BAT2D1 rs235468 23215 NM_015172.3 223434 snp C G S C 1 169781354 1623

SEC16B 89866 NM_033127.2 232130 snp C A A S 1 176169009 928

SEC16B 89866 NM_033127.2 232132 snp C T S N 1 176169347 872

ADAMTS4

dbsnp.111:rs4233367

rs4233367

ADAM metallopeptidase with thrombospondin type 1 motif, 4. Cleaves aggrecan, a cartilage proteoglycan, and may be involved in its turnover. May play an important role in the destruction of aggrecan in arthritic diseases. Could also be a critical factor in the exacerbation of neurodegeneration in Alzheimer disease. Cleaves aggrecan at the '392-Glu- -Ala-393' site. MISSEN

SE

OLFML2B

dbsnp.100:rs2499836

rs2499836

olfactomedin-like 2B; Secreted, binds to heparin and chondroitin sulfate E (By similarity) MISSEN

SE

dbsnp.126:rs35107735

rs35107735

chromosome 1 open reading frame 114. Function unknown

MISSENSE

dbsnp.107:rs3820059

rs3820059

chromosome 1 open reading frame 114. Function unknown

MISSENSE

dbsnp.52:rs6127

selectin P (granule membrane protein 140kDa, antigen CD62)

MISSENSE

dbsnp.86:rs760644 proline-rich coiled-coil 2C, Function unknown.

MISSENSE

dbsnp.79:rs235468 proline-rich coiled-coil 2C, Function unknown.

MISSENSE

dbsnp.129:rs61745560

rs61745560

SEC16 homolog B (S. cerevisiae). Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus and for normal transitional endoplasmic reticulum (tER) organization

MISSENSE

dbsnp.107:rs3813649

rs3813649


MISSENSE

http://www.genenames.org/data/hgnc_data.php?hgnc_id=24903

http://www.genenames.org/data/hgnc_data.php?hgnc_id=24903

SEC16B rs591120 89866 NM_033127.2 232133 snp G C P A 1 176169375 863

C1orf49 84066 NM_032126.2 232634 snp T G L R Function unknown. 1 176756600 170

TOR3A 64222 NM_022371.3 233417 snp T C F L 1 177317922 12

57710 NM_020950.1 236671 snp A G N D Function unknown. 1 179180219 1077

rs704326 777 NM_000721.2 238291 snp G A A T 1 180026279 1954

RNASEL rs627928 6041 NM_021133.2 239638 snp A C D E 1 180817959 540

RGS16 6004 NM_002928.3 239668 snp T C H R 1 180836248 136

dbsnp.83:rs591120


MISSENSE

dbsnp.107:rs3813636

rs3813636

MISSENSE

dbsnp.100:rs2296377

rs2296377

torsin family 3, member A/ATP-dependant interferon response protein 1. Function unknown

MISSENSE

KIAA1614

dbsnp.100:rs2331995

rs2331995

MISSENSE

CACNA1E

dbsnp.86:rs704326

calcium channel, voltage-dependent, R type, alpha 1E subunit. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death.

MISSENSE

dbsnp.83:rs627928

Ribonuclease L. encodes a component of the interferon-regulated 2-5A system that functions in the antiviral and antiproliferative roles of interferons. Mutations in this gene have been associated with predisposition to prostate cancer and this gene is a candidate for the hereditary prostate cancer 1 (HPC1) allele

MISSENSE

dbsnp.87:rs1144566

rs1144566

regulator of G-protein signaling 16. It inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits. It also may play a role in regulating the kinetics of signaling in the phototransduction cascade.

MISSENSE

ASPM rs964201 NM_018136.3 262799 snp A G Y H 1 195337523 2493

91156 NM_178275.4 269063 snp C T H Y 1 199461741 711

LGR6 rs788795 59352 271084 snp T C V A 1 200553828 591

C1orf157 NM_182579.2 274063 snp G A A V 1 202273219 97

C1orf116 79098 NM_023938.5 277974 snp A G S P Putative androgen-specific receptor 1 205262401 443

CR1 1378 NM_000573.3 278755 snp A T T S 1 205849538 1609

CR1 1378 NM_000573.3 278769 snp A G T A 1 205861942 1968

CR1L 1379 NM_175710.1 278970 snp T C L P 1 205957488 490

dbsnp.86:rs964201

259266

asp (abnormal spindle) homolog, microcephaly associated (Drosophila). Probable role in mitotic spindle regulation and coordination of mitotic processes (By similarity). May have a preferential role in regulating neurogenesis. MISSEN

SE

DKFZp434B1231

dbsnp.107:rs3738270

rs3738270

= IGFN1: immunoglobulin-like and fibronectin type III domain containing 1. Function unknown.

MISSENSE

dbsnp.86:rs788795

NM_001017403.1

leucine-rich repeat containing G protein-coupled receptor 6 , is a glycoprotein hormone receptor with a large N-terminal extracellular domain that contains leucine-rich repeats important for the formation of a horseshoe-shaped interaction motif for ligand binding

MISSENSE

dbsnp.111:rs4951039

rs4951039

284573

long intergenic non-protein coding RNA 303. Function unknown

MISSENSE

dbsnp.100:rs2842726

rs2842726

MISSENSE

dbsnp.111:rs4844609

rs4844609

complement component (3b/4b) receptor 1 (Knops blood group). Mediates cellular binding of particles and immune complexes that have activated complement. MISSEN

SE

dbsnp.100:rs2296160

rs2296160

complement component (3b/4b) receptor 1 (Knops blood group). Mediates cellular binding of particles and immune complexes that have activated complement. MISSEN

SE

dbsnp.100:rs2796257

rs2796257

complement component (3b/4b) receptor 1-like. Function unknown.

MISSENSE

rs669694 80342 NM_025228.1 281833 snp C G Q E 1 208017382 352

C1orf107 rs585627 27042 NM_014388.5 281979 snp C G Q E 1 208070821 66

TRAF3IP3

dbsnp.83:rs669694

TRAF3 interacting protein 3. Mediates cell growth by modulating the c-Jun N-terminal kinase signal transduction pathway. The encoded protein may also interact with a large multiprotein assembly containing the phosphatase 2A catalytic subunit

MISSENSE

dbsnp.83:rs585627

= DIEXF: digestive organ expansion factor homolog (zebrafish). Regulates the p53 pathway to control the expansion growth of digestive organs (By similarity). MISSEN

SE

CENPF rs335524 1063 NM_016343.3 289301 snp G A R Q 1 212892818 2728dbsnp.79:rs335524

centromere protein F, 350/400kDa (mitosin). Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potentialinhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia.

MISSENSE

USH2A 7399 NM_206933.1 291330 snp A G I T 1 214239002 2168

dbsnp.120:rs10864219

rs10864219

Usher syndrome 2A (autosomal recessive, mild). This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa.This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs.The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with sher syndrome type IIa and retinitis pigmentosa. MISSEN

SE

USH2A 7399 NM_206933.1 291599 snp C T R K 1 214415386 1485dbsnp.89:rs1805049

rs1805049


SE

USH2A 7399 NM_206933.1 291798 snp C T A T 1 214661928 124

EPRS 2058 NM_004446.2 298295 snp G T D E 1 218264247 307

FLJ43505 NM_207468.2 301898 snp T G I S 1 220986517 2

dbsnp.120:rs10779261

rs10779261


SE

dbsnp.98:rs2230301

rs2230301

glutamyl-prolyl-tRNA synthetase. Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. The protein encoded by this gene is a multifunctional aminoacyl-tRNA synthetase that catalyzes the aminoacylation of glutamic acid and proline tRNA species.

MISSENSE

dbsnp.100:rs2378607

rs2378607

400823

=FAM177B= family with sequence similarity 177, member B. Function unknown

MISSENSE

LBR 3930 NM_002296.2 306018 snp C T S N 1 223673766 153

MPN2 NM_183062.2 310360 snp A G M V 1 226099819 203

OBSCN 84033 NM_052843.2 310801 snp T A V D 1 226511187 1507

RNF187 XM_928029.3 311071 snp C T P S 1 226741196 99

C1orf124 83932 NM_032018.4 315631 snp C T P L 1 229555146 295

ZNF695 57116 NM_020394.3 345214 snp C T R K 1 245229280 83

dbsnp.98:rs2230419

rs2230419

lamin B receptor . The protein encoded by this gene belongs to the ERG4/ERG24 family. It localized in the nuclear envelope inner membrane and anchors the lamina and the heterochromatin to the membrane. It may mediate interaction between chromatin and lamin B. Mutations of this gene has been associated with autosomal recessive HEM/Greenberg skeletal dysplasia.

MISSENSE

dbsnp.119:rs9426581

rs9426581

339501

=PRSS38: protease, serine, 38. Potentially secreted. Probably serine-type endopeptidase activity. Function unknown.

MISSENSE

dbsnp.116:rs7532342

rs7532342

obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF. belongs to the family of giant sacromeric signaling proteins that includes titin and nebulin, and may have a role in the organization of myofibrils during assembly and may mediate interactions between the sarcoplasmic reticulum and myofibrils

MISSENSE

dbsnp.116:rs6684355

rs6684355

149603

ring finger protein 187 . E3 ubiquitin-protein ligase that acts as a coactivator of JUN-mediated gene activation in response to growth factor signaling via the MAP3K1 pathway, independently from MAPK8 MISSEN

SE

dbsnp.100:rs2437150

rs2437150

Zinc finger RAD18 domain-containing protein. Function unknown. Probably DNA repair/DNA binding (inferred from electronic annotation, source InterPro)

MISSENSE

dbsnp.100:rs2642973

rs2642973

Zinc finger protein 695. May be involved in transcriptional regulation MISSEN

SE

OR2B11 345854 snp T C D G 1 245681008 299

OR2B11 345855 snp G A T I 1 245681029 292

OR2B11 345857 snp C T V M 1 245681315 197

OR2G2 81470 346037 snp G C V L 1 245818641 119

OR2G2 81470 346038 snp T C L P 1 245818783 166

OR2G3 81469 346079 snp A G M V 1 245835684 58

OR11L1 346521 snp C G R P 1 246071309 170

OR11L1 346523 snp G C F L 1 246071470 116

OR11L1 346524 snp C T G S 1 246071499 107

OR2T11 347224 snp A G C R 1 246856697 118

OR5BU1 347448 snp C T S N 1 246911719 169

SH3YL1 all 2 26751 NM_015677.1 347947 snp T C M V 2 232799 0

dbsnp.120:rs12070953

rs12070953

127623

NM_001004492.1

olfactory receptor, family 2, subfamily B, member 11. Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell

MISSENSE

dbsnp.120:rs12065526

rs12065526

127623

NM_001004492.1


MISSENSE

dbsnp.116:rs6695302

rs6695302

127623

NM_001004492.1


MISSENSE

dbsnp.87:rs1151687

rs1151687

NM_001001915.1

olfactory receptor, family 2, subfamily G, member 2

MISSENSE

dbsnp.120:rs10925085

rs10925085

NM_001001915.1


MISSENSE

dbsnp.129:rs61748963

rs61748963

NM_001001914.1


MISSENSE

dbsnp.120:rs10888255

rs10888255

391189

NM_001001959.1

olfactory receptor, family 11, subfamily L, member 1

MISSENSE

dbsnp.111:rs4607924

rs4607924

391189

NM_001001959.1


MISSENSE

dbsnp.120:rs10888257

rs10888257

391189

NM_001001959.1


MISSENSE

dbsnp.92:rs1892443

rs1892443

127077

NM_001001964.1

olfactory receptor, family 2, subfamily T, member 11

MISSENSE

dbsnp.92:rs2000390

rs2000390

401994

NM_001004734.1

olfactory receptor, family 14, subfamily I, member 1

MISSENSE

dbsnp.119:rs10181051

rs10181051

SH3 domain containing, Ysc84-like 1 (S. cerevisiae). Function unknown. According to Refseq annotation SNP is in intron in the 2 isoforms, so no effect is expected

MISSTART

TPO rs732609 7173 NM_175721.1 350833 snp A C T P 2 1478933 724

RNF144A rs364891 9781 NM_014746.3 361842 snp A G T A 2 7054517 3

NAG 51594 NM_015909.2 377147 snp T C I V 2 15592136 242

KCNS3 3790 NM_002252.3 380696 snp A G T A 2 17977103 449

HS1BP3 64342 NM_022460.3 384985 snp C T V M 2 20687978 259

dbsnp.86:rs732609

Thyroid peroxidase. Iodination and coupling of the hormonogenic tyrosines in thyroglobulin to yield the thyroid hormones T(3) and T(4). Mutations in this gene are associated with several disorders of thyroid hormonogenesis, including congenital hypothyroidism, congenital goiter, and thyroid hormone organification defect IIA. MISSEN

SE

dbsnp.80:rs364891

Ring finger protein 144A. Putative E3 ubiquitin ligase. The mouse counterpart of this protein has been shown to interact with Ube2l3/UbcM4, which is an ubiquitin-conjugating enzyme involved in embryonic development.

MISSENSE

dbsnp.121:rs13029846

rs13029846

N-acetylglutamate synthase. Plays a role in the regulation of ureagenesis by producing variable amounts of N-acetylglutamate (NAG), thus modulating carbamoylphosphate synthase I (CPSI) activity. Deficiencies in N-acetylglutamate synthase have been associated with hyperammonemia. MISSEN

SE

dbsnp.111:rs4832524

rs4832524

potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3. Potassium channel subunit. Modulates channel activity and reduces the ion flow.

MISSENSE

dbsnp.100:rs2305458

rs2305458

LS1 binding protein 3. The protein encoded by this gene shares similarity with mouse Hs1bp3, an Hcls1/Hs1-interacting protein that may be involved in lymphocyte activation. May be a modulator of IL-2 signaling (By similarity). MISSEN

SE

APOB 338 NM_000384.2 385304 snp C T S N 2 21078785 4337

APOB 338 NM_000384.2 385307 snp C T R Q 2 21082331 3637

dbsnp.86:rs1042034

rs1042034

apolipoprotein B. This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. MISSEN

SE

dbsnp.89:rs1801701

rs1801701


SE

APOB 338 NM_000384.2 385336 snp G A T I 2 21117404 97

ATAD2B 54454 NM_017552.1 388509 snp T C Q R 2 23962155 206

ADCY3 109 NM_004036.3 389962 snp A G S P 2 24995041 106

GPR113 NM_153835.3 391900 snp C T A T 2 26390197 204

dbsnp.88:rs1367117

rs1367117


SE

dbsnp.116:rs7579201

rs7579201

ATPase family, AAA domain containing 2B. The protein encoded by this gene belongs to the AAA ATPase family, CDC48 subfamily. This subfamily members in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. The exact function of this protein is not known.

MISSENSE

dbsnp.120:rs11676272

rs11676272

Adenylate cyclase 3, is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This protein appears to be widely expressed in various human tissues and may be involved in a number of physiological and pathophysiological metabolic processes

MISSENSE

dbsnp.94:rs2052937

rs2052937

165082

G protein-coupled receptor 113. Orphan receptor.

MISSENSE

ABHD1 84696 NM_032604.2 393053 snp T G D E 2 27205451 136

ALK 238 NM_004304.3 395744 snp T C I V 2 29270075 1460

MTIF2 rs11357 4528 443995 snp C T V I 2 55323618 555

MTIF2 4528 444038 snp G T T N 2 55344322 58

CCDC104 NM_080667.5 444559 snp A G D G 2 55624664 242

ETAA1 54465 NM_019002.3 459828 snp G A S N 2 67484483 388

dbsnp.116:rs6715286

rs6715286

abhydrolase domain containing 1 . This gene is a member of the AB hydrolase superfamily and encodes a protein with an alpha/beta hydrolase fold. This domain is common to a number of hydrolytic enzymes of widely differing phylogenetic origins and catalytic functions

MISSENSE

dbsnp.89:rs1670283

rs1670283

Anaplastic lymphoma receptor tyrosine kinase. Orphan receptor with a tyrosine-protein kinase activity. Appears to play an important role in the normal development and function of the nervous system.

MISSENSE

dbsnp.52:rs11357

NM_001005369.1

mitochondrial translational initiation factor 2. One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. MISSEN

SE

dbsnp.86:rs1056445

rs1056445

NM_001005369.1

mitochondrial translational initiation factor 2. One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. MISSEN


rs1045910

112942

coiled-coil domain containing 104. Function unknown.

MISSENSE

dbsnp.107:rs3770657

rs3770657

Ewing tumor-associated antigen 1. Function unknown

MISSENSE

ETAA1 54465 NM_019002.3 459830 snp C T P S 2 67485628 770

CAPG rs6886 822 NM_001747.2 484404 snp T C H R 2 85475569 334

SFTPB 6439 NM_198843.1 484812 snp G A T I 2 85747251 130

THNSL2 55258 NM_018271.3 487921 snp G A G E 2 88253905 40

dbsnp.107:rs3770655

rs3770655

Ewing tumor-associated antigen 1. Function unknown

MISSENSE

dbsnp.52:rs6886

capping protein (actin filament), gelsolin-like. Calcium-sensitive protein which reversibly blocks the barbed ends of actin filaments but does not sever preformed actin filaments. May play an important role in macrophage function. May play a role in regulating cytoplasmic and/or nuclear structures through potential interactions with actin. May bind DNA. By capping the barbed ends of actin filaments, the encoded protein contributes to the control of actin-based motility in non-muscle cells. MISSEN

SE

dbsnp.86:rs1130866

rs1130866

surfactant protein B. This gene encodes the pulmonary-associated surfactant protein B (SPB), an amphipathic surfactant protein essential for lung function and homeostasis after birth. Multiple mutations in this gene have been identified, which cause pulmonary surfactant metabolism dysfunction type 1 and are associated with fatal respiratory distress in the neonatal period.

MISSENSE

dbsnp.108:rs4129190

rs4129190

Threonine synthase-like 2 (S. cerevisiae) . Acts as a catabolic phospho-lyase on both gamma- and beta-phosphorylated substrates. Degrades O-phospho-threonine (PThr) to alpha-ketobutyrate, ammonia and phosphate (by similarity). Secreted form is a potent inducer of osteoblastic production of IL6. May act to exacerbate inflammation and/or bone turnover under inflammatory conditions.

MISSENSE

EIF2AK3 9451 NM_004836.4 488473 snp C A A S 2 88656005 703

EIF2AK3 rs13045 9451 NM_004836.4 488485 snp T C Q R 2 88676237 165

ASTL 493729 snp T G K Q 2 96159334 276

ASTL rs749458 493731 snp T C Q R 2 96159583 221

dbsnp.89:rs1805165

rs1805165

Eukaryotic translation initiation factor 2-alpha kinase 3. The protein encoded by this gene phosphorylates the alpha subunit of eukaryotic translation-initiation factor 2 (EIF2), leading to its inactivation, and thus to a rapid reduction of translational initiation and repression of global protein synthesis. It is a type I membrane protein located in the endoplasmic reticulum (ER), where it is induced by ER stress caused by malfolded proteins. Mutations in this gene are associated with Wolcott-Rallison syndrome.

MISSENSE

dbsnp.52:rs13045

Eukaryotic translation initiation factor 2-alpha kinase 3. The protein encoded by this gene phosphorylates the alpha subunit of eukaryotic translation-initiation factor 2 (EIF2), leading to its inactivation, and thus to a rapid reduction of translational initiation and repression of global protein synthesis. It is a type I membrane protein located in the endoplasmic reticulum (ER), where it is induced by ER stress caused by malfolded proteins. Mutations in this gene are associated with Wolcott-Rallison syndrome.

MISSENSE

dbsnp.89:rs1657502

rs1657502

431705

NM_001002036.3

astacin-like metallo-endopeptidase (M12 family). Function unknown. Expressed in promyelocytic leukemia HL-60 cells, Burkitt's lymphoma Raji cells, and also in some ovarian carcinomas. Not detected in normal tissues.

MISSENSE

dbsnp.86:rs749458

431705

NM_001002036.3

astacin-like metallo-endopeptidase (M12 family). Function unknown. Expressed in promyelocytic leukemia HL-60 cells, Burkitt's lymphoma Raji cells, and also in some ovarian carcinomas. Not detected in normal tissues.

MISSENSE

NPAS2 4862 NM_002518.3 499050 snp A G T A 2 100957735 393

9392 NM_004257.3 504819 snp T C H R 2 105252392 724

POLR1B 84172 NM_019014.3 514332 snp C T S L 2 113025943 294

dbsnp.100:rs2305160

rs2305160

neuronal PAS domain protein 2. The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription factors. A similar mouse protein may play a regulatory role in the acquisition of specific types of memory. It also may function as a part of a molecular clock operative in the mammalian forebrain.

MISSENSE

TGFBRAP1

dbsnp.98:rs2241797

rs2241797

transforming growth factor, beta receptor associated protein 1. Plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling. May recruit SMAD4 to the vicinity of the receptor complex and facilitate its interaction with receptor-regulated Smads, such as SMAD2. MISSEN

SE

dbsnp.88:rs1545133

rs1545133

polymerase (RNA) I polypeptide B, 128kDa. DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). MISSEN

SE

NT5DC4 514611 snp A C Y S 2 113199249 572

IL1F6 rs895497 27179 NM_014440.1 515071 snp A G Q R 2 113480045 11

IL1F10 84639 NM_173161.1 515243 snp T C I T 2 113548782 43

IL1F10 84639 NM_173161.1 515244 snp C A A D 2 113548803 50

80775 NM_030577.2 525112 snp A G I V 2 120154992 31

80775 NM_030577.2 525114 snp C G D E 2 120155699 266

LCT 3938 NM_002299.2 550425 snp T C I V 2 136292003 361

NEB 4703 NM_004543.3 573691 snp C T V M 2 152235817 1490

dbsnp.111:rs4849116

rs4849116

284958

XM_001716541.1

5'-nucleotidase domain containing 4. Function unknown

MISSENSE

dbsnp.86:rs895497

interleukin 36, alpha. Secreted cytokine, function unknown.

MISSENSE

dbsnp.116:rs6761276

rs6761276

interleukin 1 family, member 10 (theta). Binds soluble IL-1 receptor type 1. The protein encoded by this gene is a member of the interleukin 1 cytokine family. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. This cytokine is thought to participate in a network of interleukin 1 family members to regulate adapted and innate immune responses.

MISSENSE

dbsnp.116:rs6743376

rs6743376

interleukin 1 family, member 10 (theta). Binds soluble IL-1 receptor type 1. The protein encoded by this gene is a member of the interleukin 1 cytokine family. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. This cytokine is thought to participate in a network of interleukin 1 family members to regulate adapted and innate immune responses.

MISSENSE

TMEM177

dbsnp.121:rs13011768

rs13011768

Transmembrane protein 177 . Function unknown.

MISSENSE

TMEM177

dbsnp.92:rs1983406

rs1983406

Transmembrane protein 177 . Function unknown.

MISSENSE

dbsnp.111:rs4954449

rs4954449

lactase , splits lactose in the small intestine.

MISSENSE

dbsnp.116:rs7426114

rs7426114

nebulin. This giant muscle protein may be involved in maintaining the structural integrity of sarcomeres and the membrane system associated with the myofibrils. Bind and stabilize F-actin.

MISSENSE

NEB 4703 NM_004543.3 573695 snp T A K N 2 152244743 1026

IFIH1 64135 NM_022168.2 588838 snp C T A T 2 162832296 945

TTC21B 79809 NM_024753.3 593262 snp T C T A 2 166496581 275

dbsnp.116:rs6735208

rs6735208

nebulin. This giant muscle protein may be involved in maintaining the structural integrity of sarcomeres and the membrane system associated with the myofibrils. Bind and stabilize F-actin.

MISSENSE

dbsnp.92:rs1990760

rs1990760

interferon induced with helicase C domain 1. RNA helicase that, through its ATP-dependent unwinding of RNA, may function to promote message degradation by specific RNases. Seems to have growth suppressive properties. Involved in innate immune defense against viruses. Upon interaction with intracellular dsRNA produced during viral replication, triggers a transduction cascade involving MAVS/IPS1, which results in the activation of NF-kappa-B, IRF3 and IRF7 and the induction of the expression of antiviral cytokines such as IFN-beta and RANTES (CCL5). ATPase activity is specifically induced by dsRNA. Essential for the production of interferons in response to picornaviruses. MISSEN

SE

dbsnp.116:rs7592429

rs7592429

tetratricopeptide repeat domain 21B. May negatively modulate SHH (Sonic Hedgehog) signal transduction and may play a role in retrograde intraflagellar transport in cilia (By similarity). SHH plays a key role in regulating vertebrate organogenesis, controls cell division of adult stem cells and has been implicated in development of some cancers. MISSEN

SE

SCN1A 6323 NM_006920.4 593379 snp C T A T 2 166601033 1055

MYO3B 600423 snp G A V I 2 170969032 769

ZAK 51776 NM_016653.2 605023 snp C T S L 2 173836758 530

TTC30B NM_152517.2 610886 snp C T R H 2 178125387 116

dbsnp.100:rs2298771

rs2298771

sodium channel, voltage-gated, type I, alpha subunit. The vertebrate sodium channel is a voltage-gated ion channel essential for the generation and propagation of action potentials, mainly in nerve and muscle.

MISSENSE

dbsnp.116:rs6736609

rs6736609

140469

NM_001083615.1

myosin IIIB. Probable actin-based motor with a protein kinase activity. MISSEN

SE

dbsnp.107:rs3769148

rs3769148

sterile alpha motif and leucine zipper containing kinase AZK. Stress-activated component of a protein kinase signal transduction cascade. Regulates the JNK and p38 pathways. Pro-apoptotic. Role in regulation of S and G2 cell cycle checkpoint by direct phosphorylation of CHEK2. Isoform 1, but not isoform 2, causes cell shrinkage and disruption of actin stress fibers. Isoform 1 may have role in neoplastic cell transformation and cancer development. Isoform 1, but not isoform 2, phosphorylates histone H3 at 'Ser-28'. MISSEN

SE

dbsnp.120:rs11694988

rs11694988

150737

tetratricopeptide repeat domain 30B. Required for polyglutamylation of axonemal tubulin (By similarity). Plays a role in anterograde intraflagellar transport (IFT), the process by which cilia precursors are transported from the base of the cilium to the site of their incorporation at the tip (By similarity). MISSEN

SE

PDE11A 50940 NM_016953.3 611884 snp C T R Q 2 178644859 183

TTN 7273 NM_133432.2 612625 snp C G A P 2 179153013 13475

dbsnp.116:rs6433711

rs6433711

phosphodiesterase 11A. Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides cAMP and cGMP. Catalyzes the hydrolysis of both cAMP and cGMP to 5'-AMP and 5'-GMP, respectively. Mutations in this gene are a cause of Cushing disease and adrenocortical hyperplasia. Their functions include vascular smooth muscle proliferation and contraction, cardiac contractility, platelet aggregation, hormonesecretion, immune cell activation, and they are involved in learning and memory. MISSEN

SE

dbsnp.110:rs4145333

rs4145333

titin. Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. MISSEN

SE

TTN 7273 NM_133432.2 612708 snp C T S N 2 179332002 3372

TTN 7273 NM_133432.2 612722 snp C T V M 2 179337705 3214

57703 NM_020943.2 614506 snp A T S R 2 180518508 772

ZNF804A 91752 NM_194250.1 622660 snp A G H R 2 185510607 746

dbsnp.100:rs2291310

rs2291310


SE

dbsnp.100:rs2291311

rs2291311


SE

KIAA1604

dbsnp.116:rs6433818

rs6433818

CWC22 spliceosome-associated protein homolog (S. cerevisiae). May be involved in pre-mRNA splicing. MISSEN

SE

dbsnp.120:rs12477430

rs12477430

zinc finger protein 804A. Function unknown.

MISSENSE

FLJ44048 NM_207482.2 623849 snp A C E D 2 186378348 54

DNAH7 56171 NM_018897.2 637634 snp A G L P 2 196381777 3318

CASP10 843 NM_032977.3 644746 snp T A L I 2 201790703 521

ALS2 57679 NM_020919.2 645668 snp C T V M 2 202333859 367

dbsnp.116:rs7576532

rs7576532

401024

fibrous sheath interacting protein 2. Function unknown.

MISSENSE

dbsnp.121:rs13411834

rs13411834

dynein, axonemal, heavy chain 7. Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP (By similarity). MISSEN

SE

dbsnp.121:rs13006529

rs13006529

caspase 10, apoptosis-related cysteine peptidase. Involved in the activation cascade of caspases responsible for apoptosis execution. Recruited to both Fas-and TNFR-1 receptors in a FADD dependent manner. May participate in the granzyme B apoptotic pathways. Cleaves and activates caspase-3, -4, -6, -7, -8, and -9. Mutations in this gene are associated with type IIA autoimmune lymphoproliferative syndrome, non-Hodgkin lymphoma and gastric cancer.

MISSENSE

dbsnp.106:rs3219156

rs3219156

amyotrophic lateral sclerosis 2 (juvenile). The protein functions as a guanine nucleotide exchange factor for the small GTPase RAB5. The protein localizes with RAB5 on early endosomal compartments, and functions as a modulator for endosomal dynamics. Mutations in this gene result in several forms of juvenile lateral sclerosis and infantile-onset ascending spastic paralysis.

MISSENSE

PARD3B NM_057177.5 649682 snp G A R K 2 205677464 191

PIP5K3 NM_015040.3 654773 snp T C L S 2 208898574 931

PIP5K3 rs893254 NM_015040.3 654774 snp A T Q L 2 208898763 994

dbsnp.100:rs2289025

rs2289025

117583

par-3 partitioning defective 3 homolog B (C. elegans). Putative adapter protein involved in asymmetrical cell division and cell polarization processes. May play a role in the formation of epithelial tight junctions. MISSEN

SE

dbsnp.100:rs2363468

rs2363468

200576

phosphoinositide kinase, FYVE finger containing. Catalyzes the phosphorylation of phosphatidylinositol-3-phosphate to phosphatidylinositol-3,5-bisphosphate. Required for endocytic-vacuolar pathway and nuclear migration. Plays a role in the biogenesis of endosome carrier vesicles (ECV)/ multivesicular bodies (MVB) transport intermediates from early endosomes. Mutations in this gene cause corneal fleck dystrophy (CFD).

MISSENSE

dbsnp.86:rs893254

200576


MISSENSE

PIP5K3 rs893253 NM_015040.3 654775 snp C G T S 2 208898772 997

PIP5K3 NM_015040.3 654776 snp C A Q K 2 208899326 1182

dbsnp.86:rs893253

200576


MISSENSE

dbsnp.88:rs1529979

rs1529979

200576


MISSENSE

BARD1 580 NM_000465.2 666315 snp C G R S 2 215353708 377

DIRC3 670785 snp A C F C 2 218312491 54

CCDC108 NM_194302.2 672636 snp T G M L 2 219611501 65

OBSL1 23363 NM_015311.1 673348 snp T C Q R 2 220127582 1577

OBSL1 23363 NM_015311.1 673383 snp C T R K 2 220138446 722

dbsnp.98:rs2229571

rs2229571

BRCA1 associated RING domain 1. Probable E3 ubiquitin-protein ligase. The BRCA1-BARD1 heterodimer specifically mediates the formation of 'Lys-6'-linked polyubiquitin chains and coordinates a diverse range of cellular pathways such as DNA damage repair, ubiquitination and transcriptional regulation to maintain genomic stability. Plays a central role in the control of the cell cycle in response to DNA damage. Acts by mediating ubiquitin E3 ligase activity that is required for its tumor suppressor function. Also forms a heterodimer with CSTF1/CSTF-50 to modulate mRNA processing and RNAP II stability by inhibiting pre-mRNA 3' cleavage. MISSEN

SE

dbsnp.111:rs4672848

rs4672848

729582

XM_001725524.1

disrupted in renal carcinoma 3. Function unknown

MISSENSE

dbsnp.116:rs6736922

rs6736922

255101

coiled-coil domain containing 108. Function unknown.

MISSENSE

dbsnp.120:rs10932814

rs10932814

obscurin-like 1. Cytoskeletal adaptor proteins function in linking the internal cytoskeleton of cells to the cell membrane. This gene encodes a cytoskeletal adaptor protein, which is a member of the Unc-89/obscurin family.Mutations in this gene cause 3M syndrome type 2.

MISSENSE

dbsnp.86:rs1039898

rs1039898

obscurin-like 1. Cytoskeletal adaptor proteins function in linking the internal cytoskeleton of cells to the cell membrane. This gene encodes a cytoskeletal adaptor protein, which is a member of the Unc-89/obscurin family.Mutations in this gene cause 3M syndrome type 2.

MISSENSE

STK11IP rs627530 NM_052902.2 673463 snp C T S F 2 220184686 751

SLC4A3 rs635311 6508 NM_201574.2 673500 snp A C D A 2 220210610 893

FARSB rs7185 10056 NM_005687.3 678064 snp C T V I 2 223144850 584

KCNE4 23704 NM_080671.2 678748 snp T G D E 2 223626226 144

57624 NM_020864.1 683398 snp A C T P 2 226200013 585

SP100 rs836237 6672 691324 snp T C M T 2 231114923 825

dbsnp.83:rs627530

114790

serine/threonine kinase 11 interacting protein. May regulate STK11 function by controlling its subcellular localization. STK11 has an essential role in G1 cell cycle arrest, phosphorylates and activates members of the AMPK-related subfamily of protein kinases, is a tumor suppressor.

MISSENSE

dbsnp.83:rs635311

solute carrier family 4, anion exchanger, member 3. Plasma membrane anion exchange protein of wide distribution. Mediates at least a part of the Cl(-)/HCO3(-) exchange in cardiac myocytes.

MISSENSE

dbsnp.52:rs7185

phenylalanyl-tRNA synthetase, beta subunit. Encodes a highly conserved enzyme that belongs to the aminoacyl-tRNA synthetase class IIc subfamily. This enzyme comprises the regulatory beta subunits that form a tetramer with two catalytic alpha subunits. In the presence of ATP, this tetramer is responsible for attaching L-phenylalanine to the terminal adenosine of the appropriate tRNA. MISSEN

SE

dbsnp.120:rs12621643

rs12621643

potassium voltage-gated channel, Isk-related family, member 4. Ancillary protein that assembles as a beta subunit with a voltage-gated potassium channel complex of pore-forming alpha subunits. Modulates the gating kinetics and enhances stability of the channel complex.

MISSENSE

KIAA1486

dbsnp.107:rs3748993

rs3748993

Hypothetical protein LOC57624. Function unknown.

MISSENSE

dbsnp.86:rs836237

NM_001080391.1

SP100 nuclear antigen. May play a role in the control of gene expression. MISSEN

SE

ECEL1 9427 NM_004826.2 693863 snp G A H Y 2 233057831 327

COL6A3 1293 NM_057164.2 701870 snp C G A P 2 237908202 2844

MLPH 79083 NM_024101.5 702397 snp A G H R 2 238107964 346

ATG4B 23192 NM_178326.2 709576 snp T A L Q 2 242259445 353

IL5RA 3568 NM_175726.1 718340 snp T C I V 3 3114956 128

PRRT3 rs279601 NM_207351.3 733085 snp G C Q E 3 9966387 137

dbsnp.88:rs1529874

rs1529874

endothelin converting enzyme-like 1. May contribute to the degradation of peptide hormones and be involved in the inactivation of neuronal peptides.

MISSENSE

dbsnp.100:rs2270669

rs2270669

collagen, type VI, alpha 3. Collagen VI acts as a cell-binding protein. Binds extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. MISSEN

SE

dbsnp.100:rs2292884

rs2292884

melanophilin. Rab effector protein involved in melanosome (pigment-producing organel) transport. Serves as link between melanosome-bound RAB27A and the motor protein MYO5A. MISSEN

SE

dbsnp.116:rs7601000

rs7601000

ATG4 autophagy related 4 homolog B (S. cerevisiae). Cysteine protease required for autophagy. Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed.

MISSENSE

dbsnp.100:rs2290610

rs2290610

interleukin 5 receptor, alpha. This is the receptor for interleukin-5, a cytokine that acts as a growth and differentiation factor for both B cells and eosinophils.

MISSENSE

dbsnp.79:rs279601

285368

proline-rich transmembrane protein 3. Function unknown.

MISSENSE

IRAK2 rs708035 3656 NM_001570.3 733477 snp T A D E 3 10251162 430

CAND2 23066 NM_012298.1 738461 snp G A A T 3 12850442 1107

NUP210 rs354479 23225 NM_024923.2 739236 snp A G L S 3 13336390 1751

FBLN2 2199 NM_001998.2 739769 snp A G T A 3 13645536 853

TBC1D5 9779 NM_014744.1 745806 snp T C I V 3 17183270 695

EFHB NM_144715.3 748602 snp G A T I 3 19934759 381

dbsnp.86:rs708035

interleukin-1 receptor-associated kinase 2. Binds to the IL-1 type I receptor following IL-1 engagement, triggering intracellular signaling cascades leading to transcriptional up-regulation and mRNA stabilization.

MISSENSE

dbsnp.120:rs12629133

rs12629133

cullin-associated and neddylation-dissociated 2 (putative) . May play a role in the assembly of ubiquitin ligase complexes and modulate the ubiquitination of target proteins. May be a transcription regulator (Potential). MISSEN

SE

dbsnp.79:rs354479

nucleoporin 210kDa. Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. MISSEN

SE

dbsnp.119:rs9843344

rs9843344

fibulin 2. This gene encodes an extracellular matrix protein, which belongs to the fibulin family. This protein binds various extracellular ligands and calcium. It may play a role during organ development, in particular, during the differentiation of heart, skeletal and neuronal structures.

MISSENSE

dbsnp.86:rs1138454

rs1138454

TBC1 domain family, member 5. May act as a GTPase-activating protein for Rab family protein(s). MISSEN

SE

dbsnp.101:rs2929366

rs2929366

151651

EF-hand domain family, member B . Function unknown.

MISSENSE

rs818818 9389 NM_004803.3 777096 snp G A V M 3 38325522 283

rs818817 9389 NM_004803.3 777097 snp A G S G 3 38325546 291

ULK4 54986 NM_017886.2 782210 snp T C I V 3 41935009 223

ULK4 54986 NM_017886.2 782298 snp T C K R 3 41971139 38

KBTBD5 NM_152393.2 783327 snp A G N S 3 42703147 344

KBTBD5 rs123509 NM_152393.2 783332 snp T C C R 3 42708471 616

FLJ36157 XM_371632.5 785496 snp C A P Q 3 44258811 87

SLC22A14

dbsnp.86:rs818818

solute carrier family 22, member 14. This gene encodes a member of the organic-cation transporter family and is a transmembrane protein which is thought to transport small molecules and since this protein is conserved among several species, it is suggested to have a fundamental role in mammalian systems.

MISSENSE

SLC22A14

dbsnp.86:rs818817

solute carrier family 22, member 14. This gene encodes a member of the organic-cation transporter family and is a transmembrane protein which is thought to transport small molecules and since this protein is conserved among several species, it is suggested to have a fundamental role in mammalian systems.

MISSENSE

dbsnp.89:rs1716975

rs1716975

unc-51-like kinase 4 (C. elegans). Function unknown.

MISSENSE

dbsnp.100:rs2272007

rs2272007

unc-51-like kinase 4 (C. elegans). Function unknown.

MISSENSE

dbsnp.116:rs6805421

rs6805421

131377

kelch repeat and BTB (POZ) domain containing 5. Function unknown.

MISSENSE

dbsnp.79:rs123509

131377

kelch repeat and BTB (POZ) domain containing 5. Function unknown.

MISSENSE

dbsnp.116:rs7645375

rs7645375

375337

chromosome 3 open reading frame 77. Function unknown.

MISSENSE

CDCP1 64866 NM_022842.3 786619 snp T C D G 3 45102518 708

CDCP1 64866 NM_022842.3 786638 snp T C Q R 3 45109825 524

dbsnp.119:rs9874077

rs9874077

B domain containing protein 1. May be involved in cell adhesion and cell matrix association. May play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. May be a novel marker for leukemia diagnosis and for immature hematopoietic stem cell subsets. Belongs to the tetraspanin web involved in tumor progression and metastasis. Is a transmembrane protein containing three extracellular CUB domains. This protein is found to be overexpressed in colon and lung cancers. Its expression level is correlated with the metastatic ability of carcinoma cells. This protein is located on the cell surface. MISSEN

SE

dbsnp.107:rs3749191

rs3749191

B domain containing protein 1. May be involved in cell adhesion and cell matrix association. May play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. May be a novel marker for leukemia diagnosis and for immature hematopoietic stem cell subsets. Belongs to the tetraspanin web involved in tumor progression and metastasis. Is a transmembrane protein containing three extracellular CUB domains. This protein is found to be overexpressed in colon and lung cancers. Its expression level is correlated with the metastatic ability of carcinoma cells. This protein is located on the cell surface. MISSEN

SE

MST1R 4486 NM_002447.2 792516 snp T C R G 3 49899943 1334

MST1R 4486 NM_002447.2 792523 snp T C Q R 3 49911105 522

HYAL2 rs709210 8692 NM_033158.2 792917 snp A C S A 3 50332872 17

STAB1 23166 NM_015136.2 795366 snp A G M V 3 52519509 911

dbsnp.86:rs1062633

rs1062633

macrophage stimulating 1 receptor (c-met-related tyrosine kinase). Receptor for macrophage stimulating protein (MSP). Has a tyrosine-protein kinase activity. MISSEN

SE

dbsnp.98:rs2230590

rs2230590

macrophage stimulating 1 receptor (c-met-related tyrosine kinase). Receptor for macrophage stimulating protein (MSP). Has a tyrosine-protein kinase activity. MISSEN

SE

dbsnp.86:rs709210

hyaluronoglucosaminidase 2. Hydrolyzes high molecular weight hyaluronic acid to produce an intermediate-sized product which is further hydrolyzed by sperm hyaluronidase to give small oligosaccharides. Displays very low levels of activity. Associates with and negatively regulates MST1R (macrophage stimulating 1 receptor) . MISSEN

SE

dbsnp.119:rs9835659

rs9835659

stabilin 1. Acts as a scavenger receptor for acetylated low density lipoprotein. Binds to both Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. When inhibited in endothelial tube formation assays, there is a marked decrease in cell-cell interactions, suggesting a role in angiogenesis. Involved in the delivery of newly synthesized CHID1/SI-CLP from the biosynthetic compartment to the endosomal/lysosomal system. MISSEN

SE

STAB1 23166 NM_015136.2 795375 snp G C A P 3 52529343 1832

STAB1 23166 NM_015136.2 795378 snp A G I V 3 52531929 2281

dbsnp.116:rs7630214

rs7630214


SE

dbsnp.111:rs4434138

rs4434138


SE

STAB1 rs13303 23166 NM_015136.2 795380 snp T C M T 3 52533047 2505

ITIH1 rs678 3697 NM_002215.2 795812 snp A T E V 3 52796020 584

ITIH1 3697 NM_002215.2 795813 snp A G Q R 3 52796050 594

dbsnp.52:rs13303


SE

dbsnp.36:rs678

inter-alpha (globulin) inhibitor H1. May act as a carrier of hyaluronan in serum or as a binding protein between hyaluronan and other matrix protein, including those on cell surfaces in tissues to regulate the localization, synthesis and degradation of hyaluronan which are essential to cells undergoing biological processes. MISSEN

SE

dbsnp.86:rs1042779

rs1042779


SE

ITIH4 3700 NM_002218.3 795856 snp G T P T 3 52827577 697

ITIH4 3700 NM_002218.3 795867 snp A T I N 3 52836250 84

CCDC66 801392 snp A G Q R 3 56602637 265

PXK 54899 NM_017771.3 803910 snp A G K R 3 58370902 480

PXK 54899 NM_017771.3 803962 snp C T A V 3 58385593 534

dbsnp.111:rs4687657

rs4687657


SE

dbsnp.121:rs13072536

rs13072536



rs1491170

285331

NM_001012506.1

coiled-coil domain containing 66 . Function unknown.

MISSENSE

dbsnp.129:rs56384862

rs56384862

PX domain containing serine/threonine kinase. Binds to and modulates brain Na,K-ATPase subunits ATP1B1 and ATP1B3 and may thereby participate in the regulation of electrical excitability and synaptic transmission. May not display kinase activity. MISSEN

SE

dbsnp.126:rs34579268

rs34579268

PX domain containing serine/threonine kinase. Binds to and modulates brain Na,K-ATPase subunits ATP1B1 and ATP1B3 and may thereby participate in the regulation of electrical excitability and synaptic transmission. May not display kinase activity. MISSEN

SE

FRMD4B 23150 NM_015123.1 822588 snp G A S L 3 69312750 946

ZNF654 55279 NM_018293.2 853511 snp T C I T 3 88272030 293

ALCAM 214 NM_001627.2 875416 snp C T T M 3 106743209 300

HHLA2 11148 NM_007072.2 879640 snp T C I T 3 109554987 29

MYH15 22989 NM_014981.1 879808 snp G A H Y 3 109671682 503

MORC1 27136 NM_014429.2 880424 snp G A H Y 3 110172910 835

BTLA 887384 snp G A P L 3 113667714 218

dbsnp.119:rs9831516

rs9831516

FERM domain containing 4B . Member of GRP1 signaling complexes that are acutely recruited to plasma membrane ruffles in response to insulin receptor signaling. May function as a scaffolding protein (By similarity) MISSEN

SE

dbsnp.116:rs7653652

rs7653652

zinc finger protein 654. May be involved in transcriptional regulation (By similarity)

MISSENSE

dbsnp.86:rs1044243

rs1044243

activated leukocyte cell adhesion molecule. Cell adhesion molecule that binds to CD6. Involved in neurite extension by neurons via heterophilic and homophilic interactions. May play a role in the binding of T- and B-cells to activated leukocytes, as well as in interactions between cells of the nervous system. MISSEN

SE

dbsnp.116:rs6779254

rs6779254

HERV-H LTR-associating 2 (Human endogenous retrovirus-H long terminal repeat-associating protein 2). Single-pass type I membrane protein (By similarity). Function unknown MISSEN

SE

dbsnp.119:rs9868484

rs9868484

myosin, heavy chain 15. Function: Muscle contraction (By similarity) MISSEN

SE

dbsnp.100:rs2593943

rs2593943

MORC family CW-type zinc finger 1. Function: required for spermatogenesis (By similarity) MISSEN

SE

dbsnp.119:rs9288952

rs9288952

151888

NM_001085357.1

B and T lymphocyte associated. Lymphocyte inhibitory receptor which inhibits lymphocytes during immune response. MISSEN

SE

CD200R1 NM_138806.3 888008 snp C G E Q 3 114125257 334

CD200R1 NM_138806.3 888011 snp A C H Q 3 114130521 199

C3orf17 25871 888107 snp A T F I Function unknown. 3 114209873 259

rs930818 889321 snp A G V A Function unknown. 3 114856619 2199

IGSF11 897143 snp C A E D 3 120104353 332

UPK1B 7348 NM_006952.3 897495 snp A G Q R 3 120391848 112

dbsnp.119:rs9865242

rs9865242

131450

CD200 receptor 1. Encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid downregulatory signal.

MISSENSE

dbsnp.119:rs9826308

rs9826308

131450

CD200 receptor 1. Encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid downregulatory signal.

MISSENSE

dbsnp.100:rs2306857

rs2306857

NM_001025073.2

MISSENSE

KIAA2018

dbsnp.86:rs930818

205717

NM_001009899.2

MISSENSE

dbsnp.126:rs36052974

rs36052974

152404

NM_001015887.1

Immunoglobulin superfamily, member 11. Functions as a cell adhesion molecule through homophilic interaction. Stimulates cell growth. MISSEN

SE

dbsnp.119:rs9840317

rs9840317

Uroplakin 1B. Encoded protein is found in the asymmetrical unit membrane (AUM) where it can form a complex with other transmembrane 4 superfamily proteins. It may play a role in normal bladder epithelial physiology, possibly in regulating membrane permeability of superficial umbrella cells or in stabilizing the apical membrane through AUM/cytoskeletal interactions.

MISSENSE

CD86 942 NM_175862.3 901450 snp G A V I 3 123307886 184

MYLK 4638 NM_053027.3 903850 snp G A P S 3 124940582 146

HEG1 57493 NM_020733.1 905777 snp C G V L 3 126214174 979

HEG1 57493 NM_020733.1 905779 snp A G F S 3 126215307 601

COL29A1 NM_153264.3 914209 snp A G Q R 3 131645084 226

dbsnp.100:rs2681417

rs2681417

Receptor involved in the costimulatory signal essential for T-lymphocyte proliferation and interleukin-2 production, by binding CD28 or CTLA-4. May play a critical role in the early events of T-cell activation and costimulation of naive T-cells, such as deciding between immunity and anergy that is made by T-cells within 24 hours after activation. Isoform 2 interferes with the formation of CD86 clusters, and thus acts as a negative regulator of T-cell activation MISSEN

SE

dbsnp.119:rs9840993

rs9840993

myosin light chain kinase. Calcium/calmodulin-dependent enzyme implicated in smooth muscle contraction via phosphorylation of myosin light chains (MLC).

MISSENSE

dbsnp.120:rs10804567

rs10804567

HEG homolog 1 (zebrafish) . Function unknown.

MISSENSE

dbsnp.116:rs6790837

rs6790837

HEG homolog 1 (zebrafish) . Function unknown.

MISSENSE

dbsnp.119:rs9883988

rs9883988

256076

collagen, type VI, alpha 5. Collagen VI acts as a cell-binding protein (By similarity). Sequence polymorphisms in this gene have been linked to atopic dermatitis (eczema). Two transcript variants,one protein-coding and the other probably not protein-coding, have been found for this gene MISSEN

SE

COL29A1 rs819085 NM_153264.3 914240 snp G A G D 3 131657023 243

COL6A6 914450 snp G A A T 3 131766973 369

TOPBP1 11073 NM_007027.2 918900 snp T C N S 3 134824677 954

dbsnp.86:rs819085

256076

collagen, type VI, alpha 5. Collagen VI acts as a cell-binding protein (By similarity). Sequence polymorphisms in this gene have been linked to atopic dermatitis (eczema). Two transcript variants,one protein-coding and the other probably not protein-coding, have been found for this gene MISSEN

SE

dbsnp.119:rs9830253

rs9830253

131873

NM_001102608.1

collagen, type VI, alpha 6. Collagen VI acts as a cell-binding protein (By similarity) MISSEN

SE

dbsnp.120:rs10935070

rs10935070

topoisomerase (DNA) II binding protein 1. Required for DNA replication. Plays a role in the rescue of stalled replication forks and checkpoint control. Binds double-stranded DNA breaks and nicks as well as single-stranded DNA. Recruits the SWI/SNF chromatin remodeling complex to E2F1-responsive promoters. Down-regulates E2F1 activity and inhibits E2F1-dependent apoptosis during G1/S transition and after DNA damage. Induces a large increase in the kinase activity of ATR MISSEN

SE

ATR 545 NM_001184.3 931725 snp A G M T 3 143764301 210

51122 NM_016094.2 943534 snp T G I L 3 150951219 112

FLJ23049 79740 NM_024687.2 967942 snp G C A G 3 168482949 635

C3orf50 rs603638 93556 969257 snp A G D G 3 170021686 58

NM_207015.2 979310 snp C T P S 3 176647772 384

dbsnp.98:rs2227928

rs2227928

ataxia telangiectasia and Rad3 related. Serine/threonine protein kinase which activates checkpoint signaling upon genotoxic stresses such as ionizing radiation (IR), ultraviolet light (UV), or DNA replication stalling, thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates BRCA1, CHEK1, MCM2, RAD17, RPA2, SMC1 and p53/TP53, which collectively inhibit DNA replication and mitosis and promote DNA repair, recombination and apoptosis. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at sites of DNA damage, thereby regulating DNA damage response mechanism. Required for FANCD2 ubiquitination. Critical for maintenance of fragile site stability and efficient regulation of centrosome duplication MISSEN

SE

COMMD2

dbsnp.119:rs9843784

rs9843784

COMM domain containing 2. May down-regulate activation of NF-kappa-B. MISSEN

SE

dbsnp.120:rs12638625

rs12638625

zinc finger, B-box domain containing. Function unknown

MISSENSE

dbsnp.83:rs603638

XM_001726230.1

EGF-like and EMI domain containing 1, pseudogene. Non-protein coding RNA 259. Function unknown

MISSENSE

NAALADL2

dbsnp.116:rs6802937

rs6802937

254827

N-acetylated alpha-linked acidic dipeptidase-like 2. May be catalytically inactive. Function unknown. MISSEN

SE

MCCC1 56922 NM_020166.3 988267 snp T G H P 3 184237902 463

HTR3D NM_182537.2 990219 snp G A R H 3 185238515 51

HTR3D NM_182537.2 990221 snp G A R H 3 185239395 259

dbsnp.100:rs2270968

rs2270968

methylcrotonoyl-CoA carboxylase 1 (alpha). This gene encodes the large subunit of 3-methylcrotonyl-CoA carboxylase. This enzyme functions as a heterodimer and catalyzes the carboxylation of 3-methylcrotonyl-CoA to form 3-methylglutaconyl-CoA. Mutations in this gene are associated with 3-Methylcrotonylglycinuria, an autosomal recessive disorder of leucine catabolism.

MISSENSE

dbsnp.86:rs1000952

rs1000952

200909

5-hydroxytryptamine (serotonin) receptor 3 family member D. This is one of the several different receptors for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor is a ligand-gated ion channel, which when activated causes fast, depolarizing responses. It is a cation-specific, but otherwise relatively nonselective, ion channel MISSEN

SE

dbsnp.116:rs6789754

rs6789754

200909

5-hydroxytryptamine (serotonin) receptor 3 family member D. This is one of the several different receptors for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor is a ligand-gated ion channel, which when activated causes fast, depolarizing responses. It is a cation-specific, but otherwise relatively nonselective, ion channel MISSEN

SE

HTR3C NM_130770.2 990287 snp C A N K 3 185257455 162

EIF4G1 1981 NM_198241.1 990616 snp A G M V 3 185522359 431

MAGEF1 64110 NM_022149.4 991375 snp T G E A 3 185911596 235

AHSG rs4918 197 NM_001622.2 994319 snp G C S T 3 187821075 255

dbsnp.116:rs6766410

rs6766410

170572

5-hydroxytryptamine (serotonin) receptor 3, family member C. This is one of the several different receptors for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor is a ligand-gated ion channel, which when activated causes fast, depolarizing responses. It is a cation-specific, but otherwise relatively nonselective, ion channel MISSEN

SE

dbsnp.96:rs2178403

rs2178403

eukaryotic translation initiation factor 4 gamma, 1. is a component of the multi-subunit protein complex EIF4F. This complex facilitates the recruitment of mRNA to the ribosome, which is a rate-limiting step during the initiation phase of protein synthesis. The recognition of the mRNA cap and the ATP-dependent unwinding of 5'-terminal secondary structure is catalyzed by factors in this complex. The subunit encoded by this gene is a large scaffolding protein that contains binding sites for other members of the EIF4F complex.

MISSENSE

dbsnp.119:rs9872799

rs9872799

melanoma antigen family F, 1. This intronless gene encodes a member of the MAGE superfamily. It is ubiquitously expressed in normal tissues and in tumor cells. This gene includes a microsatellite repeat in the coding region. Tumor antigen.

MISSENSE

dbsnp.52:rs4918

alpha-2-HS-glycoprotein. Promotes endocytosis, possesses opsonic properties and influences the mineral phase of bone. Shows affinity for calcium and barium ions MISSEN

SE

ATP13A5 NM_198505.2 1006628 snp C G E Q 3 194563107 132

MUC4 4585 NM_004532.3 1011608 snp C G M I 3 196982807 200

NKX1-1 54729 XM_926341.3 1017486 snp A G S P NK1 homeobox 1. Function unknown. 4 1392371 27

TACC3 10460 NM_006342.1 1018014 snp G A G E 4 1702775 513

GRK4 2868 NM_182982.2 1019191 snp T C L P 4 3007010 456

dbsnp.116:rs6797429

rs6797429

344905

ATPase type 13A5 . Function unknown.

MISSENSE

dbsnp.100:rs2259102

rs2259102

mucin 4, cell surface associated. May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2.

MISSENSE

dbsnp.111:rs4974560

rs4974560

MISSENSE

dbsnp.123:rs17680881

rs17680881

transforming, acidic coiled-coil containing protein 312/20/2011The function of this gene has not yet been determined; however, it is speculated that it may be involved in cell growth and differentiation. Expression of this gene is up-regulated in some cancer cell lines, and in embryonic day 15 in mice.

MISSENSE

dbsnp.126:rs34022679

rs34022679

G protein-coupled receptor kinase 4. This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family. The protein phosphorylates the activated forms of G protein-coupled receptors thus initiating its deactivation. This gene has been linked to both genetic and acquired hypertension.

MISSENSE

GRK4 2868 NM_182982.2 1019199 snp T C V A 4 3008947 485

CYTL1 54360 NM_018659.2 1023654 snp G A R C 4 5067783 135

EVC 2121 NM_153717.2 1024474 snp A C Q P 4 5771921 73

EVC 2121 NM_153717.2 1024566 snp C A T K 4 5806442 448

MAN2B2 23324 NM_015274.1 1026057 snp A C Q P 4 6645847 242

MAN2B2 23324 NM_015274.1 1026071 snp A G M V 4 6650912 445

dbsnp.89:rs1801058

rs1801058

G protein-coupled receptor kinase 4. This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family. The protein phosphorylates the activated forms of G protein-coupled receptors thus initiating its deactivation. This gene has been linked to both genetic and acquired hypertension.

MISSENSE

dbsnp.120:rs11722554

rs11722554

cytokine-like 1. C17 is a cytokine-like protein specifically expressed in bone marrow and cord blood mononuclear cells that bear the CD34 (MIM 142230) surface marker.

MISSENSE

dbsnp.100:rs2291157

rs2291157

Ellis van Creveld syndrome. This gene encodes a protein containing a leucine zipper and a transmembrane domain. May function coordinately in cardiac development . This gene has been implicated in both Ellis-van Creveld syndrome (EvC) and Weyers acrodental dysostosis.

MISSENSE

dbsnp.100:rs2302075

rs2302075

Ellis van Creveld syndrome. This gene encodes a protein containing a leucine zipper and a transmembrane domain. May function coordinately in cardiac development . This gene has been implicated in both Ellis-van Creveld syndrome (EvC) and Weyers acrodental dysostosis.

MISSENSE

dbsnp.100:rs2301796

rs2301796

mannosidase, alpha, class 2B, member 2. mannosidase II hydrolyzes (1,3)- and (1,6)-linked alpha-D-mannose residues in Man5(GlcNAc)3.

MISSENSE

dbsnp.100:rs2301790

rs2301790


MISSENSE

MAN2B2 23324 NM_015274.1 1026085 snp A G N S 4 6657764 540

SORCS2 57537 NM_020777.1 1028030 snp T C S P 4 7767831 565

SLC2A9 56606 NM_020041.2 1031020 snp G A P L 4 9519020 349

ZNF518B 85460 NM_053042.2 1032207 snp C T S N 4 10055482 522

FAM44A NM_148894.2 1036157 snp A T L I 4 13215673 649

27146 XM_039169.7 1041756 snp C T R H 4 17269179 840

CENTD1 NM_139182.1 1061676 snp C T R Q 4 35758272 694

FLJ16686 XM_379262.4 1061921 snp T A V D 4 35968412 298

dbsnp.100:rs2301788

rs2301788


MISSENSE

dbsnp.116:rs6816604

rs6816604

sortilin-related VPS10 domain containing receptor 2. Family member of vacuolar protein sorting 10 (VPS10) domain-containing receptor proteins

MISSENSE

dbsnp.100:rs2280205

rs2280205

solute carrier family 2 (facilitated glucose transporter), member 9. Transport urate and fructose. May have a role in the urate reabsorption by proximal tubules. Also transports glucose at low rate MISSEN

SE

dbsnp.119:rs9291410

rs9291410

zinc finger protein 518B. May be involved in transcriptional regulation.

MISSENSE

dbsnp.92:rs1971278

rs1971278

259282

biorientation of chromosomes in cell division 1-like. BOD1 familymember. Phosphorylated upon DNA damage, probably by ATM or ATR. Function unknown

MISSENSE

KIAA1276

dbsnp.92:rs1860596

rs1860596

family with sequence similarity 184, member B. Function unknown.

MISSENSE

dbsnp.111:rs4833069

rs4833069

116984

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2. The protein is a phosphatidylinositol (3,4,5)-trisphosphate-dependent Arf6 GAP that binds RhoA-GTP, but it lacks the predicted catalytic arginine in the RHO-GAP domain and does not have RHO-GAP activity. The protein associates with focal adhesions and functions downstream of RhoA to regulate focal adhesion dynamics

MISSENSE

dbsnp.92:rs1995319

rs1995319

401124

death domain containing 1. Function unknown

MISSENSE

TLR10 81793 1065720 snp T C I V 4 38451283 774

TLR10 81793 1065722 snp T G I L 4 38452501 368

TLR10 81793 1065724 snp T G N H 4 38452885 240

TLR1 7096 NM_003263.3 1065767 snp C A S I 4 38475042 601

TLR1 7096 NM_003263.3 1065770 snp T C N S 4 38476104 247

dbsnp.108:rs4129009

rs4129009

NM_001017388.1

toll-like receptor 10. Participates in the innate immune response to microbial agents. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response

MISSENSE

dbsnp.120:rs11096955

rs11096955

NM_001017388.1


MISSENSE

dbsnp.120:rs11096957

rs11096957

NM_001017388.1


MISSENSE

dbsnp.114:rs5743618

rs5743618

toll-like receptor 1 . Participates in the innate immune response to microbial agents. Cooperates with TLR2 to mediate the innate immune response to bacterial lipoproteins or lipopeptides. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response

MISSENSE

dbsnp.111:rs4833095

rs4833095

toll-like receptor 1 . Participates in the innate immune response to microbial agents. Cooperates with TLR2 to mediate the innate immune response to bacterial lipoproteins or lipopeptides. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response

MISSENSE

TLR6 10333 NM_006068.2 1065845 snp A G S P 4 38506744 248

N4BP2 rs794001 55728 NM_018177.2 1067500 snp G A D N 4 39797956 610

N4BP2 55728 NM_018177.2 1067501 snp A T E V 4 39798707 860

CHRNA9 55584 NM_017581.2 1067854 snp A G N S 4 40051178 441

APBB2 323 NM_173075.2 1068400 snp T C N S 4 40512935 713

ATP10D 57205 NM_020453.2 1076004 snp C T T I 4 47209441 42

ATP10D 57205 NM_020453.2 1076128 snp G A S N 4 47265632 958

dbsnp.114:rs5743810

rs5743810

toll-like receptor 6 . Participates in the innate immune response to Gram-positive bacteria and fungi. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response

MISSENSE

dbsnp.86:rs794001

NEDD4 binding protein 2. Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination MISSEN

SE

dbsnp.129:rs61748748

rs61748748

NEDD4 binding protein 2. Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination MISSEN

SE

dbsnp.119:rs10009228

rs10009228

cholinergic receptor, nicotinic, alpha 9. Ionotropic receptor with a probable role in the modulation of auditory stimuli.

MISSENSE

amyloid beta (A4) precursor protein-binding, family B, member 2. May modulate the internalization of beta-amyloid precursor protein. The protein encoded by this gene interacts with the cytoplasmic domains of amyloid beta (A4) precursor protein and amyloid beta (A4) precursor-like protein 2. This protein contains two phosphotyrosine binding (PTB) domains, which are thought to function in signal transduction. Polymorphisms in this gene have been associated with Alzheimer's disease

MISSENSE

dbsnp.126:rs33995001

rs33995001

ATPase, class V, type 10D. Function unknown

MISSENSE

dbsnp.123:rs17462252

rs17462252


MISSENSE

ATP10D 57205 NM_020453.2 1076140 snp G A R K 4 47273727 1182

CORIN 10699 NM_006587.2 1076482 snp C T C Y 4 47534685 12

SCFD2 NM_152540.3 1079298 snp A G L S 4 53706282 511

CEP135 9662 NM_025009.3 1082793 snp A C I L 4 56569273 768

57482 NM_020722.1 1083155 snp C T P L Function unknown. 4 56876385 653

57482 NM_020722.1 1083156 snp G C R P Function unknown. 4 56876388 654

57482 NM_020722.1 1083157 snp C T S L Function unknown. 4 56876751 775

dbsnp.123:rs16851681

rs16851681


MISSENSE

dbsnp.100:rs2289433

rs2289433

corin, serine peptidase. Serine-type endopeptidase involved in atrial natriuretic peptide hormone processing.

MISSENSE

dbsnp.116:rs7675987

rs7675987

152579

sec1 family domain containing 2. May be involved in protein transport MISSEN

SE

dbsnp.106:rs3214045

rs3214045

centrosomal protein 135kDa. Centrosomal protein involved in centriole biogenesis. Acts as a scaffolding protein during early centriole biogenesis. Also required for centriole-centriole cohesion during interphase by acting as a platform protein for CEP250 at the centriole. MISSEN

SE

KIAA1211

dbsnp.129:rs61750793

rs61750793

MISSENSE

KIAA1211

dbsnp.116:rs7672073

rs7672073

MISSENSE

KIAA1211

dbsnp.107:rs3796547

rs3796547

MISSENSE

CENPC1 rs11250 1060 NM_001812.2 1098444 snp G A L F 4 68062809 340

NM_207407.1 1099314 snp C T A T 4 68678123 3

C4orf35 85438 NM_033122.3 1102964 snp C T T I 4 71235976 210

SMR3A 26952 NM_012390.3 1103136 snp T C C R 4 71267018 41

SMR3A 26952 NM_012390.3 1103137 snp C T P L 4 71267289 131

dbsnp.52:rs11250

centromere protein C 1. Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENPC recruits DNA methylation and DNMT3B to both centromeric and pericentromeric satellite repeats and regulates the histone code in these regions. The protein is required for maintaining proper kinetochore size and a timely transition to anaphase. MISSEN

SE

TMPRSS11F

dbsnp.119:rs10030708

rs10030708

389208

transmembrane protease, serine 11F. Probable serine protease (By similarity). Function unknown MISSEN


rs1351419

calcium-binding protein, spermatid-specific 1. Function unknown

MISSENSE

dbsnp.119:rs10024123

rs10024123

submaxillary gland androgen regulated protein 3A . May play a role in protection or detoxification (By similarity) MISSEN

SE

dbsnp.116:rs6853742

rs6853742

submaxillary gland androgen regulated protein 3A . May play a role in protection or detoxification (By similarity) MISSEN

SE

DCK 1633 NM_000788.1 1103907 snp C T P S 4 72107103 121

25849 NM_015393.2 1108650 snp C T S L 4 76156994 126

PPEF2 5470 NM_006239.2 1110047 snp T G M L 4 77013368 480

SDAD1 55153 NM_018115.2 1110183 snp G T A D 4 77100256 489

{dbsnp.130:rs67437265;dbsnp.130:rs67437266}

rs67437265;dbsnp.130

deoxycytidine kinase . Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents MISSEN

SE

DKFZP564O0823

dbsnp.107:rs3822109

rs3822109

prostate androgen-regulated mucin-like protein 1. May regulate TLP1 expression and telomerase activity, thus enabling certain prostatic cells to resist apoptosis (By similarity) MISSEN

SE

dbsnp.116:rs6858658

rs6858658

protein phosphatase, EF-hand calcium binding domain 2. May play a role in phototransduction. May dephosphorylate photoactivated rhodopsin. May function as a calcium sensing regulator of ionic currents, energy production or synaptic transmission. MISSEN

SE

dbsnp.126:rs34627298

rs34627298

SDA1 domain containing 1 . Required for 60S pre-ribosomal subunits export to the cytoplasm (By similarity) MISSEN

SE

rs344140 57619 NM_020859.2 1111720 snp G C G A 4 77879185 277

rs344141 57619 NM_020859.2 1111721 snp C G P A 4 77879754 467

57619 NM_020859.2 1111742 snp C T P L 4 77894528 1288

SHROOM3

dbsnp.79:rs344140

shroom family member 3. Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers. Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity) MISSEN

SE

SHROOM3

dbsnp.79:rs344141


SE

SHROOM3

dbsnp.107:rs3733242

rs3733242


SE

FRAS1 80144 NM_025074.4 1112912 snp A G D G 4 79206180 31

FRAS1 80144 NM_025074.4 1113326 snp C T A V 4 79503717 816

FRAS1 80144 NM_025074.4 1113356 snp G A E K 4 79520016 1134

FRAS1 80144 NM_025074.4 1113558 snp A G K E 4 79606487 2376

BMP3 651 NM_001201.2 1116457 snp C T L F 4 82186211 204

THAP9 79725 NM_024672.3 1118826 snp G A M I 4 84057240 283

THAP9 79725 NM_024672.3 1118827 snp A G N D 4 84058822 811

dbsnp.111:rs4859905

rs4859905

Fraser syndrome 1. This gene encodes an extracellular matrix protein that appears to function in the regulation of epidermal-basement membrane adhesion and organogenesis during development. Mutations in this gene cause Fraser syndrome

MISSENSE

dbsnp.116:rs6835769

rs6835769


MISSENSE

dbsnp.120:rs12512164

rs12512164


MISSENSE

dbsnp.116:rs7684722

rs7684722


MISSENSE

dbsnp.116:rs6831040

rs6831040

bone morphogenetic protein 3. Negatively regulates bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification. MISSEN


rs1031639

THAP domain containing 9. Function unknown

MISSENSE

dbsnp.116:rs6535411

rs6535411

THAP domain containing 9. Function unknown

MISSENSE

HPSE 10855 1119493 snp T C K R 4 84449642 306

HEL308 NM_133636.2 1119699 snp C T V I 4 84593503 305

SLC10A6 NM_197965.1 1122340 snp T C I V 4 87988952 113

HERC5 51191 NM_016323.2 1124388 snp A G M V 4 89616113 497

10144 1124616 snp C T V I 4 89887881 442

TIGD2 NM_145715.2 1125229 snp A G H R 4 90254571 474

dbsnp.120:rs11099592

rs11099592

NM_001098540.1

heparanase. paran sulfate proteoglycans (HSPGs) are major components of the basement membrane and extracellular matrix. Heparanases, like HSPE, are endoglycosidases that cleave the heparan sulfate side chain of HSPGs to permit the remodeling of the extracellular matrix for cell movement or the release of bioactive molecules from the extracellular matrix or cell surface

MISSENSE

dbsnp.88:rs1494961

rs1494961

113510

helicase, POLQ-like. DNA-dependent ATPase and 5' to 3' DNA helicase. MISSEN

SE

dbsnp.121:rs13106574

rs13106574

345274

solute carrier family 10 (sodium/bile acid cotransporter family), member 6. Transports sulfoconjugated steroid hormones, as well as taurolithocholic acid-3-sulfate and sulfoconjugated pyrenes in a sodium-dependent manner

MISSENSE

dbsnp.116:rs7699006

rs7699006

hect domain and RLD 5. Major E3 ligase for ISG15 conjugation. Acts as a positive regulator of innate antiviral response in cells induced by interferon.

MISSENSE

FAM13A1

dbsnp.116:rs7657817

rs7657817

NM_001015045.1

family with sequence similarity 13, member A. Probably regulation of small GTPase mediated signal transduction.

MISSENSE

dbsnp.100:rs2280099

rs2280099

166815

tigger transposable element derived 2 . The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known.

MISSENSE

GPRIN3 NM_198281.2 1125370 snp A G V A 4 90388947 445

HADH 3033 NM_005327.2 1143954 snp T C L P 4 109150487 85

ENPEP 2028 NM_001977.3 1146946 snp T C V A 4 111629153 217

ALPK1 80216 1148816 snp G A G D 4 113571845 564

ALPK1 80216 1148817 snp A G H R 4 113572076 641

ALPK1 80216 1148818 snp G A M I 4 113572347 731

SYNPO2 NM_133477.1 1156473 snp G C G A 4 120167432 153

USP53 54532 NM_019050.2 1156944 snp T G S R 4 120433477 961

dbsnp.116:rs7653897

rs7653897

285513

GPRIN family member 3. May be involved in neurite outgrowth (By similarity) MISSEN

SE

dbsnp.111:rs4956145

rs4956145

hydroxyacyl-CoA dehydrogenase. Plays an essential role in the mitochondrial beta-oxidation of short chain fatty acids. Exerts it highest activity toward 3-hydroxybutyryl-CoA

MISSENSE

dbsnp.86:rs1126483

rs1126483

glutamyl aminopeptidase (aminopeptidase A). Appears to have a role in the catabolic pathway of the renin-angiotensin system. Probably plays a role in regulating growth and differentiation of early B-lineage cells

MISSENSE

dbsnp.96:rs2074388

rs2074388

NM_001102406.1

alpha-kinase 1. Kinases that recognize phosphorylation sites in which the surrounding peptides have an alpha-helical conformation

MISSENSE

dbsnp.121:rs13148353

rs13148353

NM_001102406.1


MISSENSE

dbsnp.96:rs2074379

rs2074379

NM_001102406.1


MISSENSE

dbsnp.120:rs12645298

rs12645298

171024

synaptopodin 2 . Has an actin-binding and actin-bundling activity (By similarity) MISSEN

SE

dbsnp.107:rs3749591

rs3749591

ubiquitin specific peptidase 53. Has no peptidase activity. Function unknown MISSEN

SE

PDE5A 8654 NM_033430.2 1157918 snp G A A V 4 120747774 50

SAR1P3 XM_293671.6 1158787 snp G A V I 4 121482946 95

GPR103 84109 NM_198179.2 1159865 snp A G L S 4 122470183 343

NM_152399.2 1160521 snp G A A V 4 122902456 10

BBS12 rs309370 NM_152618.2 1161539 snp G A R Q 4 123883653 385

BBS12 NM_152618.2 1161541 snp G A D N 4 123883895 466

dbsnp.107:rs3733526

rs3733526

phosphodiesterase 5A, cGMP-specific. Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'-GMP. MISSEN


rs1160185

344988

SAR1 homolog A (S. cerevisiae) pseudogene 3.

MISSENSE

dbsnp.100:rs2302310

rs2302310

pyroglutamylated RFamide peptide receptor. Receptor for the orexigenic neuropeptide QRFP. The activity of this receptor is mediated by G proteins that modulate adenylate cyclase activity and intracellular calcium levels.

MISSENSE

TMEM155

dbsnp.111:rs4370153

rs4370153

132332

transmembrane protein 155 . Probably secreted

MISSENSE

dbsnp.79:rs309370

166379

Bardet-Biedl syndrome 12. Probable molecular chaperone. Assists the folding of proteins upon ATP hydrolysis. As part of the BBS/CCT complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia. Involved in adipogenic differentiation

MISSENSE

dbsnp.121:rs13135778

rs13135778

166379

Bardet-Biedl syndrome 12. Probable molecular chaperone. Assists the folding of proteins upon ATP hydrolysis. As part of the BBS/CCT complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia. Involved in adipogenic differentiation

MISSENSE

FAT4 79633 NM_024582.3 1165113 snp C T H Y 4 126591263 3214

FAT4 79633 NM_024582.3 1165114 snp G A S N 4 126593238 3872

PLK4 10733 NM_014264.3 1167428 snp T A S T 4 129026668 231

PLK4 10733 NM_014264.3 1167429 snp G T E D 4 129034413 829

LARP2 55132 NM_018078.2 1167687 snp G A R H 4 129320092 659

dbsnp.130:rs73849225

rs73849225

FAT tumor suppressor homolog 4 (Drosophila), Cadherin family member 14. May function in the regulation of planar cell polarity (By similarity). Cadherins are cell-cell interaction molecules (By similarity). MISSEN

SE

dbsnp.120:rs12650153

rs12650153

FAT tumor suppressor homolog 4 (Drosophila), Cadherin family member 14. May function in the regulation of planar cell polarity (By similarity). Cadherins are cell-cell interaction molecules (By similarity). MISSEN

SE

dbsnp.107:rs3811740

rs3811740

polo-like kinase 4 . Is a member of the polo family of serine/threonine protein kinases. The protein localizes to centrioles, complex microtubule-based structures found in centrosomes, and regulates centriole duplication during the cell cycle.

MISSENSE

dbsnp.123:rs17012739

rs17012739

polo-like kinase 4 . Is a member of the polo family of serine/threonine protein kinases. The protein localizes to centrioles, complex microtubule-based structures found in centrosomes, and regulates centriole duplication during the cell cycle.

MISSENSE

dbsnp.120:rs12645577

rs12645577

La ribonucleoprotein domain family, member 1B. This gene encodes a protein containing domains found in the La related protein of Drosophila melanogaster. Lamotif-containing proteins are thought to be RNA-binding proteins. Function unknown.

MISSENSE

SCLT1 NM_144643.2 1168578 snp T A S C 4 130086729 440

CLGN 1047 NM_004362.1 1181197 snp G A R W 4 141536517 351

UCP1 7350 NM_021833.3 1181374 snp T A M L 4 141702920 228

UCP1 7350 NM_021833.3 1181380 snp C T A T 4 141708517 63

FREM3 1184648 snp G C F L 4 144838059 1072

dbsnp.119:rs10028124

rs10028124

132320

sodium channel and clathrin linker 1 . Adapter protein that links SCN10A (voltage-gated sodium channel Na(v)1.8 ) to clathrin. Regulates SCN10A channel activity, possibly by promoting channel internalization (By similarity) MISSEN

SE

dbsnp.120:rs12513290

rs12513290

calmegin. Calmegin is a testis-specific endoplasmic reticulum chaperone protein. CLGN may play a role in spermatogeneisis and infertility.

MISSENSE

dbsnp.100:rs2270565

rs2270565

uncoupling protein 1 (mitochondrial, proton carrier). UCP are mitochondrial transporter proteins that create proton leaks across the inner mitochondrial membrane, thus uncoupling oxidative phosphorylation from ATP synthesis. As a result, energy is dissipated in the form of heat. MISSEN

SE

dbsnp.127:rs45539933

rs45539933

uncoupling protein 1 (mitochondrial, proton carrier). UCP are mitochondrial transporter proteins that create proton leaks across the inner mitochondrial membrane, thus uncoupling oxidative phosphorylation from ATP synthesis. As a result, energy is dissipated in the form of heat. MISSEN

SE

dbsnp.86:rs1034494

rs1034494

166752

XM_094074.10

FRAS1 related extracellular matrix 3. Extracellular matrix protein which may play a role in cell adhesion (By similarity). MISSEN

SE

79658 NM_024605.3 1189373 snp A G M V 4 149203770 683

ESSPL - NM_183375.2 1192694 snp T G * E 4 152432052 328

TIGD4 NM_145720.2 1194230 snp T C I V 4 153910291 438

DCHS2 54798 NM_017639.2 1196104 snp G A S L 4 155461021 1204

MAP9 79884 1197495 snp T C N D 4 156493217 600

ARHGAP10

dbsnp.100:rs2276932

rs2276932

Rho GTPase activating protein 10. GTPase activator for the small GTPases RhoA and Cdc42 by converting them to an inactive GDP-bound state. Essential for PTKB2 regulation of cytoskeletal organization via Rho family GTPases. Inhibits PAK2 proteolytic fragment PAK-2p34 kinase activity and changes its localization from the nucleus to the perinuclear region. Stabilizes PAK-2p34 thereby increasing stimulation of cell death (By similarity). MISSEN

SE

dbsnp.100:rs2407221

rs2407221

345062

C-term extra amino acids: ELTGEPLLTLGDFIYNLKstop. protease, serine, 48, serine-type endopeptidase activity. Function unknown.

NONSTOP

dbsnp.111:rs4696354

rs4696354

201798

tigger transposable element derived 4. The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known.

MISSENSE

dbsnp.120:rs11935573

rs11935573

dachsous 2 (Drosophila). Calcium-dependent cell-adhesion protein (By similarity). MISSEN

SE

dbsnp.100:rs2305050

rs2305050

NM_001039580.1

microtubule-associated protein 9. Involved in organization of the bipolar mitotic spindle. Required for bipolar spindle assembly, mitosis progression and cytokinesis. May act by stabilizing interphase microtubules. MISSEN

SE

FLJ25371 rs619128 NM_152543.2 1201881 snp C T G E C4orf45. Function unknown. 4 160113699 92

FLJ25371 NM_152543.2 1201883 snp G A A V C4orf45. Function unknown. 4 160113840 45

ANP32C 23520 NM_012403.1 1208851 snp C T R K 4 165338101 70

ANP32C 23520 NM_012403.1 1208852 snp G A A V 4 165338245 22

ANXA10 11199 NM_007193.3 1214497 snp A C M L 4 169320268 70

DDX60L 91351 1214688 snp C A E D 4 169552334 1221

DDX60L 91351 1214724 snp A G C R 4 169578009 830

C4orf27 54969 NM_017867.2 1216282 snp C T R K Function unknown. 4 170899809 173

WDR17 NM_170710.3 1223989 snp G A A T 4 177310019 813

dbsnp.83:rs619128

152940

MISSENSE

dbsnp.123:rs17037864

rs17037864

152940

MISSENSE

dbsnp.100:rs2288675

rs2288675

acidic (leucine-rich) nuclear phosphoprotein 32 family, member C. Phosphoprotein 32 (PP32) is a tumor suppressor that can inhibit several types of cancers, including prostate and breast cancers.

MISSENSE

dbsnp.100:rs2288674

rs2288674

acidic (leucine-rich) nuclear phosphoprotein 32 family, member C. Phosphoprotein 32 (PP32) is a tumor suppressor that can inhibit several types of cancers, including prostate and breast cancers.

MISSENSE

dbsnp.116:rs6836994

rs6836994

annexin A10. This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. The function of this gene has not yet been determined.

MISSENSE

dbsnp.107:rs3749499

rs3749499

NM_001012967.1

DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like. Probable ATP-dependent RNA helicase.

MISSENSE

dbsnp.96:rs2130145

rs2130145

NM_001012967.1

DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like. Probable ATP-dependent RNA helicase.

MISSENSE

dbsnp.86:rs1047642

rs1047642

MISSENSE

dbsnp.111:rs4690661

rs4690661

116966

WD repeat domain 17. This gene encodes a WD repeat-containing protein. It is abundantly expressed in retina and testis, and is thought to be a candidate gene for retinal disease.

MISSENSE

NEIL3 55247 NM_018248.2 1226225 snp C T P L 4 178511743 442

NEIL3 55247 NM_018248.2 1226226 snp A C Q H 4 178511828 470

WWC2 80014 NM_024949.5 1236010 snp G A A T 4 184473861 1188

HELT 1238877 snp C G L V 4 186177945 146

25854 NM_015398.2 1240654 snp A G K E 4 187311826 40

dbsnp.121:rs13112358

rs13112358

nei endonuclease VIII-like 3 (E. coli). NEIL3 belongs to a class of DNA glycosylases homologous to the bacterial Fpg/Nei family. These glycosylases initiate the first step in base excision repair by cleaving bases damaged by reactive oxygen species and introducing a DNA strand break via the associated lyase reaction

MISSENSE

dbsnp.121:rs13112390

rs13112390

nei endonuclease VIII-like 3 (E. coli). NEIL3 belongs to a class of DNA glycosylases homologous to the bacterial Fpg/Nei family. These glycosylases initiate the first step in base excision repair by cleaving bases damaged by reactive oxygen species and introducing a DNA strand break via the associated lyase reaction

MISSENSE

dbsnp.111:rs4862155

rs4862155

WW and C2 domain containing 2. Function unknown.

MISSENSE

dbsnp.86:rs1078461

rs1078461

391723

NM_001029887.1

HES/HEY-like transcription factor. Transcriptional repressor which binds preferentially to the canonical E box sequence 5'-CACGCG-3' (By similarity)

MISSENSE

FAM149A

dbsnp.111:rs4862650

rs4862650

family with sequence similarity 149, member A. Function unknown.

MISSENSE

FAT 2195 NM_005245.3 1241301 snp C G K N 4 187756199 4058

TRIML1 NM_178556.3 1243596 snp G A E K 4 189298099 131

rs29674 NM_052909.3 1252683 snp A C T P 5 216259 668

CEP72 rs868649 55722 NM_018140.3 1253730 snp A G T A 5 693704 508

23379 NM_015325.1 1264205 snp G C C S Function unknown. 5 5513618 390

dbsnp.87:rs1280097

rs1280097

FAT tumor suppressor homolog 1 (Drosophila). This gene is an ortholog of the Drosophila fat gene, which encodes a tumor suppressor essential for controlling cell proliferation during Drosophila development. The gene product is a member of the cadherin superfamily, a group of integral membrane proteins characterized by the presence of cadherin-type repeats. Probably functions as an adhesion molecule and/or signaling receptor, and is likely to be important in developmental processes and cell communication.

MISSENSE

dbsnp.121:rs13131525

rs13131525

339976

tripartite motif family-like 1 . Probable E3 ubiquitin-protein ligase which plays an important role in blastocyst development (By similarity) MISSEN

SE

PLEKHG4B

dbsnp.76:rs29674

153478

pleckstrin homology domain containing, family G (with RhoGef domain) member 4B. Probably regulation of Rho protein signal transduction.

MISSENSE

dbsnp.89:rs868649

centrosomal protein 72kDa. Involved in the recruitment of key centrosomal proteins to the centrosome. Provides centrosomal microtubule-nucleation activity on the gamma-tubulin ring complexes (gamma-TuRCs) and has critical roles in forming a focused bipolar spindle, which is needed for proper tension generation between sister chromatids. Required for localization of KIZ/PLK1S1, AKAP9 and gamma-tubulin ring complexes (gamma-TuRCs).

MISSENSE

KIAA0947

dbsnp.100:rs2619844

rs2619844

MISSENSE

FASTKD3 79072 NM_024091.2 1269275 snp T C K R 5 7921029 55

ZFR 51663 NM_016107.3 1312622 snp C T V I 5 32439102 460

AGXT2 rs180749 64902 NM_031900.1 1317273 snp G A T I 5 35069361 211

FLJ40243 NM_173489.4 1326722 snp A G L P 5 41044536 1178

FLJ40243 rs325864 NM_173489.4 1326822 snp C T V I 5 41085153 495

MAP3K1 rs832582 4214 NM_005921.1 1344288 snp G A V I 5 56213499 905

RGS7BP rs889248 1355440 snp A G I V 5 63940823 254

dbsnp.101:rs2966952

rs2966952

FAST kinase domains 3 . Probably involved in cellular respiration.

MISSENSE

dbsnp.111:rs4867440

rs4867440

zinc finger RNA binding protein. Involved in postimplantation and gastrulation stages of development. Involved in the nucleocytoplasmic shuttling of STAU2. Binds to DNA and RNA (By similarity) MISSEN

SE

dbsnp.79:rs180749

alanine--glyoxylate aminotransferase 2, is a class III pyridoxal-phosphate-dependent mitochondrial aminotransferase. It catalyzes the conversion of glyoxylate to glycine using L-alanine as the amino donor.

MISSENSE

dbsnp.100:rs2271704

rs2271704

133558

HEAT repeat family member 7B2. Function unknown

MISSENSE

dbsnp.79:rs325864

133558

HEAT repeat family member 7B2. Function unknown

MISSENSE

dbsnp.86:rs832582

mitogen-activated protein kinase kinase kinase 1. MAP3K, or MEK kinase, is a serine/threonine kinase that occupies a pivotal role in a network of phosphorylating enzymes integrating cellular responses to a number of mitogenic and metabolic stimuli, including insulin (MIM 176730) and many growth factors .

MISSENSE

dbsnp.86:rs889248

401190

NM_001029875.1

regulator of G-protein signaling 7 binding protein. Regulator of G protein-coupled receptor (GPCR) signaling. Regulatory subunit of the R7-Gbeta5 complexes that acts by controlling the subcellular location of the R7-Gbeta5 complexes. May also act by controlling the proteolytic stability of R7 proteins, probably by protecting them from degradation (By similarity). MISSEN

SE

BDP1 55814 NM_018429.2 1363135 snp T G D E 5 70787573 37

BDP1 55814 NM_018429.2 1363205 snp G A V M 5 70836293 777

BDP1 rs715748 55814 NM_018429.2 1363219 snp G A G S 5 70842212 1179

BDP1 55814 NM_018429.2 1363220 snp T A F I 5 70842404 1243

dbsnp.107:rs3748043

rs3748043

B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB. General activator of RNA polymerase III transcription. Requires for transcription from all three types of polymerase III promoters. Requires for transcription of genes with internal promoter elements and with promoter elements upstream of the initiation site. MISSEN

SE

dbsnp.107:rs3761967

rs3761967


SE

dbsnp.86:rs715748


SE

dbsnp.92:rs1961760

rs1961760


SE

BDP1 rs715747 55814 NM_018429.2 1363221 snp C G I M 5 70842466 1263

BDP1 55814 NM_018429.2 1363222 snp G A V M 5 70842713 1346

rs637450 NM_173490.5 1365394 snp C G R G 5 72455211 85

rs636926 NM_173490.5 1365395 snp C A N K 5 72455372 138

S100Z NM_130772.3 1370425 snp A C E A 5 76207007 22

DMGDH rs532964 29958 NM_013391.2 1373588 snp A G S P 5 78376041 278

dbsnp.86:rs715747


SE

dbsnp.116:rs6886336

rs6886336


SETMEM171

dbsnp.83:rs637450

134285

transmembrane protein 171. Function unknown

MISSENSE

TMEM171

dbsnp.83:rs636926

134285

transmembrane protein 171. Function unknown

MISSENSE

dbsnp.88:rs1320308

rs1320308

170591

S100 calcium binding protein Z. Members of the S100 protein family contain 2 calcium-binding EF-hands and exhibit cell-type specific expression patterns.

MISSENSE

dbsnp.83:rs532964

methylglycine dehydrogenase. This gene encodes an enzyme involved in the catabolism of choline, catalyzing the oxidative demethylation of dimethylglycine to form sarcosine. The enzyme is found as a monomer in the mitochondrial matrix, and uses flavin adenine dinucleotide and folate as cofactors. Mutation in this gene causes dimethylglycine dehydrogenase deficiency. MISSEN

SE

JMY NM_152405.2 1373786 snp A T M L 5 78609545 87

ZFYVE16 9765 1375082 snp T C I T 5 79768834 191

ERAP1 rs27044 51752 NM_016442.3 1393687 snp G C Q E 5 96144607 729

dbsnp.121:rs13182512

rs13182512

133746

junction mediating and regulatory protein, p53 cofactor. Acts both as a nuclear p53/TP53-cofactor and a cytoplasmic regulator of actin dynamics depending on conditions. In nucleus, acts as a cofactor that increases p53/TP53 response via its interaction with p300/EP300. Increases p53/TP53-dependent transcription and apoptosis, suggesting an important role in p53/TP53 stress response such as DNA damage. In cytoplasm, acts as a nucleation-promoting factor for both branched and unbranched actin filaments. Activates the Arp2/3 complex to induce branched actin filament networks. Also catalyzes actin polymerization in the absence of Arp2/3, creating unbranched filaments. Contributes to cell motility by controlling actin dynamics.

MISSENSE

dbsnp.100:rs2544600

rs2544600

NM_001105251.1

zinc finger, FYVE domain containing 16. May be involved in regulating membrane trafficking in the endosomal pathway.

MISSENSE

dbsnp.76:rs27044

endoplasmic reticulum aminopeptidase 1. The protein encoded by this gene is an aminopeptidase involved in trimming HLA class I-binding precursors so that they can be presented on MHC class I molecules. The encoded protein acts as a monomer or as a heterodimer with ERAP2. This protein may also be involved in blood pressure regulation by inactivation of angiotensin II.

MISSENSE

ERAP1 rs30187 51752 NM_016442.3 1393728 snp T C K R 5 96150085 527

APC rs459552 324 NM_000038.3 1415748 snp T A V D 5 112204654 1821

YTHDC2 64848 NM_022828.2 1417086 snp T A L Q 5 112956911 1408

TRIM36 55521 NM_018700.3 1420217 snp C T D N 5 114490253 677

ZNF474 NM_207317.1 1431627 snp C G S C 5 121516404 273

dbsnp.76:rs30187

endoplasmic reticulum aminopeptidase 1. The protein encoded by this gene is an aminopeptidase involved in trimming HLA class I-binding precursors so that they can be presented on MHC class I molecules. The encoded protein acts as a monomer or as a heterodimer with ERAP2. This protein may also be involved in blood pressure regulation by inactivation of angiotensin II.

MISSENSE

dbsnp.80:rs459552

adenomatous polyposis coli. This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis.

MISSENSE

dbsnp.86:rs1132528

rs1132528

YTH domain containing 2. Probable ATP-dependent RNA helicase.

MISSENSE

dbsnp.101:rs2974617

rs2974617

tripartite motif containing 36. E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of target proteins. Involved in chromosome segregation and cell cycle regulation. May play a role in the acrosome reaction and fertilization (By similarity). MISSEN

SE

dbsnp.126:rs35262183

rs35262183

133923

zinc finger protein 474. Function unknown.

MISSENSE

CCDC100 NM_153223.2 1433431 snp C G Q H 5 122713625 878

CCDC100 NM_153223.2 1433509 snp G C L V 5 122746634 601

CTXN3 rs248709 1440396 snp A T E V cortexin 3. Function unknown. 5 127021161 16

rs40470 NM_175873.4 1446255 snp T G F L 5 132178846 544

PKD2L2 27039 NM_014386.2 1452740 snp G A V I 5 137272415 403

NM_198282.1 1454687 snp T C H R 5 138838102 231

dbsnp.86:rs1047437

rs1047437

153241

centrosomal protein 120kDa. Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors and for proper positioning of neurons during brain development. Also implicated in the migration and selfrenewal of neural progenitors. May play a role in centriole duplication during mitosis (By similarity).

MISSENSE

dbsnp.116:rs6595440

rs6595440

153241

centrosomal protein 120kDa. Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors and for proper positioning of neurons during brain development. Also implicated in the migration and selfrenewal of neural progenitors. May play a role in centriole duplication during mitosis (By similarity).

MISSENSE

dbsnp.79:rs248709

613212

NM_001048252.1

MISSENSE

ANKRD43

dbsnp.76:rs40470

134548

ankyrin repeat domain 43. Function unknown.

MISSENSE

dbsnp.92:rs1880458

rs1880458

polycystic kidney disease 2-like 2. May function as a subunit of a cation channel and play a role in fertilization. MISSEN

SE

TMEM173

dbsnp.86:rs1131769

rs1131769

340061

transmembrane protein 173. Facilitator of innate immune signaling that promotes the production of type I interferon.

MISSENSE

PCDHA1 56147 NM_031410.1 1455415 snp A G Y C 5 140148253 731

PCDHB6 56130 NM_018939.2 1455811 snp G A V I 5 140510712 230

PCDHB7 56129 NM_018940.2 1455852 snp G C V L 5 140533764 388

56114 NM_031993.1 1455994 snp G A V I 5 140690888 151

SPINK6 NM_205841.2 1465100 snp C A P T 5 147573689 35

SLC26A2 rs30832 1836 NM_000112.3 1467559 snp T C I T 5 149341069 573

dbsnp.98:rs2240696

rs2240696

protocadherin alpha 1. Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. MISSEN

SE

dbsnp.107:rs3776096

rs3776096

protocadherin beta 6. Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. MISSEN

SE

dbsnp.101:rs2910313

rs2910313

protocadherin beta 7. Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

MISSENSE

PCDHGA1

dbsnp.100:rs2472647

rs2472647

protocadherin gamma subfamily A, 1. Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. MISSEN

SE

dbsnp.120:rs12186491

rs12186491

404203

serine peptidase inhibitor, Kazal type 6. The protein encoded by this gene is a Kazal-type serine protease inhibitor that acts on kallikrein-related peptidases in the skin.

MISSENSE

dbsnp.76:rs30832

solute carrier family 26 (sulfate transporter), member 2. The diastrophic dysplasia sulfate transporter is a transmembrane glycoprotein implicated in the pathogenesis of several human chondrodysplasias. It apparently is critical in cartilage for sulfation of proteoglycans and matrix organization.

MISSENSE

FAT2 2196 NM_001447.1 1469364 snp A G Y H 5 150923111 1180

FAT2 2196 NM_001447.1 1469365 snp G A P L 5 150923161 1163

FAT2 2196 NM_001447.1 1469377 snp C T G S 5 150925675 1003

dbsnp.116:rs6872614

rs6872614

FAT tumor suppressor homolog 2 (Drosophila). This gene is the second identified human homolog of the Drosophila fat gene, which encodes a tumor suppressor essential for controlling cell proliferation during Drosophila development. This protein most likely functions as a cell adhesion molecule, controlling cell proliferation and playing an important role in cerebellum development.

MISSENSE

dbsnp.100:rs2304053

rs2304053


MISSENSE

dbsnp.107:rs3734055

rs3734055


MISSENSE

FAT2 2196 NM_001447.1 1469382 snp A G F S 5 150926628 685

FAT2 2196 NM_001447.1 1469383 snp G A R C 5 150926965 573

GEMIN5 25929 NM_015465.2 1473617 snp C T R Q 5 154271601 681

dbsnp.119:rs9324700

rs9324700


MISSENSE

dbsnp.88:rs1432862

rs1432862


MISSENSE

dbsnp.92:rs1974777

rs1974777

gem (nuclear organelle) associated protein 5. The SMN (survival motor neuron) complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. GEMIN5 acts as the snRNA-binding protein of the SMN complex.

MISSENSE

CCDC99 54908 NM_017785.4 1495822 snp T C Y H 5 168961058 507

CCDC99 54908 NM_017785.4 1495830 snp T C L S 5 168963727 585

MSX2 4488 NM_002449.4 1504357 snp T C M T 5 174088773 128

PRPF4B 8899 NM_003913.4 1524640 snp A G I V 6 3976996 82

FARS2 10667 NM_006567.3 1527595 snp A G N S 6 5376338 279

dbsnp.107:rs3797713

rs3797713

coiled-coil domain containing 99. Required for the localization of dynein and dynactin to the mitotic kintochore. Dynein is believed to control the initial lateral interaction between the kinetochore and spindle microtubules and to facilitate the subsequent formation of end-on kinetochore-microtubule attachments mediated by the NDC80 complex. Also required for correct spindle orientation.

MISSENSE

dbsnp.107:rs3777084

rs3777084

coiled-coil domain containing 99. Required for the localization of dynein and dynactin to the mitotic kintochore. Dynein is believed to control the initial lateral interaction between the kinetochore and spindle microtubules and to facilitate the subsequent formation of end-on kinetochore-microtubule attachments mediated by the NDC80 complex. Also required for correct spindle orientation.

MISSENSE

dbsnp.111:rs4242182

rs4242182

msh homeobox 2. Acts as a transcriptional regulator in bone development.

MISSENSE

dbsnp.119:rs9503893

rs9503893

PRP4 pre-mRNA processing factor 4 homolog B (yeast)

MISSENSE

dbsnp.120:rs11243011

rs11243011

phenylalanyl-tRNA synthetase 2, mitochondrial. Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins. MISSEN

SE

RREB1 6239 1531246 snp T C L P 6 7192246 1521

HIVEP1 3096 NM_002114.2 1540471 snp A G T A 6 12230630 872

NKAPL 1567647 snp A G E G 6 28336320 397

dbsnp.100:rs2256596

rs2256596

NM_001003699.1

ras responsive element binding protein 1. Transcription factor that binds specifically to the RAS-responsive elements (RRE) of gene promoters. May be involved in Ras/Raf-mediated cell differentiation by enhancing calcitonin expression. Represses the angiotensinogen gene. Negatively regulates the transcriptional activity of AR. Potentiates the transcriptional activity of NEUROD1. MISSEN

SE

dbsnp.116:rs6900196

rs6900196

human immunodeficiency virus type I enhancer binding protein 1. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV-1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, and interferon-beta genes. It may act in T-cell activation. Involved in activating HIV-1 gene expression. Isoform 2 and isoform 3 also bind to the IPCS (IRF1 and p53 common sequence) DNA sequence in the promoter region of interferon regulatory factor 1 and p53 genes and are involved in transcription regulation of these genes. Isoform 2 does not activate HIV-1 gene expression. Isoform 2 and isoform 3 may be involved in apoptosis. MISSEN


rs1679709

222698

NM_001007531.1

NFKB activating protein-like. Function unknown.

MISSENSE

MLN 4295 NM_002418.2 1576335 snp A G V A 6 33876874 14

C6orf1 1577121 snp C G G A 6 34322299 149

ANKS1A rs820085 23294 NM_015245.2 1578360 snp T C L S 6 35135904 693

DEF6 50619 NM_022047.3 1578820 snp A C N T 6 35393697 286

TREML4 - NM_198153.1 1589266 snp T C W R 6 41304582 72

PRPH2 - rs434102 5961 NM_000322.3 1591823 snp T C D G 6 42774038 337

PRPH2 - rs390659 5961 NM_000322.3 1591825 snp G C Q E 6 42774141 303

MUT - 4594 NM_000255.2 1602217 snp C T A T 6 49523406 498

CRISP3 - rs495335 10321 NM_006061.1 1602640 snp A G S P 6 49809481 105

dbsnp.100:rs2281820

rs2281820

motilin. This gene encodes a small peptide hormone that is secreted by cells of the small intestine to regulate gastrointestinal contractions and motility.

MISSENSE

dbsnp.87:rs1150781

rs1150781

221491

NM_001008704.1

Function unknown. (Potentially secreted).

MISSENSE

dbsnp.86:rs820085

ankyrin repeat and sterile alpha motif domain containing 1A. May play a negative role in growth factor receptor signaling pathways. MISSEN

SE

dbsnp.100:rs2395617

rs2395617

differentially expressed in FDCP 6 homolog (mouse). Phosphatidylinositol 3,4,5-trisphosphate-dependent guanine nucleotide exchange factor (GEF) which plays a role in the activation of Rho GTPases RAC1, RhoA and CDC42. Can regulate cell morphology in cooperation with activated RAC1. Plays a role in Th2 (T helper cells) development and/or activation, perhaps by interfering with ZAP-70 signaling (By similarity). MISSEN

SE

dbsnp.119:rs9369265

rs9369265

285852

Trem-like transcript 4 protein, no known functions.

MISSENSE

dbsnp.80:rs434102

Peripherin-2. Essential functions in eye morphogenesis.

MISSENSE

dbsnp.80:rs390659

Peripherin-2. Essential functions in eye morphogenesis.

MISSENSE

dbsnp.98:rs2229385

rs2229385

Methylmalonyl-CoA mutase, mitochondrial. Functions in amino acid degradation.

MISSENSE

dbsnp.83:rs495335

Cysteine-rich secretory protein 3. Possibly plays a role in innate immunity.

MISSENSE

PKHD1 all 2 5314 NM_138694.3 1606041 snp A C L V 6 51983208 1869

GSTA5 - NM_153699.1 1607514 snp C T V I 6 52809101 54

KLHL31 - 1608746 snp C T V I 6 53627563 155

C6orf142 - 90523 NM_138569.2 1609570 snp G A V I 6 54097484 158

GFRAL - NM_207410.2 1611281 snp T C S P 6 55374583 386

DST 667 NM_015548.3 1613450 snp C T M I 6 56525240 2812

DST 667 NM_015548.3 1613451 snp T C T A 6 56525503 2725

COL12A1 all 2 rs970547 1303 NM_004370.5 1649906 snp C T G S 6 75854021 3057

dbsnp.100:rs2435322

rs2435322

Polyductin. May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation.

MISSENSE

dbsnp.100:rs2397118

rs2397118

221357

Glutathion S-transferase A5. DNA suggests it's a functional gene, but mRNA could not be detected. It's one of five GSTA genes.

MISSENSE

dbsnp.107:rs3799260

rs3799260

401265

NM_001003760.4

Kelch-like protein 31. Transcriptional repressor in MAPK/JNK signaling pathway to regulate cellular functions. Overexpression inhibits the transcriptional activities of both the TPA-response element (TRE) and serum response element (SRE)

MISSENSE

dbsnp.111:rs4712056

rs4712056

Real name: MLIP. Muscular LMNA-interacting protein

MISSENSE

dbsnp.119:rs9370418

rs9370418

389400

GDNF family receptor alpha-like. No known functions. May be involved in breast and colorectal cancer.

MISSENSE

5 of 7, all long variants

dbsnp.111:rs4715630

rs4715630

Dystonin. Cytoskeletal linker protein. Acts as an integrator of intermediate filaments, actin and microtubule cytoskeleton networks.

MISSENSE

5 of 7, all long variants

dbsnp.111:rs4715631

rs4715631

Dystonin. Cytoskeletal linker protein. Acts as an integrator of intermediate filaments, actin and microtubule cytoskeleton networks.

MISSENSE

dbsnp.86:rs970547

Collagen alpha-1(XII) chain. Type XII collagen interacts with type I collagen-containing fibrils.

MISSENSE

PHIP - 55023 NM_017934.4 1656251 snp A G L P 6 79732419 1092

NT5E - 4907 NM_002526.1 1665279 snp A G T A 6 86255951 375

GABRR1 - 2569 NM_002042.2 1670128 snp T C M V 6 89983684 19

MDN1 - 23195 NM_014611.1 1670878 snp C A A S 6 90447163 4043

MDN1 - 23195 NM_014611.1 1670891 snp G A H Y 6 90459202 3422

MDN1 - 23195 NM_014611.1 1670953 snp C T S N 6 90504812 1558

FUT9 - 10690 NM_006581.3 1680321 snp A G T A 6 96758460 236

COQ3 - 51805 NM_017421.3 1684420 snp A G Y H 6 99924321 328

USP45 - 85015 1684491 snp T C N S 6 99990424 777

dbsnp.119:rs9350797

rs9350797

Pleckstrin homology domain interacting protein. Probable regulator of the insulin and insulin-like growth factor signaling pathways. Stimulates cell proliferation through regulation of cyclin transcription and has an anti-apoptotic activity through AKT1 phosphorylation and activation. Plays a role in the regulation of cell morphology and cytoskeletal organization.

MISSENSE

dbsnp.98:rs2229523

rs2229523

5'-nucleotidase. Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.

MISSENSE

dbsnp.120:rs12200969

rs12200969

Gamma-aminobutyric acid receptor subunit rho-1. Rho-1 GABA receptor could play a role in retinal neurotransmission an consists of 5 subunits amongst which this one.

MISSENSE

dbsnp.119:rs9353689

rs9353689

Midasin. Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits

MISSENSE

dbsnp.119:rs9294445

rs9294445


MISSENSE

dbsnp.110:rs4140446

rs4140446


MISSENSE

dbsnp.107:rs3811069

rs3811069

Alpha-(1,3)-fucosyltransferase. Involved in glycosphingolipid globo, lacto and neolacto series.

MISSENSE

dbsnp.110:rs4144164

rs4144164

Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial. Required for Ubiquinone biosynthesis.

MISSENSE

dbsnp.116:rs6570065

rs6570065

NM_001080481.1

Ubiquitin carboxyl-terminal hydrolase 45. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin

MISSENSE

USP45 - 85015 1684592 snp T C K E 6 1E+08 66

ASCC3 rs240780 10973 NM_006828.2 1686467 snp G C S C 6 101070867 1994

FLJ37396 NA 1698036 snp A G D G 6 109689878 921

LAMA4 3 of 5 3910 NM_002290.3 1701329 snp A G Y H 6 112600564 490

TSPYL4 - 23270 NM_021648.4 1707855 snp C A R L 6 116681775 29

RSHL3 rs784133 1708421 snp T C L P 6 117057525 588

dbsnp.116:rs7744845

rs7744845

NM_001080481.1

Ubiquitin carboxyl-terminal hydrolase 45. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin

MISSENSE

1 of 2, the long transcript

dbsnp.79:rs240780

Activating signal cointegrator 1 complex subunit 3. Enhances NF-kappa-B, SRF and AP1 transactivation.

MISSENSE

dbsnp.86:rs1040285

rs1040285

285754

XM_001722396.1

Membrane protein with unknown function. Not annotated in refseq (IGV)

MISSENSE

dbsnp.86:rs1050348

rs1050348

Laminin subunit alpha-4. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.

MISSENSE

dbsnp.98:rs2232470

rs2232470

Testis-specific Y-encoded-like protein 4. No known functions

MISSENSE

1 of two equally long transcripts. The affected one has an extra exon here.

dbsnp.86:rs784133

345895

NM_001010892.1

Real name: RSPH4A. Probable component of the axonemal radial spoke head.

MISSENSE

GPRC6A - NM_148963.2 1708641 snp G A P S 6 117237396 90

C6orf204 all 2 1711398 snp G T P T 6 118993653 250

C6orf170 - NM_152730.4 1715466 snp T C I V 6 121619068 598

LAMA2 all 2 3908 NM_000426.3 1726310 snp G A R H 6 129613022 618

- 93663 NM_033515.2 1726991 snp T C T A 6 130072907 22

dbsnp.100:rs2274911

rs2274911

222545

G-protein coupled receptor family C group 6 member A. Receptor activated by amino acids with a preference for basic amino acids such as L-Lys, L-Arg and L-ornithine but also by small and polar amino acids. The L-alpha amino acids respond is augmented by divalent cations Ca2+ and Mg2+. Activated by extracellular calcium and osteocalin. Seems to act through a G(q)/G(11) and G(i)-coupled pathway. Mediates the non-genomic effects of androgens in multiple tissue. May coordinates nutritionnal and hormonal anabolic signals through the sensing of extracellular amino acids, osteocalcin, divalents ions and its responsiveness to anabolic steroids.

MISSENSE

dbsnp.107:rs3734382

rs3734382

387119

NM_001042475.1

Coiled-coil domain-containing protein C6orf204. Probable centrosome association. Unknown function.

MISSENSE

dbsnp.116:rs7745023

rs7745023

221322

Also known as Protein Broad Minded. Required for high-level Shh responses in the developing neural tube. Together with CDK20, controls the structure of the primary cilium by coordinating assembly of the ciliary membrane and axoneme, allowing GLI2 to be properly activated in response to Shh signaling

MISSENSE

dbsnp.107:rs3816665

rs3816665

Laminin subunit alpha-2. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.

MISSENSE

ARHGAP18

dbsnp.107:rs3752536

rs3752536

Rho GTPase-activating protein 18. No known specific function.

MISSENSE

C6orf191 - 1727280 snp T C E G 6 130196359 85

C6orf191 - 1727281 snp A G F L 6 130196378 79

FLJ46906 NA 1739654 snp A G K E 6 139059507 181

FLJ46906 NA 1739657 snp A G I V 6 139059824 207

HIVEP2 - rs109836 3097 NM_006734.3 1744892 snp A G L P 6 143132955 1537

PCMT1 - rs4816 5110 NM_005389.1 1754852 snp G A V I 6 150156437 119

RAET1L - NM_130900.2 1755318 snp A G M T 6 150384903 84

dbsnp.119:rs9492393

rs9492393

253582

NM_001010876.1

Putative transmembrane protein C6orf191. Unknown function.

MISSENSE

dbsnp.111:rs4629709

rs4629709

253582

NM_001010876.1

Putative transmembrane protein C6orf191. Unknown function.

MISSENSE

dbsnp.119:rs9399249

rs9399249

441172

XM_001717879.1

Not known in refseq or Uniprot. Putative protein

MISSENSE

dbsnp.86:rs1129180

rs1129180

441172

XM_001717879.1


MISSENSE

dbsnp.79:rs109836

Human immunodeficiency virus type I enhancer-binding protein 2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.

MISSENSE

dbsnp.52:rs4816

Protein-L-isoaspartate(D-aspartate) O-methyltransferase. Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins.

MISSENSE

{dbsnp.86:rs912565;dbsnp.107:rs3734727}

rs912565;dbsnp.107

154064

Retinoic acid early transcript 1L protein. Member of a novel MHC1 family.

MISSENSE

AKAP12 all 2 9590 NM_005100.2 1757857 snp A G K E 6 151711567 116

AKAP12 all 2 9590 NM_005100.2 1757858 snp A C K Q 6 151711864 215

SYNE1 mut 23345 NM_033071.2 1759045 snp C A E D 6 152706953 3988

FNDC1 - rs370434 84624 NM_032532.2 1769817 snp C G Q E 6 159574540 1002

FNDC1 - 84624 NM_032532.2 1769821 snp T C L P 6 159575315 1260

FNDC1 - 84624 NM_032532.2 1769822 snp A G Q R 6 159575372 1279

FNDC1 - 84624 NM_032532.2 1769850 snp C A T K 6 159580868 1503

SOD2 all 3 rs4880 6648 1770771 snp A G V A 6 160033861 15

dbsnp.120:rs10872670

rs10872670

A-kinase anchor protein 12. Myasthenia gravis autoantigen. Anchoring protein that mediates the subcellular compartmentation of protein kinase A (PKA) and protein kinase C (PKC).

MISSENSE

dbsnp.107:rs3734799

rs3734799

A-kinase anchor protein 12. Myasthenia gravis autoantigen. Anchoring protein that mediates the subcellular compartmentation of protein kinase A (PKA) and protein kinase C (PKC).

MISSENSE

2 of 4, the long transcripts

{COSMIC:mut:42924;dbsnp.111:rs4645434}

Nesprin-1. Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization.

MISSENSE

dbsnp.80:rs370434

Fibronectin type III domain-containing protein 1. May be an activator of G protein signaling. Involved in tumor and psoriasis.

MISSENSE

dbsnp.101:rs3003174

rs3003174


MISSENSE

dbsnp.100:rs2501176

rs2501176


MISSENSE

{dbsnp.80:rs386360;dbsnp.129:rs63253663}

rs386360;dbsnp.129


MISSENSE

dbsnp.52:rs4880

NM_001024465.1

Superoxide dismutase [Mn], mitochondrial. Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.

MISSENSE

SLC22A1 all 2 rs628031 6580 NM_153187.1 1771459 snp A G M V 6 160480834 407

PSMB1 - rs12717 5689 NM_002793.2 1792311 snp G C P A Proteasome subunit beta type-1 6 170704224 10

all 3 1795690 snp T C * R 7 1594157 264

NA 54753 1807456 snp G A G R 7 6623354 178

NA 54753 1807457 snp A G Q R 7 6623421 200

THSD7A - rs47 NM_015204.1 1818703 snp T C N D 7 11547645 582

FLJ14712 NA XM_371878.6 1820712 snp A C F C 7 12343335 1484

FLJ14712 NA rs963323 XM_371878.6 1820807 snp G A S F 7 12376636 606

FLJ14712 NA rs848016 XM_371878.6 1820852 snp G A S F 7 12395327 141

DNAH11 - 8701 NM_003777.3 1837170 snp A G T A 7 21606929 1037

DNAH11 - 8701 NM_003777.3 1837867 snp A G M V 7 21890538 4171

dbsnp.83:rs628031

Solute carrier family 22 member 1. Translocates a broad array of organic cations with various structures and molecular weights (choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin,…).

MISSENSE

dbsnp.52:rs12717

MISSENSE

KIAA1908

dbsnp.116:rs7800178

rs7800178

114796

XM_001720885.1

Uncharacterized protein, annotated as noncoding RNA. This mutation would add 90 amino acids.

NONSTOP

DKFZp434J1015

dbsnp.100:rs2243563

rs2243563

XM_001716628.1


MISSENSE

DKFZp434J1015

dbsnp.92:rs1806552

rs1806552

XM_001716628.1


MISSENSE

dbsnp.36:rs47

221981

Thrombospondin type-1 domain-containing protein 7A. Uncharacterized, no known functions.

MISSENSE

dbsnp.96:rs2192828

rs2192828

221806


MISSENSE

dbsnp.86:rs963323

221806


MISSENSE

dbsnp.86:rs848016

221806


MISSENSE

dbsnp.119:rs10224537

rs10224537

Dynein heavy chain 11, axonemal. Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.

MISSENSE

dbsnp.116:rs6461613

rs6461613

Dynein heavy chain 11, axonemal. Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.

MISSENSE

- rs740250 9865 NM_014817.3 1849335 snp T C N S 7 28963468 239

GARS - 2617 NM_002047.2 1851608 snp C G P A 7 30601185 41

FLJ22374 NA 84182 NM_032222.2 1851903 snp C T T M 7 30797606 321

CCDC129 - NM_194300.2 1853193 snp C A A D 7 31559257 31

CCDC129 - NM_194300.2 1853236 snp A G H R 7 31584532 376

NPSR1 all 2 rs727162 NM_207172.1 1859046 snp C G S R 7 34840562 240

EEPD1 - rs196586 80820 NM_030636.2 1861690 snp G A S N 7 36287345 342

ANLN - 54443 NM_018685.2 1861907 snp G A R K 7 36412380 184

C7orf57 - 1879971 snp C T P L 7 48052601 123

KIAA0644

dbsnp.86:rs740250

TLR4 interactor with leucine rich repeats. Also known as TRIL. Component of the TLR4 signaling complex. Mediate the innate immune response to bacterial lipopolysaccharide (LPS) leading to cytokine secretion.

MISSENSE

dbsnp.86:rs1049402

rs1049402

Glycyl-tRNA synthetase. Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs.

MISSENSE

dbsnp.121:rs12701034

rs12701034


MISSENSE

dbsnp.116:rs7811042

rs7811042

223075

Coiled-coil domain-containing protein 129. Unknown function. May be involved in colorectal and breast cancer.

MISSENSE

dbsnp.119:rs10252720

rs10252720

223075

Coiled-coil domain-containing protein 129. Unknown function. May be involved in colorectal and breast cancer.

MISSENSE

dbsnp.86:rs727162

387129

Neuropeptide S receptor. May be active in signaling pathway in an autocrine or paracrine fashion in several tissues. Receptor for neuropeptide S, it may mediate its action, such as inhibitory effects, on cell growth.

MISSENSE

dbsnp.79:rs196586

Endonuclease/exonuclease/phosphatase family domain-containing protein 1. No known functions. Myristoylated at Gly2.

MISSENSE

{dbsnp.79:rs197367;dbsnp.129:rs62873663}

rs197367;dbsnp.129

Actin-binding protein anillin. Required for cytokinesis. Essential for the structural integrity of the cleavage furrow and for completion of cleavage furrow ingression.

MISSENSE

dbsnp.100:rs2708912

rs2708912

136288

NM_001100159.1

Uncharacterized protein, phosphorylated upon DNA damage.

MISSENSE

C7orf57 - 1879972 snp T C M T 7 48052685 151

C7orf57 - 1879982 snp C A P H 7 48056095 200

ABCA13 - NM_152701.2 1880426 snp A G K E 7 48516521 4445

COBL - 23242 NM_015198.2 1884860 snp C T V I 7 51064467 606

COBL - 23242 NM_015198.2 1884861 snp T G D A 7 51064556 576

ZNF117 - 51351 NM_015852.3 1903873 snp G A R * 7 64076101 427

ZNF92 all 2 NM_007139.2 1904524 snp C T A V 7 64500826 52

- NM_152559.2 1917050 snp T C Q R 7 72892747 106

- NM_182504.3 1917107 snp T A I N 7 72913500 13

PCLO all 2 rs2877 27445 NM_033026.4 1930131 snp C G S T 7 82602360 813

dbsnp.119:rs10233232

rs10233232

136288

NM_001100159.1


MISSENSE

dbsnp.100:rs2708890

rs2708890

136288

NM_001100159.1


MISSENSE

dbsnp.116:rs6583448

rs6583448

154664

ATP-binding cassette sub-family A member 13. May be involved in lipid homeostasis.

MISSENSE

dbsnp.98:rs2240090

rs2240090

Protein cordon-bleu. An Actin Nucleation Factor and Controls Neuronal Morphology.

MISSENSE

dbsnp.119:rs10230120

rs10230120

Protein cordon-bleu. An Actin Nucleation Factor and Controls Neuronal Morphology.

MISSENSE

dbsnp.88:rs1404453

rs1404453

Zinc Finger transcription factor with unknown function. This mutation deletes the last 56 amino acids.

NONSENSE

dbsnp.119:rs10265083

rs10265083

168374

Zinc Finger transcription factor with unknown function. Expressed early during embryonic development.

MISSENSE

WBSCR27

dbsnp.121:rs13241921

rs13241921

155368

Williams-Beuren syndrome chromosomal region 27 protein. Disease associated gene. The WBS is associated with loss of heterozygosity at 7q11.23. Some CNV abnormalities observed in this locus based on CG CNV data. This will have to be checked out further using raw snp array data.

MISSENSE

WBSCR28

dbsnp.120:rs11770052

rs11770052

135886

Williams-Beuren syndrome chromosomal region 28 protein. Disease associated gene. The WBS is associated with loss of heterozygosity at 7q11.23. Some CNV abnormalities observed in this locus based on CG CNV data. This will have to be checked out further using raw snp array data.

MISSENSE

dbsnp.36:rs2877

Protein piccolo. May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking

MISSENSE

STEAP4 - 79689 NM_024636.2 1936704 snp C T G D 7 87751296 74

COL1A2 - rs42524 1278 NM_000089.3 1944679 snp C G P A 7 93881174 548

ZAN all 2 rs191137 7455 NM_173059.1 1952854 snp T C W R 7 1E+08 2429

MUC12 - 10071 XM_379904.5 1953713 snp G A A T 7 1E+08 503

MUC12 - 10071 XM_379904.5 1953714 snp C G T R 7 1E+08 532

MUC17 - 1953734 snp G A A T 7 1E+08 426

NRCAM 4897 1963738 snp G C P A 7 107621848 544

CFTR - rs213950 1080 NM_000492.3 1975245 snp G A V M 7 116986768 469

dbsnp.92:rs1981529

rs1981529

Metalloreductase that has the ability to reduce both Fe3+ to Fe2+ and Cu2+ to Cu1+. Uses NAD+ as acceptor. Plays a role in systemic metabolic homeostasis, integrating inflammatory and metabolic responses. Associated with obesity and insulin-resistance. Involved in inflammatory arthritis, through the regulation of inflammatory cytokines. Inhibits anchorage-independent cell proliferation.

MISSENSE

dbsnp.76:rs42524

Collagen alpha-2(I) chain. Type I collagen is a member of group I collagen (fibrillar forming collagen).

MISSENSE

dbsnp.79:rs191137

Zonadhesin. Involved in gamete recognition and signaling.

MISSENSE

dbsnp.120:rs10953315

rs10953315

Mucin 12. Involved in epithelial cell protection, adhesion modulation, and signaling. May be involved in epithelial cell growth regulation. Stimulated by both cytokine TNF-alpha and TGF-beta in intestinal epithelium.

MISSENSE

dbsnp.120:rs11766125

rs11766125

Mucin 12. Involved in epithelial cell protection, adhesion modulation, and signaling. May be involved in epithelial cell growth regulation. Stimulated by both cytokine TNF-alpha and TGF-beta in intestinal epithelium.

MISSENSE

dbsnp.129:rs56103274

rs56103274

140453

NM_001040105.1

Mucin 17. Probably plays a role in maintaining homeostasis on mucosal surfaces.

MISSENSE

2 of 3. Only long isoforms

dbsnp.116:rs6958498

rs6958498

NM_001037132.1

Neuronal cell adhesion molecule. Cell adhesion, ankyrin-binding protein involved in neuron-neuron adhesion. May play a role in the molecular assembly of the nodes of Ranvier.

MISSENSE

dbsnp.79:rs213950

Cystic fibrosis transmembrane conductance regulator. Involved in the transport of chloride ions. No evidence for involvement in Cystic fibrosis.

MISSENSE

TAS2R16 - rs860170 50833 NM_016945.2 1980900 snp C T R H 7 122422259 221

ASB15 - NM_080928.3 1981855 snp G C G A 7 123056353 356

- 55798 NM_018396.2 1989530 snp G A V I 7 127921219 265

AGBL3 - 2000055 snp G C E Q 7 134352395 121

- 55281 NM_018295.2 2000426 snp G A R Q 7 134499752 6

CREB3L2 - rs273957 64764 NM_194071.2 2004770 snp C T V I 7 137251229 129

JHDM1D - 80853 NM_030647.1 2007908 snp G T R S 7 139443899 643

dbsnp.86:rs860170

Taste receptor type 2 member 16. Taste receptor involved in bitter perception in the mouth and gastrointestinal tract.

MISSENSE

dbsnp.111:rs4731112

rs4731112

142685

Ankyrin repeat and SOCS box protein 15. May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins

MISSENSE

METTL2B

dbsnp.100:rs2562741

rs2562741

Methyltransferase-like protein 2B. Probable methyltransferase, no known functions.

MISSENSE

dbsnp.111:rs4236655

rs4236655

340351

XM_001726650.1

Cytosolic carboxypeptidase 3. Metallocarboxypeptidase that may play a role in the processing of tubulin.

MISSENSE

TMEM140

dbsnp.107:rs3800592

rs3800592

Transmembrane protein 140. No known function, may be involved in breast and colon cancer.

MISSENSE

dbsnp.79:rs273957

Cyclic AMP-responsive element-binding protein 3-like protein 2. Transcriptional activator which is processed and activated during endoplasmic reticulum stress late phase. Regulates the transcription of unfolded protein response target genes, preventing accumulation of unfolded proteins in damaged neurons. Also regulates the expression of SEC23A, accelerating protein trafficking from the ER to the Golgi thereby playing a key role in chondrocyte differentiation and formation of epiphyseal cartilage

MISSENSE

dbsnp.116:rs6950119

rs6950119

Lysine-specific demethylase 7. Histone demethylase required for brain development.

MISSENSE

CLCN1 - 1180 NM_000083.2 2012921 snp C T P L 7 142753361 726

EPHA1 - 2041 NM_005232.3 2012974 snp T C M V 7 142798988 899

- 7984 NM_005435.3 2013908 snp A G E G 7 143692154 486

ZNF777 - 27153 NM_015694.2 2022819 snp A G V A 7 148783702 114

ZNF777 - 27153 NM_015694.2 2022820 snp G A R W 7 148783838 69

DPP6 all 3 1804 2032673 snp C T 7 154060492 0

DPP6 all 3 1804 2032775 snp A G 7 154092044 0

dbsnp.121:rs13438232

rs13438232

Chloride channel protein 1. Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.

MISSENSE

dbsnp.116:rs6967117

rs6967117

Ephrin type-A receptor 1. Receptor tyrosine kinase which binds promiscuously membrane-bound ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Upon activation by EFNA1 induces cell attachment to the extracellular matrix inhibiting cell spreading and motility through regulation of ILK and downstream RHOA and RAC. Plays also a role in angiogenesis and regulates cell proliferation. May play a role in apoptosis. This mutation is Met to Val. Probably low impact.

MISSENSE

ARHGEF5

dbsnp.87:rs1209412

rs1209412

Rho guanine nucleotide exchange factor 5. No known function, expressed in organs.

MISSENSE

dbsnp.107:rs3735319

rs3735319

Zinc finger protein 777. Zinc Finger transcription factor with unknown function.

MISSENSE

dbsnp.107:rs3735318

rs3735318


MISSENSE

dbsnp.120:rs11243339

rs11243339

NM_001039350.1

Dipeptidyl aminopeptidase-like 6. No aminopeptidase activity. May be involved in physiological processes of brain function. According to refseq, this mutation is in an intron.

UNKNOWN-TR

dbsnp.107:rs3807218

rs3807218

NM_001039350.1

Dipeptidyl aminopeptidase-like 6. No aminopeptidase activity. May be involved in physiological processes of brain function. This is a silent mutation

UNKNOWN-TR

DPP6 all 3 1804 2033328 snp A G 7 154298560 0

MCPH1 all 3 rs930557 79648 NM_024596.2 2065492 snp G C D H 8 6289590 313

MCPH1 all 3 79648 NM_024596.2 2065493 snp A G D G 8 6289825 391

RP1L1 - 94137 NM_178857.5 2074236 snp G T A E 8 10503180 1945

RP1L1 - 94137 NM_178857.5 2074240 snp C A R S 8 10504616 1466

RP1L1 - 94137 NM_178857.5 2074247 snp G A R W 8 10505581 1145

C8orf79 all 2 rs528255 57604 NM_020844.2 2079500 snp A G H R 8 12923007 149

C8orf79 all 2 57604 NM_020844.2 2079502 snp T G C G 8 12923177 206

C8orf79 all 2 rs608052 57604 NM_020844.2 2079507 snp A G R G 8 12923909 450

DLC1 all 2 10395 NM_182643.1 2080957 snp G A T I 8 13401172 259

dbsnp.100:rs2293353

rs2293353

NM_001039350.1

Dipeptidyl aminopeptidase-like 6. No aminopeptidase activity. May be involved in physiological processes of brain function. This is a silent mutation

UNKNOWN-TR

dbsnp.86:rs930557

Microcephalin. Implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex.

MISSENSE

dbsnp.100:rs2515569

rs2515569

Microcephalin. Implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex.

MISSENSE

dbsnp.120:rs11785822

rs11785822

Retinitis pigmentosa 1-like 1 protein. Required for the differentiation of photoreceptor cells.

MISSENSE

dbsnp.111:rs4840498

rs4840498


MISSENSE

dbsnp.111:rs4840502

rs4840502


MISSENSE

dbsnp.83:rs528255

Putative methyltransferase KIAA1456. No known functions.

MISSENSE

dbsnp.107:rs3739310

rs3739310

Putative methyltransferase KIAA1456. No known functions.

MISSENSE

dbsnp.83:rs608052

Putative methyltransferase KIAA1456. No known functions. Mutation in 3' UTR.

MISSENSE

dbsnp.107:rs3816747

rs3816747

Rho GTPase-activating protein 7. Frequently deleted in Liver Cancer, also involved in ovarian cancer. Functions as a GTPase-activating protein specific for Rho and an activator of PLCD1 in vivo and induces morphological changes and detachment through cytoskeletal reorganization.

MISSENSE

FGL1 all 4 2267 NM_201553.1 2093033 snp T C I V 8 17783817 71

FGL1 all 4 rs484373 2267 NM_201553.1 2093037 snp G A T I 8 17787299 14

PCM1 - rs208753 5108 NM_006197.3 2093244 snp A G M V 8 17859194 596

NAT2 - 10 NM_000015.2 2094412 snp T C I T 8 18302133 113

SH2D4A - 63898 NM_022071.2 2096778 snp A G E G 8 19263045 215

SLC18A1 all 4 6570 NM_003053.1 2097863 snp A G I T 8 20080992 135

NUDT18 - 79873 NM_024815.3 2100559 snp T C M V 8 22021057 223

- 8797 NM_003844.2 2101907 snp T C H R 8 23116200 140

LOXL2 - 4017 NM_002318.2 2102131 snp T G M L 8 23223297 569

NKX2-6 - 2103047 snp C T G S 8 23620199 144

C8orf80 - 2110825 snp T C S G 8 27981122 179

C8orf80 - 2110828 snp C G R P 8 27983767 22

dbsnp.107:rs3739406

rs3739406

Fibrinogen-like protein 1. Has hepatocyte mitogenic activity.

MISSENSE

dbsnp.83:rs484373

Fibrinogen-like protein 1. Has hepatocyte mitogenic activity.

MISSENSE

dbsnp.79:rs208753

Pericentriolar material 1 protein. Required for centrosome assembly and function. Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2.

MISSENSE

dbsnp.89:rs1801280

rs1801280

Arylamine N-acetyltransferase 2. detoxification of hydrazine and arylamine drugs. Can bioactivate certain carcinogens.

MISSENSE

dbsnp.111:rs4921637

rs4921637

SH2 domain-containing protein 4A. Inhibits estrogen-induced cell proliferation. May play a role in T cell function.

MISSENSE

dbsnp.88:rs1390938

rs1390938

Chromaffin granule amine transporter. Involved in the vesicular transport of biogenic amines.

MISSENSE

dbsnp.107:rs3739435

rs3739435

Nucleoside diphosphate-linked moiety X motif 18. Probably mediates the hydrolysis of some nucleoside diphosphate derivatives.

MISSENSE

TNFRSF10A

dbsnp.116:rs6557634

rs6557634

Tumor necrosis factor receptor superfamily member 10A. Receptor for the cytotoxic ligand TNFSF10/TRAIL.

MISSENSE

dbsnp.86:rs1063582

rs1063582

Lysyl oxidase homolog 2. Involved in cell adhesion and senescence?

MISSENSE

dbsnp.98:rs2228696

rs2228696

137814

XM_070619.11

Homeobox protein Nkx-2.6. In conjunction with NKX2-5, may play a role in both pharyngeal and cardiac embryonic development

MISSENSE

dbsnp.111:rs4732620

rs4732620

389643

NM_001010906.1

GTPase SLIP-GC. Plays a role as replication-related GTPase protein in germinal center B-cell.

MISSENSE

dbsnp.116:rs6998705

rs6998705

389643

NM_001010906.1

GTPase SLIP-GC. Plays a role as replication-related GTPase protein in germinal center B-cell.

MISSENSE

MBOAT4 - 2113878 snp T C T A 8 30115797 34

MCM4 all 2 rs762679 4173 NM_005914.2 2134557 snp T A L M 8 49047988 649

FLJ39080 NA XM_499117.3 2171018 snp A G E G 8 75777171 25

CNGB3 - 54714 NM_019098.3 2186437 snp T G T P 8 87735366 297

CNGB3 - 54714 NM_019098.3 2186462 snp A C C W 8 87748418 233

CDH17 all 2 1015 NM_004063.2 2195347 snp C G E D 8 95212361 733

MATN2 all 2 4147 NM_030583.2 2201518 snp A G K E 8 99060396 355

VPS13B 1 of 4 NM_181661.2 2202486 snp T G Y * 8 1E+08 412

ENPP2 all 3 5168 NM_006209.3 2228622 snp A G S P 8 120665203 544

ANXA13 all 2 312 NM_004306.2 2234815 snp C T V I 8 124766047 271

dbsnp.116:rs7813902

rs7813902

619373

XM_001125855.2

Ghrelin O-acyltransferase. Mediates the octanoylation of ghrelin at 'Ser-3'. Can use a variety of fatty acids as substrates including octanoic acid, decanoic acid and tetradecanoic acid.

MISSENSE

dbsnp.86:rs762679

Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells.

MISSENSE

dbsnp.96:rs2162147

rs2162147

441355


MISSENSE

dbsnp.111:rs4961206

rs4961206

Cyclic nucleotide-gated cation channel beta-3. Involved in visual signal transduction.

MISSENSE

dbsnp.116:rs6471482

rs6471482

Cyclic nucleotide-gated cation channel beta-3. Involved in visual signal transduction.

MISSENSE

dbsnp.86:rs1051623

rs1051623

Cadherin 17. Involved in cell cell adhesion.

MISSENSE

dbsnp.92:rs1869609

rs1869609

Matrilin 2. Involved in matrix assembly.

MISSENSE

dbsnp.116:rs7460625

rs7460625

157680

Vacuolar protein sorting-associated protein 13B. Protein sorting in post golgi traffic? Mutation adds 6 extra amino acids in the shortest splice variants (415 aa). This isoform is widely expressed. Others 3 variants remain unchanged on of them is also widely expressed.

NONSENSE

dbsnp.119:rs10283100

rs10283100

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2. Hydrolyzes lysophospholipids to produce lysophosphatidic acid (LPA) in extracellular fluids. Tumor cell motility-stimulating factor.

MISSENSE

dbsnp.100:rs2294015

rs2294015

Annexin A13. Intestine specific expression.

MISSENSE

ANXA13 all 2 312 NM_004306.2 2234839 snp C T R H 8 124779909 85

FER1L6 - 2235360 snp T G D E 8 125145769 1109

EFR3A - 23167 NM_015137.3 2246376 snp A G N D 8 133052005 364

OC90 - 2246480 snp T C S G 8 133122490 130

OC90 - 2246481 snp T C N D 8 133122499 127

TG 1 of 4 rs180223 7038 NM_003235.4 2247484 snp T G S A 8 133969433 733

FLJ43860 - NM_207414.2 2264247 snp C T G E Uncharacterized protein. 8 142528995 837

FLJ43860 - NM_207414.2 2264317 snp G T L M Uncharacterized protein. 8 142559301 288

FLJ43860 - NM_207414.2 2264358 snp C A G C Uncharacterized protein. 8 142574759 89

FLJ43860 - NM_207414.2 2264362 snp A G L P Uncharacterized protein. 8 142575642 73

TOP1MT - NM_052963.1 2268831 snp C T V I 8 144478079 255

ZNF707 all 3 2269617 snp C A P H 8 144847858 95

dbsnp.100:rs2294013

rs2294013

Annexin A13. Intestine specific expression.

MISSENSE

dbsnp.116:rs7012186

rs7012186

654463

NM_001039112.2

Fer-1-like protein 6. Function unknown.

MISSENSE

dbsnp.86:rs1051221

rs1051221

Protein EFR3 homolog A. Function unknown.

MISSENSE

dbsnp.116:rs7386782

rs7386782

729330

NM_001080399.1

Otoconin-90. Phospholipase 2 homolog, It is unlikely that this protein has phospholipase A2 activity. May be involved in Teratocarcinoma's

MISSENSE

dbsnp.116:rs7386783

rs7386783

729330

NM_001080399.1

Otoconin-90. Phospholipase 2 homolog, It is unlikely that this protein has phospholipase A2 activity. May be involved in Teratocarcinoma's

MISSENSE

dbsnp.79:rs180223

Thyroglobulin, Precursor of the iodinated thyroid hormones.

MISSENSE

dbsnp.116:rs7003306

rs7003306

389690

MISSENSE

dbsnp.100:rs2748416

rs2748416

389690

MISSENSE

dbsnp.100:rs2748404

rs2748404

389690

MISSENSE

dbsnp.100:rs2613637

rs2613637

389690

MISSENSE

dbsnp.120:rs11544484

rs11544484

116447

DNA topoisomerase I, mitochondrial. Releases the supercoiling and torsional tension of DNA introduced during duplication of mitochondrial DNA by transiently cleaving and rejoining one strand of the DNA duplex.

MISSENSE

dbsnp.116:rs6987308

rs6987308

286075

NM_001100598.1


MISSENSE

PARP10 - 84875 NM_032789.3 2270064 snp A G L P 8 145130973 394

FREM1 - NM_144966.4 2302127 snp T G Q P 9 14727505 2142

FREM1 - NM_144966.4 2302398 snp C G V L 9 14836035 438

- 54914 NM_017794.3 2313869 snp C G T S Uncharacterized protein. 9 20856973 717

- 54914 NM_017794.3 2313969 snp A G T A Uncharacterized protein. 9 20943048 1372

- 54914 NM_017794.3 2314011 snp A G K E Uncharacterized protein. 9 20978425 1667

UBAP2 - rs307692 55833 NM_018449.2 2336285 snp G A A V 9 33917898 755

KIF24 NM_194313.2 2336877 snp G A S F 9 34247094 836

KIF24 NM_194313.2 2336958 snp T C M V 9 34300926 139

OR13J1 2338838 snp T C H R Olfactory receptor 13J1. 9 35860000 132

219 NM_000692.3 2342975 snp G A V M 9 38386501 252

TRPM3 80036 NM_206947.3 2350876 snp C T R Q 9 72340803 1531

dbsnp.120:rs11136343

rs11136343

Poly [ADP-ribose] polymerase 10. May play a role in cell proliferation. May be required for the maintenance of cell cycle progression

MISSENSE

dbsnp.120:rs10961689

rs10961689

158326

FRAS1-related extracellular matrix protein 1, role in epidermal differentiation.

MISSENSE

dbsnp.100:rs2779500

rs2779500

158326

FRAS1-related extracellular matrix protein 1, role in epidermal differentiation.

MISSENSE

KIAA1797

dbsnp.116:rs7875872

rs7875872

MISSENSE

KIAA1797

dbsnp.105:rs3206852

rs3206852

MISSENSE

KIAA1797

dbsnp.111:rs4977881

rs4977881

MISSENSE

dbsnp.79:rs307692

Ubiquitin associated protein 2. Function unknown.

MISSENSE

dbsnp.127:rs41274041

rs41274041

347240

Kinesin-like protein KIF24. Function unknown.

MISSENSE

dbsnp.120:rs10972048

rs10972048

347240

Kinesin-like protein KIF24. Function unknown.

MISSENSE

dbsnp.116:rs7044405

rs7044405

392309

NM_001004487.1

MISSENSE

ALDH1B1

dbsnp.111:rs4878199

rs4878199

Aldehyde dehydrogenase X, mitochondrial. ALDHs play a major role in the detoxification of alcohol-derived acetaldehyde. They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation.

MISSENSE

dbsnp.116:rs6560142

rs6560142

Transient receptor potential cation channel subfamily M member 3. Calcium channel mediating constitutive calcium ion entry.

MISSENSE

RMI1 80010 NM_024945.2 2370268 snp A G N S 9 85807084 454

ROR2 4920 NM_004560.2 2382129 snp C T V I 9 93526141 818

NINJ1 4814 NM_004148.3 2383437 snp G T A D 9 94927140 109

FBP2 rs573212 8789 NM_003837.2 2386087 snp C G V L 9 96389486 85

ANKS6 NM_173551.3 2391247 snp C T V I 9 100573040 643

BAAT 570 NM_001701.2 2394337 snp C T R Q 9 103173448 19

OR13D1 2400623 snp A C Q H Olfactory receptor 13D1. 9 106497095 190

OR13D1 2400624 snp C T S L Olfactory receptor 13D1. 9 106497352 276

C9orf84 2410629 snp A G I T Uncharacterized protein. 9 113494400 1122

C9orf84 2410646 snp A G L P Uncharacterized protein. 9 113502142 928

C9orf84 2410651 snp T C Y C Uncharacterized protein. 9 113504307 892

C9orf84 2410706 snp T C H R Uncharacterized protein. 9 113530128 376

FKBP15 23307 NM_015258.1 2413721 snp G A L F 9 114989976 433

dbsnp.92:rs1982151

rs1982151

RecQ-mediated genome instability protein 1. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Interacts with TOP3A

MISSENSE

dbsnp.120:rs10761129

rs10761129

Tyrosine-protein kinase transmembrane receptor ROR2. Involved in the formation of chondrocytes

MISSENSE

dbsnp.100:rs2275848

rs2275848

Nerve injury induced 1. Homophilic cell adhesion molecule that promotes axonal growth.

MISSENSE

dbsnp.83:rs573212

Fructose-1,6-bisphosphatase isozyme 2.

MISSENSE

dbsnp.116:rs6415847

rs6415847

203286

Ankyrin repeat and SAM domain-containing protein 6. Required for renal function.

MISSENSE

dbsnp.88:rs1572983

rs1572983

Bile acid-CoA:amino acid N-acyltransferase. Involved in bile acid metabolism.

MISSENSE

dbsnp.120:rs10820709

rs10820709

286365

NM_001004484.1

MISSENSE

dbsnp.120:rs10761073

rs10761073

286365

NM_001004484.1

MISSENSE

dbsnp.88:rs1475110

rs1475110

158401

NM_001080551.1

MISSENSE

dbsnp.116:rs6477845

rs6477845

158401

NM_001080551.1

MISSENSE

dbsnp.88:rs1407390

rs1407390

158401

NM_001080551.1

MISSENSE

dbsnp.116:rs7470491

rs7470491

158401

NM_001080551.1

MISSENSE

dbsnp.119:rs10465129

rs10465129

FK506-binding protein 15. May be involved in the cytoskeletal organization of neuronal growth cones.

MISSENSE

FKBP15 23307 NM_015258.1 2413722 snp A C H Q 9 114990526 412

RNF183 NM_145051.3 2413871 snp T C Q R 9 115099944 113

DFNB31 25861 2415696 snp G C H Q 9 116206158 368

TNC rs13321 3371 NM_002160.2 2416787 snp C G E Q 9 116832403 2007

TNC 3371 NM_002160.2 2416905 snp T C Q R 9 116886400 679

55755 2425570 snp C G E Q 9 122330856 288

OR1N2 2428407 snp C T T M Olfactory receptor 1N2 9 124356170 300

OR1L8 2428512 snp C G R P Olfactory receptor 1L8 9 124369945 210

OR1Q1 rs972925 NM_012364.1 2428573 snp A G Q R Olfactory receptor 1Q1 9 124416907 23

OR1Q1 NM_012364.1 2428574 snp A G I M Olfactory receptor 1Q1 9 124417325 162

dbsnp.119:rs10435864

rs10435864

FK506-binding protein 15. May be involved in the cytoskeletal organization of neuronal growth cones.

MISSENSE

dbsnp.107:rs3750534

rs3750534

138065

RING finger protein 183. Function unknown.

MISSENSE

dbsnp.116:rs6478078

rs6478078

NM_001083885.1

Whirlin, real name: WHRN. Necessary for elongation and maintenance of inner and outer hair cell stereocilia in the organ of Corti in the inner ear.

MISSENSE

dbsnp.52:rs13321

Tenascin. Extracellular matrix protein implicated in guidance of migrating neurons as well as axons during development, synaptic plasticity as well as neuronal regeneration.

MISSENSE

dbsnp.86:rs1061494

rs1061494

Tenascin. Extracellular matrix protein implicated in guidance of migrating neurons as well as axons during development, synaptic plasticity as well as neuronal regeneration.

MISSENSE

CDK5RAP2

dbsnp.111:rs4836822

rs4836822

NM_001011649.1

CDK5 regulatory subunit-associated protein 2. Potential regulator of CDK5 activity via its interaction with CDK5R1. Negative regulator of centriole disengagement (licensing) which maintains centriole engagement and cohesion. Involved in regulation of mitotic spindle orientation. Plays a role in the spindle checkpoint activation by acting as a transcriptional regulator of both BUBR1 and MAD2 promoter.

MISSENSE

dbsnp.88:rs1411272

rs1411272

138882

NM_001004457.1

MISSENSE

dbsnp.120:rs10739614

rs10739614

138881

NM_001004454.1

MISSENSE

dbsnp.86:rs972925

158131

MISSENSE

dbsnp.88:rs1329957

rs1329957

158131

MISSENSE

OR1B1 2428606 snp A C V G Olfactory receptor 1B1 9 124430694 313

OR1B1 2428609 snp A G L S Olfactory receptor 1B1 9 124431189 148

OR1L6 2428673 snp C A Q K Olfactory receptor 1L6 9 124552013 58

WDR38 2431079 snp C G A G 9 126658659 192

SH2D3C 10044 NM_170600.1 2434899 snp G A L F 9 129576537 22

LAMC3 10319 NM_006059.3 2441410 snp A G E G 9 132917698 543

LAMC3 10319 NM_006059.3 2441493 snp A G S G 9 132937869 1081

NA 84726 NM_013318.3 2442283 snp C G T S 9 133340143 935

NA 84726 NM_013318.3 2442287 snp C T A V 9 133341163 1275

SETX rs543573 23064 NM_015046.5 2443531 snp T C I V 9 134192649 1385

dbsnp.88:rs1556189

rs1556189

347169

NM_001004450.1

MISSENSE

dbsnp.88:rs1536929

rs1536929

347169

NM_001004450.1

MISSENSE

dbsnp.120:rs10760252

rs10760252

392390

NM_001004453.1

MISSENSE

dbsnp.120:rs10760381

rs10760381

401551

NM_001045476.1

WD repeat-containing protein 38. Function unknown.

MISSENSE

dbsnp.120:rs10760500

rs10760500

SH2 domain-containing protein 3C. Eph receptor-binding protein which may be a positive regulator of TCR signaling

MISSENSE

dbsnp.120:rs10901333

rs10901333

Laminin subunit gamma-3. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.

MISSENSE

dbsnp.100:rs2275140

rs2275140

Laminin subunit gamma-3. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.

MISSENSE

KIAA0515

dbsnp.120:rs10736851

rs10736851

Protein PRRC2B, uncharacterized protein.

MISSENSE

KIAA0515

dbsnp.120:rs11243403

rs11243403

Protein PRRC2B, uncharacterized protein.

MISSENSE

dbsnp.83:rs543573

Probable helicase senataxin. Involved in DNA double-strand breaks damage response generated by oxidative stress. Probable helicase, which may be involved in RNA maturation.

MISSENSE

SETX 23064 NM_015046.5 2443532 snp C T G R 9 134193051 1251

GLT6D1 NM_182974.2 2450755 snp G A P S 9 137655939 218

C9orf86 55684 NM_024718.2 2453113 snp G C E Q 9 138852151 338

FLJ20433 NA 54932 NM_017820.3 2453900 snp C T C Y Uncharacterized protein. 9 139363664 544

FLJ20433 NA 54932 NM_017820.3 2453902 snp T G E D Uncharacterized protein. 9 139366963 321

FLJ20433 NA 54932 NM_017820.3 2453927 snp C T A T Uncharacterized protein. 9 139382246 159

ENTPD8 2454014 snp A G L P 9 139452298 61

PITRM1 rs6901 10531 NM_014889.2 2460490 snp T C Q R 10 3170226 1036

PITRM1 10531 NM_014889.2 2460545 snp T C I V 10 3192064 327

tAKR XM_372302.4 2463254 snp A G C R 10 4908181 331

dbsnp.87:rs1183768

rs1183768

Probable helicase senataxin. Involved in DNA double-strand breaks damage response generated by oxidative stress. Probable helicase, which may be involved in RNA maturation.

MISSENSE

dbsnp.123:rs17040344

rs17040344

360203

Glycosyltransferase 6 domain-containing protein 1. Susceptibilty gene for periodontitis

MISSENSE

dbsnp.100:rs2811741

rs2811741

Putative GTP-binding protein Parf. May reduce growth inhibitory activity of CDKN2A.

MISSENSE

dbsnp.125:rs28545754

rs28545754

MISSENSE

dbsnp.116:rs7020732

rs7020732

MISSENSE

dbsnp.120:rs11533158

rs11533158

MISSENSE

dbsnp.116:rs6606582

rs6606582

377841

NM_001033113.1

Ectonucleoside triphosphate diphosphohydrolase 8. Canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity.

MISSENSE

dbsnp.52:rs6901

Presequence protease, mitochondrial. ATP-independent protease that degrades mitochondrial transit peptides after their cleavage. Also degrades other unstructured peptides. Specific for peptides in the range of 10 to 65 residues.

MISSENSE

dbsnp.111:rs4242746

rs4242746

Presequence protease, mitochondrial. ATP-independent protease that degrades mitochondrial transit peptides after their cleavage. Also degrades other unstructured peptides. Specific for peptides in the range of 10 to 65 residues.

MISSENSE

dbsnp.116:rs7092190

rs7092190

389932

truncated Aldo Keto reductase. Only 14 amino acids long. Not in Uniprot.

MISSENSE

tAKR XM_372302.4 2463261 snp T C N S 10 4908856 305

tAKR XM_372302.4 2463290 snp G A R C 10 4917651 206

AKR1C4 1109 NM_001818.2 2463992 snp A G Q R 10 5245024 249

CALML5 51806 NM_017422.3 2464393 snp T C S G 10 5531229 57

C10orf18 54906 NM_017782.3 2464852 snp T G C G Protein FAM208B. Function unknown. 10 5821633 498

C10orf18 54906 NM_017782.3 2464868 snp T C V A Protein FAM208B. Function unknown. 10 5830425 1678

54522 NM_019046.1 2465000 snp T C Q R 10 5960126 352

IL15RA 3601 NM_002189.2 2465156 snp T G N T 10 6042373 181

PRKCQ 5588 NM_006257.2 2466110 snp G A P L 10 6567148 329

ITIH5 80760 NM_032817.3 2467879 snp A G F S 10 7645106 710

dbsnp.111:rs4242778

rs4242778

389932


MISSENSE

dbsnp.116:rs7092182

rs7092182

389932


MISSENSE

dbsnp.111:rs4880718

rs4880718

Aldo-keto reductase family 1 member C4. Catalyzes the transformation of the potent androgen dihydrotestosterone (DHT) into the less active form

MISSENSE

dbsnp.120:rs11546426

rs11546426

Calmodulin-like protein 5. Binds calcium. May be involved in terminal differentiation of keratinocytes.

MISSENSE

dbsnp.100:rs2254067

rs2254067

MISSENSE

dbsnp.100:rs2669142

rs2669142

MISSENSE

ANKRD16

dbsnp.86:rs1052420

rs1052420

Ankyrin repeat domain-containing protein 16. Function unknown.

MISSENSE

dbsnp.98:rs2228059

rs2228059

Interleukin-15 receptor subunit alpha. High-affinity receptor for interleukin-15. Can signal both in cis and trans where IL15R from one subset of cells presents IL15 to neighboring IL2RG-expressing cells. Expression of different isoforms may alter or interfere with signal transduction. Shorter isoforms lack IL15 binding activity.

MISSENSE

dbsnp.98:rs2236379

rs2236379

Protein kinase C theta type. This is a calcium-independent, phospholipid-dependent, serine- and threonine-specific enzyme. Essential for T-cell receptor (TCR)-mediated T-cell activation, but is dispensable during TCR-dependent thymocyte development.

MISSENSE

dbsnp.120:rs10795551

rs10795551

Inter-alpha-trypsin inhibitor heavy chain H5. May act as a tumor suppressor.

MISSENSE

ITIH5 80760 NM_032817.3 2467904 snp T G T P 10 7658691 355

ITIH2 3698 NM_002216.2 2468133 snp A G N S 10 7803666 262

TAF3 83860 NM_031923.2 2468565 snp A G N S 10 8046803 441

DHTKD1 55526 NM_018706.5 2474504 snp T G Y D 10 12171086 271

DHTKD1 55526 NM_018706.5 2474539 snp C G I M 10 12183110 606

MEIG1 2479338 snp A C K T 10 15048498 8

CUBN 8029 NM_001081.3 2481971 snp G C S W 10 16983376 2716

CUBN 8029 NM_001081.3 2482110 snp G A P S 10 17064508 1558

CUBN 8029 NM_001081.3 2482351 snp A G F S 10 17196156 252

NM_152725.2 2483890 snp G A V I 10 18306994 303

XM_295865.6 2485640 snp A C D A 10 19660412 293

dbsnp.100:rs2275069

rs2275069


MISSENSE

dbsnp.116:rs7075296

rs7075296


MISSENSE

dbsnp.111:rs4747647

rs4747647

Transcription initiation factor TFIID subunit 3. Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II

MISSENSE

dbsnp.107:rs3740015

rs3740015

Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial. Catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO2.

MISSENSE

dbsnp.94:rs2062988

rs2062988

Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial. Catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO2.

MISSENSE

dbsnp.111:rs4750568

rs4750568

644890

NM_001080836.2

Meiosis expressed gene 1 protein homolog. Involved in germ cell differentiation?

MISSENSE

dbsnp.100:rs2796835

rs2796835

Cubilin, Intrinsic factor-vitamin B12 receptor. Cotransporter which plays a role in lipoprotein, vitamin and iron metabolism, by facilitating their uptake.

MISSENSE

dbsnp.89:rs1801231

rs1801231


MISSENSE

dbsnp.89:rs1801222

rs1801222


MISSENSE

SLC39A12

dbsnp.100:rs2478568

rs2478568

221074

Zinc transporter ZIP12. Acts as a zinc-influx transporter.

MISSENSE

C10orf112

dbsnp.116:rs7100382

rs7100382

340895

MAM and LDL-receptor class A domain-containing protein. Function unknown.

MISSENSE

XM_295865.6 2485807 snp G A V I 10 19718502 629

PIP4K2A 5305 NM_005028.4 2488911 snp T C N S 10 22879633 250

GPR158 57512 NM_020752.2 2490889 snp C G A G 10 25741346 424

MYO3A 53904 NM_017433.4 2492238 snp C A R S 10 26503135 1312

PTCHD3 - 2494039 snp A G * Q 10 27727230 767

PTCHD3 - 2494041 snp A G M T 10 27727970 520

PTCHD3 - 2494073 snp A C C G 10 27732284 406

SVIL 6840 NM_021738.2 2497464 snp C T V I 10 29862037 421

57608 NM_020848.1 2498088 snp T C R G Uncharacterized protein. 10 30356213 956

C10orf68 79741 NM_024688.2 2501267 snp A G I V Uncharacterized protein. 10 33014974 38

C10orf68 79741 NM_024688.2 2501458 snp G C G A Uncharacterized protein. 10 33163829 387

C10orf112

dbsnp.120:rs10763975

rs10763975

340895

MAM and LDL-receptor class A domain-containing protein. Function unknown.

MISSENSE

dbsnp.120:rs10828317

rs10828317

Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha. Catalyzes the phosphorylation of phosphatidylinositol-5-phosphate (PtdIns5P) on the fourth hydroxyl of the myo-inositol ring, to form phosphatidylinositol-4,5-biphosphate (PtdIns(4,5)P2).

MISSENSE

dbsnp.100:rs2480345

rs2480345

Probable G-protein coupled receptor 158. Function unknown.

MISSENSE

dbsnp.92:rs1999240

rs1999240

Myosin-IIIa. Probable actin-based motor with a protein kinase activity. Probably plays a role in vision and hearing.

MISSENSE

dbsnp.100:rs2505323

rs2505323

374308

NM_001034842.2

Putative role in sperm development or function. Mutation adds 35 extra amino acids, till the endo of the 3' UTR of the mRNA. If longer mRNA, then maximally ~150 amino acids added till next stop codon.

NONSTOP

dbsnp.100:rs2505327

rs2505327

374308

NM_001034842.2

Putative role in sperm development or function.

MISSENSE

dbsnp.100:rs2484180

rs2484180

374308

NM_001034842.2

Putative role in sperm development or function.

MISSENSE

dbsnp.87:rs1247696

rs1247696

Supervillin. Forms a high-affinity link between the actin cytoskeleton and the membrane. Involved in invadopodia of cancer cells.

MISSENSE

KIAA1462

dbsnp.96:rs2185724

rs2185724

MISSENSE

dbsnp.89:rs1762526

rs1762526

MISSENSE

dbsnp.111:rs4448627

rs4448627

MISSENSE

ZNF33A 7581 NM_006974.2 2508161 snp C G Q E 10 38384705 548

CCNYL2 XM_374787.5 2509895 snp G T D E 10 42290836 7

ZNF33B rs210280 7582 NM_006955.1 2510011 snp G A R C 10 42409970 144

MARCH8 2513342 snp A G Y H 10 45273772 265

ZNF488 NM_153034.2 2515851 snp C T A V 10 47990752 71

WDFY4 57705 2517151 snp T C S P 10 49683407 772

WDFY4 57705 2517166 snp G A R Q 10 49695401 1060

WDFY4 57705 2517296 snp G A S N 10 49779907 1771

C10orf73 2517616 snp G T D E 10 50009759 289

C10orf73 2517617 snp A T L Q 10 50009967 220

C10orf71 NM_199459.2 2517979 snp G T R L 10 50201554 319

C10orf71 NM_199459.2 2517982 snp A C D A 10 50201977 460

dbsnp.100:rs2505232

rs2505232

Zinc finger protein 33A. ZNF with unknown function.

MISSENSE

dbsnp.100:rs2801951

rs2801951

414194

Cyclin-Y-like protein 2. Function unknown.

MISSENSE

dbsnp.79:rs210280

Zinc finger protein 33B. ZNF with unknown function.

MISSENSE

dbsnp.116:rs7908745

rs7908745

220972

NM_001002266.1

E3 ubiquitin-protein ligase MARCH8. Mediates ubiquitination of CD86 and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. Functions in immune response.

MISSENSE

dbsnp.126:rs35618062

rs35618062

118738

Zinc finger protein 448. ZNF with unknown function.

MISSENSE

dbsnp.96:rs2170132

rs2170132

XM_001714299.1

WD repeat- and FYVE domain-containing protein 4. Function unknown.

MISSENSE

dbsnp.116:rs7097397

rs7097397

XM_001714299.1


MISSENSE

dbsnp.100:rs2663046

rs2663046

XM_001714299.1


MISSENSE

dbsnp.130:rs73302786

rs73302786

170370

XM_096317.11

Putative protein FAM170B. Function unknown.

MISSENSE

170370

XM_096317.11

Putative protein FAM170B. Function unknown.

MISSENSE

dbsnp.129:rs56206226

rs56206226

118461

Uncharacterized protein C10orf71. Function unknown.

MISSENSE

dbsnp.127:rs45554335

rs45554335

118461


MISSENSE

CHAT 1103 NM_020984.2 2518316 snp G A V M 10 50526657 342

C10orf53 NM_182554.2 2518432 snp A G R G 10 50586489 98

ZWINT 11130 NM_032997.2 2527378 snp T C R G 10 57788635 186

BICC1 80114 2530946 snp T C S P 10 60258558 942

SLC16A9 NM_194298.1 2531449 snp G T T K 10 61084016 257

RTKN2 NM_145307.2 2534269 snp T C H R 10 63628117 461

JMJD1C NM_004241.2 2535792 snp A T S T 10 64644542 244

PBLD 64081 NM_022129.3 2542679 snp T C H R 10 69714036 256

HKDC1 rs906219 80201 NM_025130.3 2544587 snp C A N K 10 70696515 916

dbsnp.111:rs4838544

rs4838544

Choline O-acetyltransferase. Catalyzes the reversible synthesis of acetylcholine (ACh) from acetyl CoA and choline at cholinergic synapses.

MISSENSE

dbsnp.87:rs1258236

rs1258236

282966

UPF0728 protein C10orf53.Function unknown.

MISSENSE

dbsnp.98:rs2241666

rs2241666

ZW10 interactor. Part of the MIS12 complex, which is required for kinetochore formation and spindle checkpoint activity. Required to target ZW10 to the kinetochore at prometaphase. ZW10 is an essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis.

MISSENSE

dbsnp.111:rs4948550

rs4948550

NM_001080512.1

Protein bicaudal C homolog 1. Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.

MISSENSE

dbsnp.98:rs2242206

rs2242206

220963

Monocarboxylate transporter 9. Proton-linked monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates

MISSENSE

dbsnp.103:rs3125734

rs3125734

219790

Rhotekin-2. May play an important role in lymphopoiesis.

MISSENSE

dbsnp.120:rs10761725

rs10761725

221037

Probable histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. May be involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes

MISSENSE

dbsnp.110:rs4142048

rs4142048

Phenazine biosynthesis-like domain-containing protein. Function unknown.

MISSENSE

dbsnp.86:rs906219

Putative hexokinase. Involved in glycolysis?

MISSENSE

NM_139155.2 2547218 snp T C L P 10 72170768 592

NM_139155.2 2547242 snp C A L M 10 72183640 939

SLC29A3 55315 NM_018344.4 2547982 snp A G R G 10 72752568 17

SLC29A3 rs780668 55315 NM_018344.4 2548045 snp C T S F 10 72781413 157

SLC29A3 55315 NM_018344.4 2548069 snp A G I V 10 72791918 325

CDH23 64072 NM_022124.3 2548636 snp C G T S 10 73220122 1998

LIPN 2563657 snp C A T N 10 90520639 243

IFIT2 rs1727 3433 NM_001547.4 2564167 snp C A D E 10 91056748 351

9585 NM_016195.2 2564746 snp T C C R 10 91488106 1136

ADAMTS14

dbsnp.120:rs10823607

rs10823607

140766

A disintegrin and metalloproteinase with thrombospondin motifs 14. Secreted, Has a aminoprocollagen type I activity processing activity in the absence of ADAMTS2.

MISSENSE

ADAMTS14

dbsnp.121:rs12774070

rs12774070

140766

A disintegrin and metalloproteinase with thrombospondin motifs 14. Secreted, Has a aminoprocollagen type I activity processing activity in the absence of ADAMTS2.

MISSENSE

dbsnp.100:rs2277257

rs2277257

Equilibrative nucleoside transporter 3. Mediates transport of adenine, adenosine and uridine, as well as several nucleoside analog drug over plasma membrane.

MISSENSE

dbsnp.86:rs780668


MISSENSE

dbsnp.100:rs2487068

rs2487068


MISSENSE

dbsnp.120:rs11592462

rs11592462

Cadherin 23. Required for establishing and/or maintaining the proper organization of the stereocilia bundle of hair cells in the cochlea and the vestibule during late embryonic/early postnatal development

MISSENSE

dbsnp.120:rs10788611

rs10788611

643418

NM_001102469.1

Lipase member N plays a highly specific role in the last step of keratinocyte differentiation.

MISSENSE

dbsnp.36:rs1727

Interferon-induced protein with tetratricopeptide repeats 2. Function unknown.

MISSENSE

MPHOSPH1

dbsnp.92:rs1886996

rs1886996

Kinesin-like protein KIF20B. Plus end directed motor protein, required for cytokinesis.

MISSENSE

9585 NM_016195.2 2564747 snp A G N S 10 91488233 1178

EXOC6 54536 2567510 snp G A V I 10 94584544 23

CYP26C1 NM_183374.2 2567813 snp G A R Q 10 94814155 244

PLCE1 51196 NM_016341.3 2569423 snp G C R P 10 96029586 1574

PLCE1 51196 NM_016341.3 2569439 snp C T T I 10 96048287 1776

PLCE1 51196 NM_016341.3 2569450 snp A G H R 10 96056330 1926

MPHOSPH1

dbsnp.92:rs1886997

rs1886997

Kinesin-like protein KIF20B. Plus end directed motor protein, required for cytokinesis.

MISSENSE

dbsnp.100:rs2490741

rs2490741

NM_001013848.1

Exocyst complex component 6, involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.

MISSENSE

dbsnp.120:rs11187265

rs11187265

340665

Cytochrome P450 26C1. Involved in retinoic acid metabolism.

MISSENSE

dbsnp.100:rs2274224

rs2274224

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase epsilon-1. PLCE1 is a bifunctional enzyme which also regulates small GTPases of the Ras superfamily through its Ras guanine-exchange factor (RasGEF) activity. As an effector of heterotrimeric and small G-protein, it may play a role in cell survival, cell growth, actin organization and T-cell activation

MISSENSE

dbsnp.107:rs3765524

rs3765524


MISSENSE

dbsnp.100:rs2274223

rs2274223


MISSENSE

DNTT 1791 2571190 snp A G R G 10 98068228 111

MMS19 64210 NM_022362.3 2572418 snp G C A G 10 99230747 88

ANKRD2 26287 NM_020349.2 2572567 snp G A A T 10 99327561 61

ZFYVE27 NM_144588.4 2572677 snp G T G V 10 99494619 137

C10orf28 27291 NM_014472.4 2573193 snp A G H R 10 99959557 565

LOXL4 84171 NM_032211.6 2573235 snp T G D A 10 1E+08 404

HPS1 3257 NM_000195.2 2573460 snp A G V A 10 1E+08 3

ABCC2 1244 NM_000392.2 2575779 snp G A V I 10 101553804 416

SCD 6319 NM_005063.4 2575974 snp A C M L 10 102106300 223

dbsnp.116:rs6584066

rs6584066

NM_001017520.1

DNA nucleotidylexotransferase. One of the in vivo functions of this enzyme is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells.

MISSENSE

dbsnp.100:rs2275586

rs2275586

MMS19 nucleotide excision repair protein homolog. May play a role in nucleotide excision repair (NER) and RNA polymerase II (POL II) transcription

MISSENSE

dbsnp.116:rs7094973

rs7094973

Ankyrin repeat domain-containing protein 2. May play an important role in skeletal muscle hypertrophy.

MISSENSE

dbsnp.120:rs10882993

rs10882993

118813

Protrudin. Functions as an upstream inhibitor of RAB11, regulating directional protein transport to the forming neurites.

MISSENSE

dbsnp.120:rs11189513

rs11189513

Growth inhibition and differentiation-related protein 88. Function unclear. Expressed in placenta.

MISSENSE

dbsnp.92:rs1983864

rs1983864

Lysyl oxidase homolog 4. May modulate the formation of a collagenous extracellular matrix.

MISSENSE

dbsnp.129:rs58548334

rs58548334

Hermansky-Pudlak syndrome 1 protein. Component of multiple cytoplasmic organelles. Apparently crucial for their normal development and function. May be involved in intracellular protein sorting.

MISSENSE

dbsnp.100:rs2273697

rs2273697

Canalicular multispecific organic anion transporter 1. Mediates hepatobiliary excretion of numerous organic anions.

MISSENSE

dbsnp.98:rs2234970

rs2234970

Scavenger receptor cysteine-rich type 1 protein M130. Acute phase-regulated receptor involved in clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages and may thereby protect tissues from free hemoglobin-mediated oxidative damage.

MISSENSE

WNT8B 7479 NM_003393.3 2576159 snp G C C S 10 102212946 10

SEC31B 25956 NM_015490.3 2576199 snp C A A S 10 102237397 1168

SEC31B 25956 NM_015490.3 2576218 snp G A P S 10 102255172 371

SEC31B 25956 NM_015490.3 2576221 snp A C S A 10 102255836 331

SEC31B 25956 NM_015490.3 2576225 snp C A L F 10 102259074 128

SEC31B 25956 NM_015490.3 2576226 snp A G V A 10 102259195 88

C10orf6 55719 NM_018121.3 2576594 snp C A S Y 10 102674369 540

KAZALD1 rs807037 81621 NM_030929.3 2576740 snp G C G A 10 102814338 254

C10orf26 rs284860 54838 2578470 snp T C S P 10 104562952 322

FAM26A 2578772 snp C T D N 10 105223099 298

COL17A1 rs805722 1308 NM_000494.3 2579536 snp T C M V 10 105800389 702

COL17A1 rs805708 1308 NM_000494.3 2579563 snp G A T M 10 105814322 209

CCDC147 2579671 snp T A S T 10 106142100 495

dbsnp.107:rs3793771

rs3793771

Wnt-8b. Ligand for members of the frizzled family of seven transmembrane receptors. May play an important role in the development and differentiation of the hippocampus.

MISSENSE

dbsnp.100:rs2298075

rs2298075

Protein transport protein Sec31B. Component of CopII vesicles, functions in ER cargo export to golgi.

MISSENSE

dbsnp.100:rs2295772

rs2295772


MISSENSE

dbsnp.100:rs2295774

rs2295774


MISSENSE

dbsnp.107:rs3793706

rs3793706


MISSENSE

dbsnp.107:rs3763695

rs3763695


MISSENSE

dbsnp.120:rs10883563

rs10883563

Protein FAM178A. Involved in Inherited Infantile Onset Spinocerebellar Ataxia (IOSCA)

MISSENSE

dbsnp.86:rs807037

Kazal-type serine protease inhibitor domain-containing protein 1. Involved in the proliferation of osteoblasts

MISSENSE

dbsnp.79:rs284860

NM_001083913.1

Outcome predictor in acute leukemia 1. High expression of this protein is associated with favourable prognosis in Acute Lymphoblastic Leukemia (ALL), but is treatment dependent.

MISSENSE

dbsnp.101:rs2986035

rs2986035

119395

XM_001725818.1

Calcium homeostasis modulator protein 3. Function unknown.

MISSENSE

dbsnp.86:rs805722

Collagen alpha-1(XVII) chain. May play a role in the integrity of hemidesmosome.

MISSENSE

dbsnp.86:rs805708

Collagen alpha-1(XVII) chain. May play a role in the integrity of hemidesmosome.

MISSENSE

dbsnp.120:rs11192036

rs11192036

159686

NM_001008723.1

Coiled-coil domain-containing protein 147. Function unknown.

MISSENSE

RBM20 XM_291671.8 2586551 snp G C W S 10 112562447 767

RBM20 rs942077 XM_291671.8 2586607 snp G C E Q 10 112585708 1222

PDCD4 27250 NM_145341.2 2586662 snp A G I V 10 112631042 24

GPAM 57678 NM_020918.3 2588352 snp T C E G 10 113925368 130

GUCY2G 2588554 snp A C V G 10 114062080 261

NRAP 4892 NM_198060.2 2589831 snp G A S L 10 115383918 489

NRAP 4892 NM_198060.2 2589877 snp T C Q R 10 115395604 359

dbsnp.88:rs1417635

rs1417635

282996

Probable RNA-binding protein 20. Expressed in heart, function unknown.

MISSENSE

dbsnp.86:rs942077

282996

Probable RNA-binding protein 20. Expressed in heart, function unknown.

MISSENSE

dbsnp.116:rs7081726

rs7081726

Programmed cell death protein 4. Inhibits translation initiation and cap-dependent translation. May excert its function by hindering the interaction between EIF4A1 and EIF4G. Inhibits the helicase activity of EIF4A. Modulates the activation of JUN kinase. Down-regulates the expression of MAP4K1, thus inhibiting events important in driving invasion, namely, MAPK85 activation and consequent JUN-dependent transcription. May play a role in apoptosis. Tumor suppressor. Inhibits tumor promoter-induced neoplastic transformation.

MISSENSE

dbsnp.120:rs10787428

rs10787428

Glycerol-3-phosphate acyltransferase 1, mitochondrial. Involved in glycerolipid biosynthesis.

MISSENSE

dbsnp.120:rs10885329

rs10885329

390003

XM_001718434.1

Real name: GUCY2GP. Not in uniprot, only in NCBI. Guanylate cyclase 2G homolog (mouse or rat), pseudogene

MISSENSE

dbsnp.105:rs3189030

rs3189030

Nebulin-related-anchoring protein. May be involved in anchoring the terminal actin filaments in the myofibril to the membrane and in transmitting tension from the myofibrils to the extracellular matrix.

MISSENSE

dbsnp.103:rs3127106

rs3127106


MISSENSE

NRAP 4892 NM_198060.2 2589878 snp C T A T 10 115395653 343

NRAP 4892 NM_198060.2 2589899 snp T C Y C 10 115400223 248

NRAP 4892 NM_198060.2 2589902 snp A G V A 10 115401603 207

CASP7 840 NM_033340.2 2590009 snp C G T S 10 115479141 243

CASP7 840 NM_033340.2 2590010 snp G A R K 10 115479156 248

TRUB1 NM_139169.4 2591062 snp A C E A 10 116692414 102

TRUB1 NM_139169.4 2591085 snp G A R K 10 116709532 166

ATRNL1 26033 NM_207303.2 2591444 snp G A S N 10 117065164 988

dbsnp.103:rs3121478

rs3121478


MISSENSE

dbsnp.96:rs2185913

rs2185913


MISSENSE

dbsnp.96:rs2154028

rs2154028


MISSENSE

dbsnp.98:rs2227310

rs2227310

Involved in the activation cascade of caspases responsible for apoptosis execution. Overexpression promotes programmed cell death.

MISSENSE

dbsnp.98:rs2227309

rs2227309

Involved in the activation cascade of caspases responsible for apoptosis execution. Overexpression promotes programmed cell death.

MISSENSE

dbsnp.126:rs34393297

rs34393297

142940

Probable tRNA pseudouridine synthase 1. May be responsible for synthesis of pseudouridine from uracil in transfer RNAs

MISSENSE

dbsnp.116:rs7099565

rs7099565

142940

Probable tRNA pseudouridine synthase 1. May be responsible for synthesis of pseudouridine from uracil in transfer RNAs

MISSENSE

dbsnp.92:rs1953758

rs1953758

Attractin-like protein 1. May play a role in melanocortin signaling pathways that regulate energy homeostasis

MISSENSE

INPP5F 22876 NM_014937.2 2597693 snp A G N D 10 121576871 996

TACC2 10579 NM_206862.2 2601553 snp T C W R 10 123835311 1102

TACC2 10579 NM_206862.2 2601554 snp C T P L 10 123836479 1491

TACC2 10579 NM_206862.2 2601818 snp G A A T 10 123986965 2731

BTBD16 NM_144587.2 2602000 snp G A R Q 10 124079025 317

dbsnp.105:rs3188055

rs3188055

Inositol polyphosphate 5-phosphatase OCRL-1. Converts phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 4-phosphate. May function in lysosomal trafficking.

MISSENSE

dbsnp.116:rs7073433

rs7073433

Transforming acidic coiled-coil-containing protein 2. Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors By similarity. May play a role in organizing centrosomal microtubules. May act as a tumor suppressor protein. May represent a tumor progression marker.

MISSENSE

dbsnp.116:rs7920896

rs7920896


MISSENSE

dbsnp.100:rs2295879

rs2295879


MISSENSE

dbsnp.100:rs2421013

rs2421013

118663

BTB/POZ domain-containing protein 16. Function unknown.

MISSENSE

BTBD16 rs986178 NM_144587.2 2602001 snp G A G D 10 124079064 330

DOCK1 rs869801 1793 NM_001380.3 2610348 snp G A A T 10 129135673 1792

MGMT rs12917 4255 NM_002412.2 2614161 snp C T L F 10 131396272 83

GLRX3 10539 NM_006541.3 2614676 snp C T P S 10 131849139 122

KNDC1 85442 NM_152643.6 2619745 snp A G E G 10 134850148 435

ADAM8 101 NM_001109.3 2619942 snp A G F L 10 134932335 656

MTG1 92170 NM_138384.2 2620189 snp A G I V 10 135083530 292

2621226 snp A G C R 11 418384 398

2621227 snp T C I V 11 418488 390

EFCAB4A NM_173584.3 2621905 snp G A R Q 11 818915 76

EFCAB4A NM_173584.3 2621906 snp A G K E 11 819538 152

OR52I1 2629874 snp C T T I Olfactory receptor 52I1 11 4571965 40

dbsnp.86:rs986178

118663

BTB/POZ domain-containing protein 16. Function unknown.

MISSENSE

dbsnp.86:rs869801

Downstream of CRK 180kb protein. Involved in cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility.

MISSENSE

dbsnp.52:rs12917

Methylated-DNA-protein-cysteine methyltransferase. Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) in DNA.

MISSENSE

dbsnp.100:rs2274217

rs2274217

Glutaredoxin-3. Does not posses any thioredoxin activity since it lacks the conserved motif that is essential for catalytic activity. Critical negative regulator of cardiac hypertrophy and a positive inotropic regulator.

MISSENSE

dbsnp.107:rs3810964

rs3810964

Protein very KIND. Probable guanine nucleotide exchange factor (GEF). Function unknown.

MISSENSE

dbsnp.100:rs2275720

rs2275720

Disintegrin and metalloproteinase domain-containing protein 8. Possible involvement in extravasation of leukocytes.

MISSENSE

dbsnp.100:rs2255246

rs2255246

Mitochondrial GTPase 1. May be involved in assembly of the large ribosomal subunit.

MISSENSE

TMEM16J

dbsnp.120:rs10794323

rs10794323

338440

NM_001012302.2

Anoctamin-9. May act as a calcium-activated chloride channel. Is induced by p53.

MISSENSE

TMEM16J

dbsnp.120:rs10794324

rs10794324

338440

NM_001012302.2

Anoctamin-9. May act as a calcium-activated chloride channel. Is induced by p53.

MISSENSE

dbsnp.116:rs7126805

rs7126805

283229

EF-hand calcium-binding domain-containing protein 4A. Plays a role in store-operated Ca2+ entry.

MISSENSE

dbsnp.125:rs28558789

rs28558789

283229

EF-hand calcium-binding domain-containing protein 4A. Plays a role in store-operated Ca2+ entry.

MISSENSE

dbsnp.92:rs2010722

rs2010722

390037

NM_001005169.1

MISSENSE

OR52A4 2631238 snp A G C R Olfactory receptor 52A4 11 5098555 276

OR52A4 2631241 snp T C D G Olfactory receptor 52A4 11 5099124 86

OR52A1 23538 NM_012375.2 2631281 snp A G S P Olfactory receptor 52A1 11 5129361 271

OR51B2 79345 NM_033180.4 2631864 snp C G C S Olfactory receptor 51B2 11 5301477 208

OR51B2 79345 NM_033180.4 2631866 snp A G C R Olfactory receptor 51B2 11 5301745 119

OR51B6 2631971 snp G A S N Olfactory receptor 52I1 11 5329689 125

UBQLNL rs393044 NM_145053.4 2632712 snp A C W G 11 5493112 378

UBQLNL NM_145053.4 2632713 snp G A A V 11 5493423 274

OR52H1 2632831 snp A G C R Olfactory receptor 52H1 11 5522605 241

OR52H1 2632834 snp T C H R Olfactory receptor 52H1 11 5522940 129

OR52B6 2632998 snp A G T A Olfactory receptor 52B6 11 5558850 56

OR52B6 2632999 snp T A L H Olfactory receptor 52B6 11 5559013 110

OR52B6 2633000 snp G A A T Olfactory receptor 52B6 11 5559180 166

OR52B6 2633001 snp A G H R Olfactory receptor 52B6 11 5559190 169

OR52B6 2633005 snp G A V I Olfactory receptor 52B6 11 5559543 287

dbsnp.111:rs4426129

rs4426129

390053

NM_001005222.1

MISSENSE

dbsnp.116:rs7947334

rs7947334

390053

NM_001005222.1

MISSENSE

dbsnp.120:rs10768611

rs10768611

MISSENSE

dbsnp.116:rs7937237

rs7937237

MISSENSE

dbsnp.116:rs7952293

rs7952293

MISSENSE

dbsnp.113:rs5006888

rs5006888

390058

NM_001004750.1

MISSENSE

dbsnp.80:rs393044

143630

Ubiquitin-like protein. Function unknown.

MISSENSE

dbsnp.92:rs2017433

rs2017433

143630

Ubiquitin-like protein. Function unknown.

MISSENSE

dbsnp.92:rs1995158

rs1995158

390067

NM_001005289.1

MISSENSE

dbsnp.88:rs1566275

rs1566275

390067

NM_001005289.1

MISSENSE

dbsnp.86:rs1077126

rs1077126

340980

NM_001005162.2

MISSENSE

dbsnp.100:rs2341432

rs2341432

340980

NM_001005162.2

MISSENSE

dbsnp.100:rs2341433

rs2341433

340980

NM_001005162.2

MISSENSE

dbsnp.100:rs2341434

rs2341434

340980

NM_001005162.2

MISSENSE

dbsnp.120:rs10769086

rs10769086

340980

NM_001005162.2

MISSENSE

OR56B1 2633488 snp T C C R Olfactory receptor 56B1 11 5714637 105

OR52E4 2634116 snp G A V I Olfactory receptor 52E4 11 5862623 175

OR52E4 2634117 snp G T R M Olfactory receptor 52E4 11 5862648 183

OR56A4 2634412 snp T C I V Olfactory receptor 56A4 11 5980215 246

OR52W1 2634974 snp A G H R Olfactory receptor 52W1 11 6177744 238

C11orf56 84067 NM_032127.3 2634987 snp G A T M 11 6195919 504

SMPD1 6609 NM_000543.3 2635273 snp G A G R 11 6372038 507

OR2D2 NM_003700.1 2636292 snp A G I T Olfactory receptor 2D2. 11 6869819 162

ZNF214 7761 NM_013249.2 2636524 snp A G C R 11 6978735 251

NLRP14 NM_176822.3 2636620 snp A C N T 11 7016535 47

NLRP14 NM_176822.3 2636668 snp G A E K 11 7035613 807

CYB5R2 51700 NM_016229.3 2637870 snp T C N D 11 7644290 208

dbsnp.116:rs7397032

rs7397032

387748

NM_001005180.1

MISSENSE

dbsnp.111:rs4758168

rs4758168

390081

NM_001005165.1

MISSENSE

dbsnp.111:rs4757986

rs4757986

390081

NM_001005165.1

MISSENSE

dbsnp.120:rs11040249

rs11040249

120793

NM_001005179.2

MISSENSE

dbsnp.120:rs10839531

rs10839531

120787

NM_001005178.1

MISSENSE

dbsnp.107:rs3750944

rs3750944

FTS and Hook-interacting protein. Component of the FTS/Hook/FHIP complex, which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting complex (the HOPS complex).

MISSENSE

dbsnp.86:rs1050239

rs1050239

Sphingomyelin phosphodiesterase. Converts sphingomyelin to ceramide.

MISSENSE

dbsnp.92:rs1965208

rs1965208

120776

MISSENSE

dbsnp.100:rs2857919

rs2857919

Zinc finger protein 214. ZNF with unknown function.

MISSENSE

dbsnp.121:rs12801277

rs12801277

338323

NACHT, LRR and PYD domains-containing protein 14. May be involved in inflammation and spermatogenesis.

MISSENSE

dbsnp.120:rs10839708

rs10839708

338323

NACHT, LRR and PYD domains-containing protein 14. May be involved in inflammation and spermatogenesis.

MISSENSE

dbsnp.121:rs12801394

rs12801394

NADH-cytochrome b5 reductase 2, involved in desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.

MISSENSE

OVCH2 NM_198185.2 2637981 snp T A N Y 11 7673430 409

OVCH2 NM_198185.2 2637992 snp G A P S 11 7678445 291

OVCH2 NM_198185.2 2638002 snp C T R Q 11 7684461 18

OR10A6 2638523 snp A G L P Olfactory receptor 10A1 11 7905925 286

C11orf16 56673 NM_020643.2 2640431 snp A G L P 11 8903596 397

SWAP70 rs415895 23075 NM_015055.2 2642195 snp C G Q E 11 9726137 504

MICALCL 84953 NM_032867.2 2646883 snp G A A T 11 12272466 304

KCNJ11 rs5219 3767 NM_000525.3 2654672 snp T C K E 11 17366147 22

ABCC8 rs757110 6833 NM_000352.3 2654691 snp C A A S 11 17375052 1368

HTATIP2 10553 NM_006410.4 2660580 snp T G S R 11 20361188 196

dbsnp.111:rs4528317

rs4528317

341277

Ovochymase-2, function unknown, some proteolysis activity.

MISSENSE

dbsnp.120:rs10839849

rs10839849

341277


MISSENSE

dbsnp.116:rs7927138

rs7927138

341277


MISSENSE

dbsnp.111:rs4758258

rs4758258

390093

NM_001004461.1

MISSENSE

dbsnp.100:rs2653588

rs2653588


MISSENSE

dbsnp.80:rs415895

Switch-associated protein 70. Phosphatidylinositol 3,4,5-trisphosphate-dependent guanine nucleotide exchange factor (GEF), Regulates the actin cytoskeleton as an effector or adapter protein.

MISSENSE

dbsnp.88:rs1493953

rs1493953

MICAL C-terminal-like protein. Involved in spermatid differentiation.

MISSENSE

dbsnp.52:rs5219

ATP-sensitive inward rectifier potassium channel 11

MISSENSE

dbsnp.86:rs757110

ATP-binding cassette sub-family C member 8. Putative subunit of the beta-cell ATP-sensitive potassium channel (KATP). Regulator of ATP-sensitive K+ channels and insulin release.

MISSENSE

dbsnp.107:rs3824886

rs3824886

Oxidoreductase HIV-Tat interactiong protein 2. Oxidoreductase required for tumor suppression. 242 aa isoform is a metastasis suppressor with proapoptotic as well as antiangiogenic properties. 133 aa isoform has an antiapoptotic effect.

MISSENSE

SLC6A5 9152 NM_004211.3 2661084 snp C G A G 11 20579731 161

NM_213599.1 2664315 snp A T L F 11 22228445 321

QSER1 79832 2682159 snp G A V I 11 32910919 384

QSER1 79832 2682161 snp A G N S 11 32912819 1017

CD44 960 2686166 snp A G K R 11 35182730 373

CD44 960 2686172 snp T C I T 11 35186248 435

ALX4 60529 NM_021926.2 2701428 snp C G R T 11 44288084 34

LRP4 4038 NM_002334.2 2704817 snp C T R Q 11 46846740 1645

dbsnp.88:rs1443549

rs1443549

Sodium- and chloride-dependent glycine transporter 2. May be responsible for the termination of neurotransmission at strychnine-sensitive glycinergic synapses.

MISSENSE

TMEM16E

dbsnp.116:rs7481951

rs7481951

203859

Anoctamin-5. May act as a calcium-activated chloride channel.

MISSENSE

dbsnp.86:rs1022586

rs1022586

NM_001076786.1

Glutamine and serine-rich protein 1. Function unknown.

MISSENSE

dbsnp.116:rs7940077

rs7940077

NM_001076786.1

Glutamine and serine-rich protein 1. Function unknown.

MISSENSE

dbsnp.119:rs9666607

rs9666607

NM_001001389.1

CD44 antigen. Hyaluronate receptor. Adhesion with HA plays an important role in cell migration, tumor growth and progression. Also involved in lymphocyte activation, recirculation and homing, and in hematopoiesis. Altered expression or dysfunction causes numerous pathogenic phenotypes.

MISSENSE

dbsnp.88:rs1467558

rs1467558

NM_001001389.1

CD44 antigen. Hyaluronate receptor. Adhesion with HA plays an important role in cell migration, tumor growth and progression. Also involved in lymphocyte activation, recirculation and homing, and in hematopoiesis. Altered expression or dysfunction causes numerous pathogenic phenotypes.

MISSENSE

dbsnp.107:rs3824915

rs3824915

Homeobox protein aristaless-like 4, Transcription factor involved in skull and limb development

MISSENSE

dbsnp.107:rs3816614

rs3816614

Low-density lipoprotein receptor-related protein 4. Potential cell surface endocytic receptor, which binds and internalizes extracellular ligands for degradation by lysosomes.

MISSENSE

LRP4 4038 NM_002334.2 2704819 snp T C S G 11 46849683 1553

LRP4 4038 NM_002334.2 2704829 snp T C I V 11 46855346 1085

NUP160 23279 NM_015231.1 2706172 snp T C T A 11 47813828 350

OR4X1 2706863 snp A G R G Olfactory receptor 4X1 11 48242417 143

OR5D13 rs297118 2718351 snp G A C Y Olfactory receptor 5D13 11 55297673 61

OR5T2 2720559 snp C G V L Olfactory receptor 5T2 11 55756978 86

OR5T2 2720561 snp G A T I Olfactory receptor 5T2 11 55757046 63

OR8K1 - 2720865 snp T C M T 11 55870091 0

OR9G4 rs577576 2721919 snp T C N D Olfactory receptor 9G4 11 56267247 205

OR5AK2 2722453 snp G A M I Olfactory receptor 5AK2 11 56513239 91

OR10Q1 2724134 snp C G E D Olfactory receptor 10Q1 11 57752887 11

OR5B3 2724301 snp C G G A Olfactory receptor 5B3 11 57926718 246

OR5B3 2724302 snp T C I V Olfactory receptor 5B3 11 57926866 197

dbsnp.100:rs2306029

rs2306029


MISSENSE

dbsnp.116:rs6485702

rs6485702


MISSENSE

dbsnp.107:rs3816605

rs3816605

Nuclear pore complex protein Nup160. Involved in mRNA nuclear export.

MISSENSE

dbsnp.88:rs1503193

rs1503193

390113

NM_001004726.1

MISSENSE

dbsnp.79:rs297118

390142

NM_001001967.1

MISSENSE

dbsnp.120:rs10791893

rs10791893

219464

NM_001004746.1

MISSENSE

dbsnp.120:rs11227599

rs11227599

219464

NM_001004746.1

MISSENSE

dbsnp.92:rs1905055

rs1905055

390157

NM_001002907.1

Olfactory receptor 8K1. First 20 amino acids are lost till next start codon.

MISSTART

dbsnp.83:rs577576

283189

NM_001005284.1

MISSENSE

dbsnp.100:rs2853083

rs2853083

390181

NM_001005323.1

MISSENSE

dbsnp.111:rs4245219

rs4245219

219960

NM_001004471.1

MISSENSE

dbsnp.120:rs11229409

rs11229409

441608

NM_001005469.1

MISSENSE

dbsnp.120:rs11229410

rs11229410

441608

NM_001005469.1

MISSENSE

OR5B3 2724306 snp A G W R Olfactory receptor 5B3 11 57927313 48

OR5B2 2724417 snp A G V A Olfactory receptor 5B2 11 57946687 207

OR5B2 2724418 snp A G M T Olfactory receptor 5B2 11 57946711 199

ZFP91 rs8373 80829 NM_053023.3 2724645 snp A G S G 11 58134999 206

GLYAT rs675815 10249 NM_201648.2 2724886 snp T C N S 11 58234659 155

OR10V1 rs499033 2726428 snp T C Q R Olfactory receptor 10V1 11 59237526 122

84689 2727373 snp A T N Y 11 59939545 159

84689 2727374 snp G A G R 11 59940766 566

MS4A13 2727630 snp A G I V 11 60042150 6

DAK 26007 NM_015533.3 2728730 snp G A A T 11 60865549 184

NA 2731399 snp T C I V 11 62604028 538

dbsnp.120:rs11229413

rs11229413

441608

NM_001005469.1

MISSENSE

dbsnp.119:rs10466659

rs10466659

390190

NM_001005566.1

MISSENSE

dbsnp.111:rs4298923

rs4298923

390190

NM_001005566.1

MISSENSE

dbsnp.52:rs8373

E3 ubiquitin-protein ligase ZFP91. typical E3 ubiquitin-protein ligase that mediates 'Lys-63'-linked ubiquitination of MAP3K14/NIK. May also play an important role in cell proliferation and/or anti-apoptosis.

MISSENSE

dbsnp.83:rs675815

Glycine N-acyltransferase. Mitochondrial acyltransferase which transfers the acyl group to the N-terminus of glycine.

MISSENSE

dbsnp.83:rs499033

390201

NM_001005324.1

MISSENSE

NYD-SP21

dbsnp.116:rs7131283

rs7131283

NM_001079692.1

Membrane-spanning 4-domains subfamily A member 14. Involved in signal transduction?

MISSENSE

NYD-SP21

dbsnp.107:rs3825020

rs3825020

NM_001079692.1


MISSENSE

dbsnp.120:rs10736706

rs10736706

503497

NM_001100909.1


MISSENSE

dbsnp.100:rs2260655

rs2260655

Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing). Catalyzes both the phosphorylation of dihydroxyacetone and the splitting of ribonucleoside diphosphate-X compounds among which FAD is the best substrate. Involved in innate immune system?

MISSENSE

MGC34821

dbsnp.116:rs7945121

rs7945121

283238

XM_001720420.1

Not annotated, putative uncharacterized protein.

MISSENSE

NA 2731403 snp A C Y * 11 62605062 500

NM_199352.3 2731670 snp T C M V 11 62688059 485

NM_199352.3 2731706 snp C G R T 11 62707796 299

NM_199352.3 2731769 snp T C S G 11 62741443 249

2734050 snp G T R L 11 64760876 449

rs624307 NM_182556.2 2734120 snp T C M V 11 64900650 223

EHBP1L1 2734293 snp A T D V 11 65106424 568

CD248 57124 NM_020404.2 2735441 snp T C H R 11 65839704 456

ACY3 rs948445 91703 NM_080658.1 2736797 snp C T R Q 11 67171067 7

222 NM_000695.3 2736858 snp T C H R 11 67187337 360

TPCN2 NM_139075.3 2739488 snp T C L P 11 68607989 563

55191 NM_018161.4 2743402 snp G C V L 11 70847194 73

MGC34821

dbsnp.120:rs11231341

rs11231341

283238

XM_001720420.1

Not annotated, putative uncharacterized protein.

NONSENSE

SLC22A25

dbsnp.116:rs6591771

rs6591771

387601

Solute carrier family 22 member 25, for organic anions. Further specificity unknown.

MISSENSE

SLC22A25

dbsnp.120:rs11231397

rs11231397

387601


MISSENSE

SLC22A25

dbsnp.120:rs11231409

rs11231409

387601


MISSENSE

SLC22A20

dbsnp.101:rs2904982

rs2904982

440044

NM_001004326.2

Solute carrier family 22 member 20, for estrone sulfate.

MISSENSE

SLC25A45

dbsnp.83:rs624307

283130

Solute carrier family 25 member 45, specificity unknown.

MISSENSE

dbsnp.87:rs1194099

rs1194099

254102

NM_001099409.1

EH domain-binding protein 1-like protein 1. Function unknown.

MISSENSE

dbsnp.107:rs3741367

rs3741367

Endosialin, tumor endothelial marker. May play a role in tumor angiogenesis.

MISSENSE

dbsnp.86:rs948445

Aspartoacylase-2. Plays an important role in deacetylating mercapturic acids in kidney proximal tubules

MISSENSE

ALDH3B2

dbsnp.88:rs1551886

rs1551886

Aldehyde dehydrogenase family 3 member B2. Function in alchohol metabolism.

MISSENSE

dbsnp.100:rs2376558

rs2376558

219931

Voltage-dependent calcium channel protein TPC2. Nicotinic acid adenine dinucleotide phosphate (NAADP) receptor that may function as one of the major voltage-gated Ca2+ channels (VDCC) across the lysosomal membrane. May be involved in smooth muscle contraction.

MISSENSE

NADSYN1

dbsnp.100:rs2276360

rs2276360

Glutamine-dependent NAD(+) synthetase. NAD+ biosynthesis.

MISSENSE

55191 NM_018161.4 2743432 snp A C Q H 11 70862325 203

DNAJB13 NM_153614.2 2747123 snp G A M I 11 73358782 308

UCP2 rs660339 7351 NM_003355.2 2747135 snp G A A V 11 73366751 54

C2CD3 rs826058 26005 NM_015531.4 2747253 snp C T R Q 11 73474564 1218

TSKU 25987 NM_015516.3 2750313 snp T A D E 11 76185339 343

USP35 57558 NM_020798.1 2752296 snp G C A P 11 77599174 875

rs494791 60492 NM_021825.3 2760240 snp A C F L 11 82674633 9

SYTL2 rs641393 54843 NM_206927.1 2763295 snp G A T M 11 85113999 382

NADSYN1

dbsnp.116:rs7950441

rs7950441

Glutamine-dependent NAD(+) synthetase. NAD+ biosynthesis.

MISSENSE

dbsnp.130:rs72982975

rs72982975

374407

DnaJ homolog subfamily B member 13. May be involved in inhibiting testis spermatogenesis apoptosis.

MISSENSE

dbsnp.83:rs660339

Mitochondrial uncoupling protein 2. By uncoupling OxPhos from ATP synthesis, energy is dissipated as heat.

MISSENSE

dbsnp.86:rs826058

C2 domain-containing protein 3. Function unknown.

MISSENSE

dbsnp.87:rs1149621

rs1149621

Tsukushin. Secreted upon estrogen induction. Function unknown.

MISSENSE

dbsnp.100:rs2512526

rs2512526

Ubiquitin carboxyl-terminal hydrolase 35. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin. Further details unknown.

MISSENSE

CCDC90B

dbsnp.83:rs494791

Coiled-coil domain-containing protein 90B, mitochondrial. Function unknown.

MISSENSE

dbsnp.83:rs641393

Synaptotagmin-like protein 2. Isoform 1 acts as a RAB27A effector protein and plays a role in cytotoxic granule exocytosis in lymphocytes. It is required for cytotoxic granule docking at the immunologic synapse. Isoform 4 binds phosphatidylserine (PS) and phosphatidylinositol-4,5-bisphosphate (PIP2) and promotes the recruitment of glucagon-containing granules to the cell membrane in pancreatic alpha cells. Binding to PS is inhibited by Ca2+ while binding to PIP2 is Ca2+ insensitive.

MISSENSE

SYTL2 rs556669 54843 NM_206927.1 2763296 snp T C D G 11 85114041 368

SYTL2 rs597480 54843 NM_206927.1 2763299 snp G C A G 11 85114515 210

FAT3 2774846 snp A G I V 11 92174089 2754

HEPHL1 2777008 snp A G N D 11 93437266 250

- 57562 NM_020802.2 2790229 snp G A S N Uncharacterized protein. 11 101362967 1076

dbsnp.83:rs556669


MISSENSE

dbsnp.83:rs597480


MISSENSE

dbsnp.108:rs3847531

rs3847531

120114

NM_001008781.2

Protocadherin Fat 3. May play a role in the interactions between neurites derived from specific subsets of neurons during development

MISSENSE

dbsnp.92:rs1945783

rs1945783

341208

NM_001098672.1

Hephaestin-like protein 1. May function as a ferroxidase and may be involved in copper transport and homeostasis

MISSENSE

KIAA1377

dbsnp.116:rs6590942

rs6590942

MISSENSE

MMP20 9313 NM_004771.3 2791021 snp T G K T 11 102001207 17

MMP27 64066 NM_022122.2 2791240 snp G A T M 11 102081584 23

NPAT 4863 NM_002519.2 2800763 snp C T V I 11 107549197 574

C11orf52 91894 NM_080659.2 2806812 snp C G T R 11 111300294 22

DLAT 1737 NM_001931.2 2806888 snp C T A V 11 111401533 42

DLAT 1737 NM_001931.2 2806920 snp G A D N 11 111421856 450

BCDO2 83875 NM_031938.4 2807117 snp T C L P 11 111570643 230

BCDO2 83875 NM_031938.4 2807162 snp A C I L 11 111593708 547

80975 NM_030770.1 2809737 snp C T R Q 11 113075594 45

dbsnp.100:rs2245803

rs2245803

Matrix metalloproteinase-20. Degrades amelogenin, the major protein component of the enamel matrix and two of the macromolecules characterizing the cartilage extracellular matrix: aggrecan and the cartilage oligomeric matrix protein (COMP). May play a central role in tooth enamel formation.

MISSENSE

dbsnp.92:rs1939015

rs1939015

Matrix metalloproteinase-27. Specific target unknown.

MISSENSE

dbsnp.96:rs2070661

rs2070661

Nuclear protein of the ataxia telangiectasia mutated locus. Required for progression through the G1 and S phases of the cell cycle and for S phase entry.

MISSENSE

dbsnp.116:rs7124407

rs7124407


MISSENSE

dbsnp.100:rs2303436

rs2303436

Pyruvate dehydrogenase complex component E2 (dihydrolipoamide acetyltransferase, E2).

MISSENSE

dbsnp.120:rs10891314

rs10891314

Pyruvate dehydrogenase complex component E2 (dihydrolipoamide acetyltransferase, E2).

MISSENSE

dbsnp.120:rs10891338

rs10891338

Beta-carotene dioxygenase 2. The apocarotenals formed by this enzyme may be the precursors for the biosynthesis of retinoic acid or exert unknown physiological effects.

MISSENSE

dbsnp.96:rs2217401

rs2217401

Beta-carotene dioxygenase 2. The apocarotenals formed by this enzyme may be the precursors for the biosynthesis of retinoic acid or exert unknown physiological effects.

MISSENSE

TMPRSS5

dbsnp.120:rs11601425

rs11601425

Transmembrane protease serine 5. May play a role in hearing

MISSENSE

CEP164 rs573455 22897 NM_014956.4 2815492 snp A G Q R 11 116773093 1118

AMICA1 NM_153206.2 2816934 snp A G V A 11 117579546 182

AMICA1 NM_153206.2 2816951 snp A T I N 11 117586554 83

OAF NM_178507.2 2820504 snp A G H R 11 119604867 209

OAF NM_178507.2 2820505 snp G A R H 11 119604888 216

POU2F3 25833 NM_014352.2 2820612 snp A G H R 11 119680958 151

TECTA rs526433 7007 NM_005422.2 2821628 snp G A S N 11 120538187 1723

2825569 snp T C N S 11 123260053 133

OR8D4 2825628 snp G A R K Olfactory receptor 8D4 11 123283240 297

dbsnp.83:rs573455

Centrosomal protein of 164 kDa. Plays a critical role in G2/M checkpoint and nuclear divisions. A key player in the DNA damage-activated ATR/ATM signaling cascade since it is required for the proper phosphorylation of H2AX, RPA, CHEK2 and CHEK1. Plays a critical role in chromosome segregation, acting as a mediator required for the maintenance of genomic stability through modulation of MDC1, RPA and CHEK1.

MISSENSE

dbsnp.89:rs1793174

rs1793174

120425

Junctional adhesion molecule-like. May function in transmigration of leukocytes through epithelial and endothelial tissues.

MISSENSE

dbsnp.123:rs17121881

rs17121881

120425

Junctional adhesion molecule-like. May function in transmigration of leukocytes through epithelial and endothelial tissues.

MISSENSE

dbsnp.100:rs2508489

rs2508489

220323

Out at first protein homolog. Function unknown.

MISSENSE

dbsnp.100:rs2508490

rs2508490

220323

Out at first protein homolog. Function unknown.

MISSENSE

dbsnp.116:rs7110845

rs7110845

POU domain, class 2, transcription factor 3. Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3'). Regulated the expression of a number of genes such as SPRR2A or placental lactogen.

MISSENSE

dbsnp.83:rs526433

Alpha-tectorin. One of the major non-collagenous components of the tectorial membrane (inner ear).

MISSENSE

PMP22CD

dbsnp.120:rs10893099

rs10893099

338661

NM_001013743.1

Transmembrane protein 225. Function unknown.

MISSENSE

dbsnp.116:rs7927385

rs7927385

338662

NM_001005197.1

MISSENSE

KCNJ5 3762 NM_000890.3 2833858 snp C G Q E 11 128287221 281

11095 NM_007037.4 2835910 snp G A A V 11 129786697 524

SNX19 NM_014758.2 2836856 snp T C N S 11 130281733 752

SNX19 NM_014758.2 2836872 snp C G V L 11 130289963 360

GLB1L3 2842251 snp G A V M 11 133687584 514

CCDC77 rs735295 84318 NM_032358.2 2844247 snp T C M T 12 417943 334

WNK1 rs956868 65125 NM_018979.2 2845246 snp A C T P 12 861172 1055

WNK1 65125 NM_018979.2 2845263 snp G T M I 12 868625 1807

dbsnp.116:rs7102584

rs7102584

G protein-activated inward rectifier potassium channel 4. Somatic mutations in KCNJ5 have been found in aldosterone-producing adrenal adenomas and can be responsible for aldosteronism associated with cell autonomous proliferation. These are typically solitary, well circumscribed tumors diagnosed between ages 30 and 70.

MISSENSE

ADAMTS8

dbsnp.96:rs2131535

rs2131535

A disintegrin and metalloproteinase with thrombospondin motifs 8. Has anti-angiogenic properties.

MISSENSE

dbsnp.111:rs4414223

rs4414223

399979

Sorting nexin-19. Involved in intracellular trafficking.

MISSENSE

dbsnp.107:rs3751037

rs3751037

399979

Sorting nexin-19. Involved in intracellular trafficking.

MISSENSE

dbsnp.100:rs2509062

rs2509062

112937

NM_001080407.1

Beta-galactosidase-1-like protein 3. Glycosyl hydrolase with unknown function.

MISSENSE

dbsnp.86:rs735295

Coiled-coil domain-containing protein 77. Unknown function.

MISSENSE

dbsnp.86:rs956868

Serine/threonine-protein kinase WNK1, plays an important role in the regulation of electrolyte homeostasis, cell signaling, survival, and proliferation, as an activator and inhibitor of sodium-coupled chloride cotransporters and potassium-coupled chloride cotransporters respectively.

MISSENSE

dbsnp.121:rs12828016

rs12828016

Serine/threonine-protein kinase WNK1, plays an important role in the regulation of electrolyte homeostasis, cell signaling, survival, and proliferation, as an activator and inhibitor of sodium-coupled chloride cotransporters and potassium-coupled chloride cotransporters respectively.

MISSENSE

AKAP3 10566 NM_006422.2 2851544 snp C T E K 12 4606755 524

AKAP3 10566 NM_006422.2 2851546 snp G C T S 12 4606937 463

AKAP3 10566 NM_006422.2 2851551 snp C T G E 12 4607975 117

GALNT8 26290 NM_017417.1 2851715 snp T G Y D 12 4700260 52

VWF rs216311 7450 NM_000552.3 2854147 snp T C T A 12 5998703 1380

VWF 7450 NM_000552.3 2854227 snp T C H R 12 6042462 483

SCNN1A 6337 NM_001038.4 2854835 snp T C T A 12 6327322 662

TAPBPL 55080 NM_018009.4 2855034 snp A G M V 12 6433013 145

TAPBPL 55080 NM_018009.4 2855035 snp A G T A 12 6433070 164

dbsnp.92:rs1990312

rs1990312

A-kinase anchor protein 3. May function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction.

MISSENSE

dbsnp.120:rs11063266

rs11063266


MISSENSE

dbsnp.96:rs2072355

rs2072355


MISSENSE

dbsnp.120:rs10849133

rs10849133

Probable polypeptide N-acetylgalactosaminyltransferase 8. Probably catalyzes the initial reaction in O-linked oligosaccharide biosynthesis.

MISSENSE

dbsnp.79:rs216311

von Willebrand factor. Important in the maintenance of hemostasis, it promotes adhesion of platelets to the sites of vascular injury by forming a molecular bridge between sub-endothelial collagen matrix and platelet-surface receptor complex GPIb-IX-V.

MISSENSE

dbsnp.89:rs1800378

rs1800378

von Willebrand factor. Important in the maintenance of hemostasis, it promotes adhesion of platelets to the sites of vascular injury by forming a molecular bridge between sub-endothelial collagen matrix and platelet-surface receptor complex GPIb-IX-V.

MISSENSE

dbsnp.98:rs2228576

rs2228576

Amiloride-sensitive sodium channel subunit alpha. Controls the reabsorption of sodium in kidney, colon, lung and sweat glands.

MISSENSE

dbsnp.100:rs2532501

rs2532501

Tapasin-related protein, involved in immune system/antigen processing.

MISSENSE

dbsnp.100:rs2532500

rs2532500

Tapasin-related protein, involved in immune system/antigen processing.

MISSENSE

LEPREL2 10536 NM_014262.3 2855679 snp A G T A 12 6810110 300

A2ML1 NM_144670.3 2859367 snp A G M V 12 8911755 1256

PHC1 1911 NM_004426.2 2859508 snp A G T A 12 8978164 692

PZP 5858 NM_002864.1 2859804 snp T G T P 12 9198639 1204

CLEC1B rs583903 51266 NM_016509.3 2861884 snp C T G D 12 10041117 63

TAS2R10 rs597468 50839 NM_023921.1 2863847 snp G A T M 12 10869668 155

PRR4 2/2 11272 NM_007244.2 2863879 snp T C Q R 12 10890974 119

LRMP 1/1 4033 NM_006152.2 2889827 snp C G L V 12 25133861 140

OVCH1 1/1 NM_183378.2 2898477 snp G A T I 12 29521347 443

dbsnp.120:rs10744716

rs10744716

Prolyl 3-hydroxylase activity catalyzing the post-translational formation of 3-hydroxyproline in -Xaa-Pro-Gly-sequences in collagens, especially types IV and V

MISSENSE

dbsnp.116:rs7308811

rs7308811

144568

Alpha-2-macroglobulin-like protein 1. Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism.

MISSENSE

dbsnp.86:rs1049925

rs1049925

Early development regulatory protein 1. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development.

MISSENSE

dbsnp.100:rs2377741

rs2377741

Pregnancy zone protein. Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism.

MISSENSE

dbsnp.83:rs583903

C-type lectin domain family 1 member B. Acts as an attachment factor for human immunodeficiency virus type 1 (HIV-1) and facilitates its capture by platelets.

MISSENSE

dbsnp.83:rs597468

Taste receptor type 2 member 10, involved in bitter perception.

MISSENSE

dbsnp.86:rs1047699

rs1047699

Proline-rich gene prob. Involved in lacrimal functions in eye, this homozygous variant is the most common one for asian and european populations and minor in african.

MISSENSE

dbsnp.116:rs7969931

rs7969931

Common homoz. variant in all populations. Membane PR in ER membrane (cyt. face), role in development of lymphoid cells

MISSENSE

dbsnp.116:rs7975356

rs7975356

341350

Most frequent variant in all populations. Occurs in exon 12/28. Gene function unknown, role in proteolysis inferred from electronic annot.

MISSENSE

OVCH1 1/1 NM_183378.2 2898526 snp G A R C 12 29539541 132

LRRK2 1/1 NM_198578.2 2913282 snp T C M T 12 39044918 2396

MUC19 NA XM_497341.4 2913428 snp G A G E 12 39107442 132

MUC19 NA XM_497341.4 2913446 snp T C I T 12 39118427 566

MUC19 NA XM_497341.4 2913459 snp C G C W 12 39120642 571

MUC19 NA XM_497341.4 2913460 snp C A C * 12 39121221 653

MUC19 NA XM_497341.4 2913465 snp C G I M 12 39122000 693

MUC19 NA XM_497341.4 2913474 snp T C V A 12 39124482 908

MUC19 NA XM_497341.4 2913538 snp A C E A 12 39144209 1177

VDR 2/2 7421 2924339 snp A G M - 12 46559161 0

H1FNT 1/1 NM_181788.1 2925044 snp C T S F 12 47010050 236

dbsnp.120:rs10843438

rs10843438

341350

frequent variant in all populations. Occurs in exon 6/28. Gene function unknown, role in proteolysis inferred from electronic annot.

MISSENSE

dbsnp.107:rs3761863

rs3761863

120892

in exon 49/51, frequent in all populations. Gene (aka PARK8) is kinase, mutations in this gene (but not this one) are the most common cause of hereditary Parkinsons disease.

MISSENSE

dbsnp.116:rs7955308

rs7955308

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. This AA variant is the most freq one and the ancestral allele.

MISSENSE

dbsnp.120:rs11176635

rs11176635

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. This CC variant is a minor allele.

MISSENSE

dbsnp.120:rs10878592

rs10878592

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. Relatively frequent genotype.

MISSENSE

dbsnp.120:rs10784618

rs10784618

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. Minor genotype.

NONSENSE

dbsnp.116:rs7966110

rs7966110

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. Minor genotype at this locus.

MISSENSE

dbsnp.120:rs10784621

rs10784621

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. Minor genotype.

MISSENSE

dbsnp.101:rs2933353

rs2933353

283463

GENE UNANNOTATED IN REFSEQ/IGV but is a mucin. Lots of diff splice variants. Relatively frequent genotype.

MISSENSE

dbsnp.98:rs2228570

rs2228570

NM_001017535.1

Vitamin D receptor. Very frequent genotype, causes alternate protein start (instead of MEAMAA it starts MAA)

MISSTART

dbsnp.100:rs2291483

rs2291483

341567

Frequent genotype in the middle of the only exon of this histone gene. This member is testis-specific.

MISSENSE

C12orf41 1/1 54934 NM_017822.3 2925589 snp G T P T 12 47335004 444

ELA1 1/1 1990 NM_001971.4 2928861 snp T C M V 12 50023828 58

KRT75 1/1 rs298109 9119 NM_004693.2 2930396 snp T C R G 12 51114084 90

KRT6B 3854 NM_005555.3 2930435 snp T C I V 12 51129002 364

KRT74 rs670741 NM_175053.3 2930887 snp T G E D keratin, not interesting 12 51251439 270

KRT76 51350 NM_015848.3 2931428 snp C T A T keratin, not interesting 12 51452206 358

ESPL1 9700 NM_012291.4 2932183 snp C A A D 12 51948890 24

ESPL1 2/2 9700 NM_012291.4 2932198 snp C A S R 12 51956811 613

ESPL1 2/2 9700 NM_012291.4 2932221 snp G A R H 12 51972969 2036

C12orf10 rs711316 60314 NM_021640.3 2932260 snp A G H R 12 51987126 352

dbsnp.107:rs3741628

rs3741628

HYPOTHETICAL PROTEIN. Genotype frequent in European and Asian descent, not African. Occurs in exon 9 of 10.

MISSENSE

dbsnp.123:rs17860300

rs17860300

In exon 3/8. Actually relatively rare genotype for this locus. Gene is chymotrypsin-like elastase family member

MISSENSE

dbsnp.79:rs298109

Gene of keratin family, this one typical for epithelial cells. Exon number 1/9. Relatively frequent variant.

MISSENSE

{dbsnp.80:rs437014;dbsnp.123:rs17099476}

rs437014;dbsnp.123

Keratin, exon 6/9. Very frequent genotype.

MISSENSE

dbsnp.83:rs670741

121391

MISSENSE

dbsnp.116:rs6580904

rs6580904

MISSENSE

1/2, though second is not confirmed

dbsnp.116:rs6580942

rs6580942

aka separase or separin, with crucial role in cleavage of cohesin just before anaphase. Separase overexpression causes ploidy changes and chromosome amplifications. Lots of tumor samples also show elevated separase levels. Most frequent genotype, more than the C refseq genotype. Unfortunately no more info on gene structure. SIFT says tolerated.

MISSENSE

dbsnp.88:rs1318648

rs1318648

see above. Frequent genotype. Present in armadillo repeats that may be the binding place for separin. SIFT says tolerated. No info in literature.

MISSENSE

dbsnp.86:rs1056685

rs1056685

see above. Location correlates with caspase fold. By far most common and ancestral genotype though, unlikely to be deleterious.

MISSENSE

dbsnp.86:rs711316

function unknown, prob related to melanocytes

MISSENSE

LRP1 1/1 4035 NM_002332.2 2937354 snp A C Q P 12 55876050 2899

GLI1 3/3 2735 NM_005269.1 2937585 snp G A G D 12 56151587 932

1/1 64333 2937597 snp A C S A 12 56156421 185

HELB 1/1 92797 NM_033647.2 2950585 snp T C L P 12 64985161 190

dbsnp.116:rs7397167

rs7397167

aa2899/4544 (Extracellular LDLR domain class A19). LDL receptor related protein, clears ApoE4, b-amyloid. Role in apoptosis ao. Some mutations related with increased risk for Alzheimers, but not this one.

MISSENSE

dbsnp.98:rs2228224

rs2228224

relatively commone genotype. Lots of disease-related variants described, but always far from the region of this SNP. Protein plays role in protein folding and in cilio-homeostasis.

MISSENSE

ARHGAP9

dbsnp.120:rs11544238

rs11544238

NM_001080156.1

aa185/750, in PH domain. Least common genotype. Gene is GTPase activating Rho-GAP, implicated in adhesion regulation of hematopoietic cells. STRANGE: The exact opposite mutation (AlatoSer) is associated with coronary spasms in japanese people! But RefSeq says standard is Ser. The Ser variant inhibits cell migration, cell spreading and reduces binding to fibronectin.

MISSENSE

dbsnp.111:rs4430553

rs4430553

DNA helicase. A dominant-negative version of this gene (mutations in Walker A or B motifs) is known, and blocks chromosomal DNA replication (function required for S phase entry). Is also phopshorylated upon DNA damage. This mutation is aa 190/1086, exon 2. Genotype relatively common in population. No OMIM entry. Site is not in one of the Walker motifs (ATPase activity), nor in the helicase motifs, nor at phosphorylation site, and SIFT predicts it to be tolerated.

MISSENSE

BBS10 1/1 79738 NM_024685.3 2964319 snp G A P L 12 75264279 538

C12orf64 NM_173591.2 2969134 snp A G I V 12 79271372 1775

C12orf64 NM_173591.2 2969142 snp A G I V 12 79276790 2009

PTPRQ 2969374 snp T A V D 12 79413959 427

DUSP6 1/2 rs770087 1848 NM_001946.2 2981289 snp A C S A 12 88268903 143

HAL 3034 NM_002108.2 2992295 snp C T V I 12 94898744 438

UTP20 27340 NM_014503.2 2999069 snp T A L Q 12 1E+08 1881

ACACB 32 NM_001093.3 3011298 snp G A V I 12 108181220 2140

dbsnp.126:rs35676114

rs35676114

probable molecular chaperone, also involved in BBSome= cilogenesis complex. A couple of mutations in this gene are disease-associated, but not this one. Genotype distribution: few data, not detected in ESP cohort population, nor Watson/Venter genomes. No domain info on protein, so unclear effect.

MISSENSE

dbsnp.116:rs7297767

rs7297767

283310

by far most frequent genotype. Function unknown. Aka otogelin-like, otogelin being an N-glycosylated ear-specific membrane protein.

MISSENSE

dbsnp.94:rs2034528

rs2034528

283310

by far most frequent genotype. Function unknown. Aka otogelin-like, otogelin being an N-glycosylated ear-specific membrane protein.

MISSENSE

dbsnp.120:rs10778752

rs10778752

374462

XM_001134446.2

PI phosphatase required for auditory function, and adipogenesis in mesenchymal stem cells. SNP localizes to Fibronectin typeIII 4 domain. Genotype is rel frequent, less in Asian populations, and SIFT prediction says its tolerated.

MISSENSE

dbsnp.86:rs770087

dual-specific phosphatase that inactivates MAPK, specifically ERK family, has been suggested to work as a tumor suppressor. KO MEFs show reduced rate of apoptosis. Common genotype.

MISSENSE

dbsnp.116:rs7297245

rs7297245

histidine ammonia-lyase. SNP not in important part of protein.

MISSENSE

dbsnp.119:rs10082778

rs10082778

by far most common genotype in population. Part of snoRNA complex involved in processing rRNA.

MISSENSE

dbsnp.96:rs2075260

rs2075260

acteyl-CoA carboxylase beta, regulation of fatty acid oxidation.

MISSENSE

OAS1 4938 NM_002534.2 3013882 snp G A G S 12 111833252 161

OAS3 4940 NM_006187.2 3014005 snp G A R K 12 111860770 17

OAS2 1/3 4939 3014089 snp C G S R 12 111909536 162

CCDC60 NM_178499.2 3024355 snp A G I V unknown role, rel rare SNP. 12 118350915 45

STX2 2054 NM_194356.1 3047525 snp C G S T 12 129872266 41

SFRS8 6433 NM_004592.2 3050371 snp T C L P 12 130803800 420

DDX51 NM_175066.3 3050799 snp T C Q R 12 131192620 294

POLE 5426 NM_006231.2 3052017 snp T C N S 12 131730598 1395

dbsnp.86:rs1131454

rs1131454

protein using ATP to make 2-5As, activating latent Rnase L resulting in viral degradation. VIB in innate immune response to virus. Mutations have been associated with viral susceptibility. The opposite S162G mutation has been associated with susc to diabetes type I, is located in a conserved region of the gene and close to the DNA binding domain, corr with diff innate immune response. dbSNP says this is a probable-pathogenic allele. SIFT predicts it to be tolerated.

MISSENSE

dbsnp.92:rs1859330

rs1859330

see above. Frequent genotype. No disease correlations.

MISSENSE

dbsnp.87:rs1293767

rs1293767

NM_001032731.1

see above. Not so common genotype. No disease correlation. End of protein (which is one of 3 variants)

MISSENSE

dbsnp.86:rs1064319

rs1064319

160777

MISSENSE

dbsnp.116:rs6486602

rs6486602

protein with role in epithelial morphogenesis. Only small change, (S to T). Frequent genotype.

MISSENSE

dbsnp.92:rs1982528

rs1982528

Splicing regulatory protein, regulating ao fibronectin and CD45 splicing. Most frequent genotype by far. No disease correlation.

MISSENSE

dbsnp.86:rs1133690

rs1133690

317781

ATP-binding RNA helicase involved in biogenesis of 60S ribosomal subunits. Frequent genotype. No OMIM entry.

MISSENSE

dbsnp.114:rs5744934

rs5744934

DNA repair polymerase. Very rare genotype, but no known disease correlations. SIFT predictions based on orthologues says the S on this position is damaging, but the homologue-based prediction says it's tolerated. One paper found no relationship between this SNP and meningioma.

MISSENSE

PARP4 143 NM_006437.3 3067259 snp G A R C 13 23918862 1107

PARP4 143 NM_006437.3 3067325 snp C T S N see above, but very rare genotype. 13 23927294 872

FLT3 2/2 2322 NM_004119.2 3075175 snp G A T M 13 27522293 226

NBEA 2/2 26960 NM_015678.3 3088053 snp A G I V 13 35100268 2500

FREM2 2/2 NM_207361.4 3094619 snp C T T I 13 38328313 2325

CPB2 2/2 1361 NM_001872.3 3106135 snp C T A T 13 45546094 168

RCBTB1 2/2 55213 NM_018191.3 3111608 snp G A A V 13 49039345 23

dbsnp.119:rs9318554

rs9318554

Poly-ADP ribosyl transferase-LIKE protein. This protein cannot bind DNA directly, so transferase activity prob via PPI. Region of SNP is not catalytic/for interactions. Very common genotype. No disease associations known.

MISSENSE

dbsnp.116:rs7140044

rs7140044

MISSENSE

dbsnp.92:rs1933437

rs1933437

Class III receptor Tyr kinase. Mutations resulting in constitutive activation are correlated with leukemia -but this SNP is in the extracellular domain and has no known relation to cancer. Frequent genotype.

MISSENSE

dbsnp.120:rs11538677

rs11538677

Neurobeachin, binds to typeII regulatory units of PKA and targets them to membrane. This SNP is located in the BEACH domain, this genotype is very rare. However, as I to V effect considered minimal, and the mutations in this gene associated with myeloma involve frameshifts and complete gene disruption.

MISSENSE

dbsnp.119:rs9548509

rs9548509

341640

Very frequent genotype. Membrane protein required for skin epithelium integrity and poss for epidermal adhesion. This SNP has no known disease associations.

MISSENSE

dbsnp.107:rs3742264

rs3742264

carboxypeptidase B (cleaves basic AA) that downregulated fibrinolysis. Relatively rare genotype. No disease correlations.

MISSENSE

dbsnp.111:rs4942848

rs4942848

regulator of chromatin condensation, gene frequently deleted in lymphoid malignancies. Frequent genotype, unassociated with disease.

MISSENSE

ATP7B 4/4 540 3114550 snp A G V A 13 51413354 932

ATP7B 4/4 540 3114565 snp T C K R 13 51422488 669

ATP7B 4/4 540 3114591 snp C G V L 13 51442805 455

ATP7B 4/4 540 3114599 snp A C S A 13 51446140 405

TBC1D4 9882 NM_014832.2 3155195 snp C T V I 13 74782216 818

LMO7 4008 NM_005358.4 3156163 snp T C M T 13 75321248 1112

COL4A1 rs536174 1282 NM_001845.4 3216217 snp T G T P 13 109637550 554

FLJ44054 3223550 snp C T V M 13 113490062 314

OR4K2 3225818 snp A T N I uninteresting orf 14 19415185 306

OR4L1 3226336 snp G T R S uninteresting orf 14 19598198 51

OR11H6 3226796 snp G T L F uninteresting orf 14 19762292 194

dbsnp.89:rs1801249

rs1801249

NM_001005918.1

membrane Cu++-transport protein. Huge amount of natural variants can be found, some correlated with Wilson's Disease. This SNP's genotype is frequent, not clearly corr with WD.

MISSENSE

dbsnp.86:rs1061472

rs1061472

NM_001005918.1

see above, common genotype. Not disease- associated

MISSENSE

dbsnp.89:rs1801244

rs1801244

NM_001005918.1

see above, not so frequent genotype.Not disease-ass

MISSENSE

dbsnp.89:rs1801243

rs1801243

NM_001005918.1

see above, common genotype. Not disease- associated

MISSENSE

dbsnp.86:rs1062087

rs1062087

Very common genotype.Correlated with insulin.

MISSENSE

dbsnp.116:rs7986131

rs7986131

Most frequent genotype. At end of gene (aa1112 of 1300) in PDZ domain. Has mulitple isoforms. Some mutations linked to colorectal cancer, but these are on positions 354 and 785. SIFT says this one is tolerated. Role not clear, ubiquitin-medtiation degradation related. No literature on this SNP.

MISSENSE

dbsnp.83:rs536174

The GG (or CC for other sense) genotype is the exclusive genotype - this is again a case where refseq is 'sick'. SIFT prediction says tolerated when using orthologues in protein alignment, but T is damaging using homologues in the protein aligment (however low confidence). One paper says T iso P destroys the typical collagen motif.

MISSENSE

dbsnp.116:rs7399982

rs7399982

643365

XM_001721577.1

HYPOTHETICAL PROTEIN, unknown function

MISSENSE

dbsnp.121:rs12883767

rs12883767

390431

NM_001005501.1

MISSENSE

dbsnp.92:rs1959630

rs1959630

122742

NM_001004717.1

MISSENSE

dbsnp.123:rs17211285

rs17211285

122748

NM_001004480.1

MISSENSE

OR11H6 3226797 snp T C Y H uninteresting orf 14 19762413 235

OR11H6 3226799 snp T C C R uninteresting orf 14 19762482 258

RNASE9 3227379 snp A G S P ANNOTATED AS NON-ACTIVE GENE 14 20094458 203

RNASE9 3227380 snp A G F S ANNOTATED AS NON-ACTIVE GENE 14 20094625 147

OR6S1 3227589 snp C T V I uninteresting orf 14 20179224 155

RNASE7 1/1 84659 NM_032572.3 3228508 snp G C A P 14 20581297 102

FLJ10357 55701 NM_018071.3 3228580 snp G C V L 14 20619732 955

FLJ10357 55701 NM_018071.3 3228582 snp T C L S same as above 14 20620908 1188

MYH6 rs365990 4624 NM_002471.2 3232814 snp A G V A 14 22931650 1100

ZFHX2 85446 3233075 snp A G V A 14 23064356 1678

ZFHX2 85446 3233076 snp A G I T see above. 14 23066611 1080

23351 NM_015299.2 3234171 snp G T W L 14 23971115 269

COCH 1690 NM_004086.1 3243563 snp C G T S 14 30424846 351

dbsnp.123:rs17277221

rs17277221

122748

NM_001004480.1

MISSENSE

dbsnp.123:rs17277228

rs17277228

122748

NM_001004480.1

MISSENSE

dbsnp.87:rs1243647

rs1243647

390443

NM_001001673.3

MISSENSE

dbsnp.120:rs12590446

rs12590446

390443

NM_001001673.3

MISSENSE

dbsnp.120:rs11622969

rs11622969

341799

NM_001001968.1

MISSENSE

dbsnp.87:rs1263872

rs1263872

has broad antimicrobial activity (secreted protein, innate immunity). AA 102/130. Is by far the most frequent genotype. No OMIM-related SNPs.

MISSENSE

dbsnp.116:rs7143633

rs7143633

is likely to be a RhoGEF (name is ARHGEF40). Genotype CC is frequent, GG a bit less. Gene has been found to be significantly amplified in a set of 3000 tumours, but not mutated so unlikely to be relevant

MISSENSE

dbsnp.92:rs1958396

rs1958396

MISSENSE

dbsnp.80:rs365990

myosin heavy chain 6. Both genotypes are frequent and known polymorhisms unrelated to disease.

MISSENSE

dbsnp.111:rs4982766

rs4982766

XM_001720095.1

not annotated in igv, most likely ZFN TF, genotype is frequent.

MISSENSE

dbsnp.116:rs8016202

rs8016202

XM_001720095.1

MISSENSE

KIAA0323

dbsnp.116:rs7151995

rs7151995

KH and NYN domain containing protein, evidence at protein level but function unknown. TT genotype by far the most common (refseq is the outsider).

MISSENSE

dbsnp.86:rs1045644

rs1045644

protein important for hearing, not relevant here

MISSENSE

STRN3 29966 3243595 snp T C N S 14 30451101 470

PAX9 1/1 5083 NM_006194.2 3252262 snp G C A P 14 36205503 239

SEC23A 10484 NM_006364.2 3255750 snp G C L V 14 38625935 210

NID2 1/1 22795 NM_007361.3 3276753 snp C T G D 14 51590117 452

54916 NM_017799.3 3284749 snp G A S N 14 56169611 564

9786 NM_014749.3 3287595 snp T C L P uncharacterized protein 14 58007168 766

rs8660 NM_144581.1 3289306 snp T C I V 14 59009479 340

C14orf38 3289426 snp C T S N uncharacterized protein 14 59058076 688

dbsnp.100:rs2273171

rs2273171

NM_001083893.1

striatin3, binds calmodulin in calcium dependent manner, and has been shown to influence RNA pol II transcription. Polymorphism is well known and not associated to disease. Frequent genotype.

MISSENSE

dbsnp.111:rs4904210

rs4904210

aa239 of 341. Gene very important in fetal development and cancer growth, though function unknown. Lots of deleterious mutations in OMIM, but none is this one. SIFT says tolerated. Literature suggests it is only a polymorphism, though one paper claims it to be a risk factor, if not cause for oligodontia (absence of 6 or more teeth).

MISSENSE

dbsnp.116:rs8018720

rs8018720

component of COPII coat that covers ER-derived vesicles to Golgi. CC is most frequent genotype. No published info on this mutation. SIFT says tolerated. A missense mutation 170 aa downstream does cause a loss of function.

MISSENSE

dbsnp.96:rs2101919

rs2101919

aa 452 of 1340. Rel freq SNP. Important in basement membrane structure and in adhesion and migration, apoptosis, and differentiation. However, null mice are completely viable and show no phenotype. Frequent SNP.

MISSENSE

C14orf101

dbsnp.86:rs1041316

rs1041316

existing protein but of unknown function

MISSENSE

KIAA0586

dbsnp.89:rs1748986

rs1748986

MISSENSE

C14orf149

dbsnp.52:rs8660

112849

probable proline racemase. Frequent genotype, no info on effect, no OMIM entry

MISSENSE

dbsnp.121:rs12887189

rs12887189

729665

XM_001726950.1

MISSENSE

TRMT5 57570 NM_020810.2 3291324 snp A G S P 14 60515719 216

SYNE2 23224 NM_182914.2 3295270 snp T C M T 14 63561447 1968

SYNE2 23224 NM_182914.2 3295277 snp C T A V 14 63566501 2283

SYNE2 23224 NM_182914.2 3295281 snp G A S N same as above 14 63567682 2358

SYNE2 23224 NM_182914.2 3295282 snp G A A T 14 63567789 2394

SYNE2 23224 NM_182914.2 3295331 snp A G S G same as A2284V 14 63588787 2801

SYNE2 23224 NM_182914.2 3295332 snp A G I V same as above 14 63589207 2941

SYNE2 23224 NM_182914.2 3295340 snp G C D H 14 63592426 3252

AKAP5 9495 NM_004857.3 3295857 snp C T T I 14 64005472 202

PLEKHH1 57475 NM_020715.2 3298614 snp A G H R 14 67112326 734

dbsnp.116:rs7142228

rs7142228

tRNA methymtransferase, no relation to disease. GG genotype by far most frequent, again refseq is the odd one out here.

MISSENSE

dbsnp.111:rs4902264

rs4902264

Huge protein with multiple isoforms. Important for spacial organization of cell, and during migration, but KO mice are viable and only hyperactive in new environment, only DKO with SYNE1 is required for neuronal migration. Rel frequent genotype.

MISSENSE

dbsnp.108:rs4027402

rs4027402

see above for function. Relatively frequent genotype. Located in potential coiled coil. No OMIM entry on this SNP, no disease correlation in lit, SIFT says tolerated

MISSENSE

dbsnp.108:rs4027404

rs4027404

MISSENSE

dbsnp.108:rs4027405

rs4027405

see above for function. Most frequent genotype. Not in coiled coil. No OMIM, no disease in lit, SIFT says tolerated

MISSENSE

dbsnp.92:rs1890908

rs1890908

MISSENSE

dbsnp.107:rs3829767

rs3829767

MISSENSE

dbsnp.116:rs8010911

rs8010911

same as above, except that SIFT predicts the H to be damaging, but only when using alignment with homologues.

MISSENSE

dbsnp.87:rs1256149

rs1256149

protein necessary for anchoring PKA to discrete locations in the cell, in this case at postsynaptic densities. By far most frequent genotype (refseq is rare). This SNP is outside the region critical for anchoring function. SIFT says tolerated.

MISSENSE

dbsnp.120:rs11158685

rs11158685

gene with pleckstrin homology domain but furthermore uknown. Frequent genotype, no OMIM entry.

MISSENSE

FLJ44817 XM_929437.3 3300814 snp T C L P unknown function 14 69079471 521

PAPLN rs177389 89932 NM_173462.3 3306583 snp T G M R 14 72797261 665

PAPLN 4/6 89932 NM_173462.3 3306588 snp C T T M 14 72805118 1173

MLH3 rs175081 27030 NM_014381.2 3309586 snp T C N D 14 74583635 825

TTLL5 2/3 23093 NM_015072.3 3310619 snp C T A V 14 75226361 148

GSTZ1 2954 NM_145870.1 3313761 snp T C M T 14 76864035 81

THSD3 NM_199265.1 3313980 snp C T A T 14 77020876 5

TSHR 7253 3319419 snp C A R S 14 80644757 247

dbsnp.116:rs6573888

rs6573888

400224

MISSENSE

dbsnp.79:rs177389

papilin, extracellular glycoprotein. Genotype relatively frequent. No info on potential effect of snp in lit, nor OMIM. SIFT says tolerated.

MISSENSE

dbsnp.111:rs4903104

rs4903104

see above for function. This TT genotype is very rare. Interestingly SIFT says this Met is tolerated when using orthologues in protein aligment, but damaging when using homologues in protein alignment. No literature on this SNP though. This change is located in an Ig-like domain C2 type3.

MISSENSE

dbsnp.79:rs175081

Part of the MutL homolog family of mismatch repair genes. Functions as a heterodimer with other members, and somatic mutations (not this one though) in this gene are frequently associated with microsattelite instability, and germline mutations are correlated with HNPCC type 7. Very frequent genotype. SIFT says tolerated. No lit suggests this SNP could be cancer related.

MISSENSE

dbsnp.100:rs2303345

rs2303345

glucocorticoid receptor. Not super frequent genotype. SIFT says tolerated. No OMIM disease for this gene.

MISSENSE

dbsnp.86:rs1046428

rs1046428

glutathion S-transferase. CC genotype by far the most frequent. SIFT says the M version is damaging (both methods), so not a problem here.

MISSENSE

dbsnp.107:rs3742728

rs3742728

145501

protein with thrombospondin domain but function unknown.

MISSENSE

dbsnp.107:rs3783941

rs3783941

NM_001018036.1

receptor for thyothropin, role in controlling thyroid cell metabolism. Frequent genotype.

MISSENSE

TSHR 7253 NM_000369.2 3319464 snp G C E D 14 80680335 726

STON2 85439 NM_033104.2 3319647 snp A G S P 14 80814488 306

GALC rs421262 2581 NM_000153.2 3330300 snp T C T A 14 87470965 640

57578 NM_020818.3 3339633 snp G A V I 14 93158339 1492

NM_175739.3 3340886 snp A G V A 14 94000857 347

ATG2B `1/1 55102 NM_018036.5 3344783 snp T C N D 14 95851664 1123

AK7 NM_152327.2 3344933 snp C G N K 14 95992504 388

EML1 2009 NM_004434.2 3351180 snp T C S P 14 99450700 555

dbsnp.92:rs1991517

rs1991517

Interestingly, this SNP is associated with Graves disease, but again it's refseq who's sick: it's the E allele that gives higher risk for this disease. It is functionally inert in WT, but gives GOF in when A593N SNP is there too.

MISSENSE

dbsnp.107:rs3813535

rs3813535

regulator of endocytosis. Frequent genotype, tolerated says SIFT. No disease association.

MISSENSE

dbsnp.80:rs421262

galactosylceramidase, hydrolyzes galactose ester bonds in lysosomes. Activity is very low but enzyme is however responsible for the lysososmal catabolism of a major lipid in myelin. Defects cause Krabbe disease. This SNP only causes a significant reduction in activity when associated with T 562, which is not the case here.

MISSENSE

KIAA1409

dbsnp.111:rs4905081

rs4905081

NALCN sodium channel complex part, cation channel activated by neurotensin or substance P.AA genotype is not very frequent, but there. SIFT says tolerated. No further info in lit.

MISSENSE

SERPINA9

dbsnp.120:rs11628722

rs11628722

327657

protease inhibitor (ao trypsin). Frequent genotype. SIFT says tolerated. No OMIM entry.

MISSENSE

dbsnp.119:rs9323945

rs9323945

Very (and most) frequent genotype. Aa1123/2078. Autophagy protein from atg2 family but individual role unknown.

MISSENSE

dbsnp.100:rs2369679

rs2369679

122481

adenylate kinase 7. no OMIM entry. This SNP is located in the adenylate kinase domain but is annotated as natural variant. In fact, frquency is by far the largest, refseq is the odd one out. SIFT says tolerated. No lit on it.

MISSENSE

dbsnp.100:rs2250718

rs2250718

microtubuli associated protein. Frequent genotype. Though gene itself is associated with Usher syndromes, this NSP isn't.

MISSENSE

3320 3353952 snp T A M L 14 101638119 70

MARK3 5/5 4140 NM_002376.4 3355816 snp T C F S 14 103004240 409

AHNAK2 NM_138420.2 3358318 snp G C P A unknown function 14 104476643 5396

AHNAK2 NM_138420.2 3358321 snp C T G E unknown function 14 104477416 5138

AHNAK2 NM_138420.2 3358326 snp T G M L unknown function 14 104479226 4535

AHNAK2 NM_138420.2 3358333 snp T C M V unknown function 14 104481227 3868

AHNAK2 NM_138420.2 3358336 snp C T G E unknown function 14 104481871 3653

AHNAK2 NM_138420.2 3358339 snp A G V A unknown function 14 104482744 3362

ATP10A 57194 NM_024490.3 3373451 snp C G R S 15 23476186 1297

HSP90AA1

dbsnp.116:rs8005905

rs8005905

NM_001017963.2

Hsp90A, a major Hsp90. Functions as a homodimer, but this SNP is far from that region. AA is frequent genotype. For some reason SIFT cannot score this protein.

MISSENSE

dbsnp.119:rs10137161

rs10137161

aa409/753. Regulator of microtubuli associated proteins like tau, loss of this protein is related to pancreas cancer, possible involvement in cell cycle regulation. Frequency of this genotype is almost 100% in all world populations.

MISSENSE

dbsnp.107:rs3742935

rs3742935

113146

MISSENSE

dbsnp.129:rs61421370

rs61421370

113146

MISSENSE

dbsnp.119:rs9672139

rs9672139

113146

MISSENSE

dbsnp.119:rs10438246

rs10438246

113146

MISSENSE

dbsnp.125:rs28380382

rs28380382

113146

MISSENSE

dbsnp.111:rs4264326

rs4264326

113146

MISSENSE

dbsnp.107:rs3816800

rs3816800

in cytoplasmic domain of this multi-pass membrane protein, which is a P-type cation transport ATPase. Maternally expressed, mutations cause Angelman syndrome. Frequent phenotype. Cannot find association of this SNP with disease, but SNP array says T, Flp and A are diploid here, while S, SG and SGendoT have 3.

MISSENSE

TRPM1 4308 NM_002420.4 3379767 snp C T S N 15 29149643 31

9824 NM_014783.2 3381748 snp A G I V 15 30716915 883

FMN1 3382509 snp C T G E 15 31146661 238

FMN1 3382510 snp C A G V 15 31146865 170

RYR3 6263 NM_001036.3 3383555 snp G A G E 15 31803565 2269

EIF2AK4 3391373 snp A G E G 15 38053090 555

BAHD1 22893 NM_014952.3 3391976 snp C A Q K 15 38538846 297

dbsnp.98:rs2241493

rs2241493

cation channel part of the GRM6 signaling cascde. Expression is inversely correlated with melanoma aggressiveness. SNP is in extracellular part. TT is by far most frequent genotype. No associations with disease.

MISSENSE

ARHGAP11A

dbsnp.126:rs34173159

rs34173159

Rho-GTPase but no known other function. Although this genotype seems very rare, only 2 populations have been tested for this SNP. SIFT says mutation is tolerated. It's at the end of the protein.

MISSENSE

dbsnp.120:rs11072170

rs11072170

342184

NM_001103184.1

role i adherens junctions and polymerization of linear actin cables. Tt genotype is rather rare. Sift says tolerated. No other hints in lit.

MISSENSE

dbsnp.120:rs11858145

rs11858145

342184

NM_001103184.1

very common genotype. Sift says tolerated.

MISSENSE

dbsnp.116:rs6495228

rs6495228

intracellular calcium channel (aka ryanodine receptor 3). Most frequent genotype, gg is very rare. SIFT says tolerated.

MISSENSE

dbsnp.100:rs2307105

rs2307105

440275

NM_001013703.2

GG is by far the most frequent genotype, refseq is rare. This protein is a kinase of eIF2 (translation initiation factor), downregulating protein synthesis in response to stresses. SIFT says tolerated. This entry has an experimental sequence conflict at this position (sequencing error?)

MISSENSE

dbsnp.107:rs3803357

rs3803357

frequent genotype. This protein is a heterochromatin protein acting as a transcriptional repressor. This SNP is in a Proline rich region. SIFT says tolerated. No further info in lit.

MISSENSE

CASC5 57082 NM_144508.3 3392092 snp G C R T 15 38685934 42

CASC5 57082 NM_144508.3 snp G T A S 15 38701132

CASC5 57082 NM_144508.3 snp T C M T 15 38701469

ZFYVE19 rs690347 84936 3392340 snp T G S A 15 38893217 375

EXDL1 rs522063 NM_152596.2 3392916 snp T C T A 15 39263500 488

SPTBN5 51332 NM_016642.2 3393416 snp G A H Y 15 39958774 1052

SPTBN5 51332 NM_016642.2 3393417 snp A G C R 15 39958828 1034

dbsnp.116:rs7177192

rs7177192

gene with 2 crucial functions in mitosis: essential for spindle-assembly checkpoint signaling and for correct chromosome alignment. A translocation is involving this gene has been associated with leukemia. Unfortunately, this is a frequent genotype, tolerated acc to SIFT.

MISSENSE

dbsnp.116:rs7177192

rs7177192

rs2412541

SPECIAL CASE: SNP caller says all lines except S are homozygous (S has no call), but alignment at S clearly shows homozygosity. TT is a relatively frequent genotype. SIFT says tolerated, uniprot says it's a natural variant.It's in the region where it interacts with BUB1 and BUB1B for interaction with kinetochores. Cannot find any lit on it though.

460 or 486

MISSENSE

dbsnp.116:rs7177192

rs7177192

rs11858113

SPECIAL CASE: same case as above. CC is not such a frequent genotype. It is however noted as a natural variant in Uniprot. SIFT says toelrated. Again this is in the interaction region with BIB1 and BUB1B. No lit on it.

572 or 598

MISSENSE

dbsnp.83:rs690347

NM_001077268.1

zinc finger protein with FYVE domain. Frequent genotype. Function unknown.

MISSENSE

dbsnp.83:rs522063

161829

exonuclease 3-5 domain containing, natural variant. Specific role unknown.

MISSENSE

dbsnp.87:rs1197682

rs1197682

spectrin beat chain, role in actin capping. AA genotype is rare. Interestingly, both SIFT predictions say its damaging. No additional lit on this. Region is in between two spectrin repeat domains. No OMIM disease.

MISSENSE

dbsnp.87:rs1197683

rs1197683

see above for function. Not a lot of genotype info here, though GG seems to be common.SIFT says tolerated.

MISSENSE

GANC 2595 NM_198141.2 3393934 snp A G Q R 15 40358009 43

ZSCAN29 NM_152455.3 3394674 snp C T G S 15 41446226 198

TP53BP1 7158 NM_005657.1 3394733 snp T G K Q 15 41511937 1135

TP53BP1 rs560191 7158 NM_005657.1 3394790 snp G C D E same as above. 15 41555065 352

MAP1A 4130 NM_002373.5 3394833 snp G A A T 15 41605370 1469

SORD 6652 NM_003104.4 3395726 snp A C N T 15 43151825 268

DUOX2 rs269868 50506 NM_014080.4 3395742 snp G A S L dual oxidase 2. not a disease SNP 15 43179366 1066

DUOX2 50506 NM_014080.4 3395759 snp G A P L same as above 15 43191357 137

DUOX1 53905 NM_017434.3 3395807 snp C T L F same as above 15 43233447 1177

dbsnp.116:rs8024732

rs8024732

glucosidase alpha neutral C, key enzyme in glycogen metabolism. Is in region associated with diabetes susceptibility. GG is very common genotype. There has been no indication of disease effect because of this SNP?

MISSENSE

{dbsnp.108:rs3917221;dbsnp.121:rs12912744}

rs3917221;dbsnp.121

146050

zinc finger with SCAN domain. Role unknown.

MISSENSE

dbsnp.100:rs2602141

rs2602141

p53 binding protein, that associates to sites of dsbreaks, also interacts with H2AFX and the kinetochores. This SNP is a natural variant acc to uniprot, TT is frequent genotype. SIFT says tolerated. No disease corr in lit (one found no correlation with increased cancer risk).

MISSENSE

dbsnp.83:rs560191

MISSENSE

dbsnp.129:rs62020612

rs62020612

microtubuli associated protein, expressed almot exclusively in the brain. No genotype info, not a modified residue, no lit.

MISSENSE

{dbsnp.92:rs930337;dbsnp.98:rs2229659;dbsnp.130:rs74011346}

rs930337;dbsnp.98

sorbitol dehydrogenase. No genotype info.

MISSENSE

dbsnp.79:rs269868

MISSENSE

dbsnp.92:rs2001616

rs2001616

MISSENSE

dbsnp.100:rs2458236

rs2458236

MISSENSE

SLC12A1 6557 NM_000338.2 3399324 snp T C V A 15 46368004 957

FBN1 2200 NM_000138.3 3399547 snp C T C Y 15 46594928 471

ATP8B4 79895 NM_024837.2 3400685 snp G T H N 15 48013604 451

ATP8B4 79895 NM_024837.2 3400752 snp T C N S same as above. 15 48066953 224

GLDN NM_181789.2 3402626 snp G A S N 15 49477063 264

DMXL2 23312 NM_015263.2 3402715 snp A G S P 15 49578850 1287

MYO5A 4644 NM_000259.2 3404016 snp T G E D 15 50476922 361

56204 NM_019600.2 3404266 snp C T V I uncharacterized protein 15 50688724 559

UNC13C 3406130 snp G A G S 15 52094216 608

NEDD4 2/2 4734 NM_198400.2 3409131 snp T C N S 15 53940020 625

dbsnp.88:rs1552311

rs1552311

mediates KCl cotransport when activated by cell swelling. May play role in volume homeostasis in single cells.CC is clearly the most frequent genotype, refseq is odd one out. SIFT says tolerated.

MISSENSE

dbsnp.111:rs4775765

rs4775765

fibrillin, extracellular matrix protein important for structural support of connective tissue. Mutations can cause Marfan syndrome. Natural variant.

MISSENSE

dbsnp.100:rs2452524

rs2452524

atpase class I type 8B member 4. Natural variant. Genotype frequent.

MISSENSE

dbsnp.123:rs16963151

rs16963151

MISSENSE

dbsnp.123:rs17648128

rs17648128

342035

role in formation of nodes of ranvier in myelin sheet. Not relevant.

MISSENSE

dbsnp.120:rs12102203

rs12102203

may play role as scaffold protein for MADD on synaptic vesicles. Known natural variant. Frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.89:rs1724577

rs1724577

myosin. GG is by far most frequent genotype. SIFT says tolerated.

MISSENSE

KIAA1370

dbsnp.121:rs12915981

rs12915981

MISSENSE

dbsnp.120:rs12437941

rs12437941

440279

NM_001080534.1

probable role in vesicle maturation during exocytosis, target of DAG pathway? Known natural variant. AA is clearly the most frequent genotype, no GG. SIFT says tolerated.

MISSENSE

dbsnp.100:rs2303579

rs2303579

Very frequent genotype. A somatic mutation only 2AA downstream (Y to H) is associated with breast cancer. Gene is an E3 ubiquitin ligase, degrading VEGFR2, TNK2, EGFR, TNF2. Involved in budding of many viruses, role in neuronal dendrite extension. KO in mice causes embryonal death.

MISSENSE

NEDD4 2/2 4734 NM_198400.2 3409132 snp C T R Q See above. Genotype rel. Frequent. 15 53940163 606

CGNL1 84952 NM_032866.3 3411211 snp A G T A 15 55519019 510

AQP9 366 NM_020980.3 3412022 snp A G T A 15 56263572 278

LACTB NM_032857.2 3418568 snp G A R K 15 61220818 468

HERC1 8925 NM_003922.3 3419155 snp C G E D 15 61724261 3721

HERC1 8925 NM_003922.3 3419194 snp T C I V same as above 15 61757508 2219

HERC1 8925 NM_003922.3 3419211 snp C G G A same as above 15 61775409 1695

ITGA11 22801 3425918 snp G A P L 15 66392222 971

NOX5 79400 NM_024505.2 3427178 snp C T L F 15 67115279 361

MYO9A 4649 NM_006901.2 3431755 snp C T G E 15 69978319 1192

CCDC33 80125 NM_025055.3 3434652 snp G A S N unknown function 15 72409730 479

PPCDC 60490 NM_021823.3 3435294 snp A G I M 15 73123781 77

dbsnp.100:rs2303580

rs2303580

MISSENSE

dbsnp.87:rs1280396

rs1280396

GG is most frequent genotype. SIFT says tolerated. Role in tight junctions.

MISSENSE

dbsnp.92:rs1867380

rs1867380

aquaporin 9. known natural variant, SIFT says tolerated.

MISSENSE

dbsnp.100:rs2729835

rs2729835

114294

protein from the 39S mitochondrial ribosome.

MISSENSE

dbsnp.98:rs2229749

rs2229749

a GEF for Arf and Rab. No diseases correlated with it. Known natural variant, SIFT says tolerated, genotype is frequent.

MISSENSE

dbsnp.98:rs2228510

rs2228510

MISSENSE

{dbsnp.100:rs2255243;dbsnp.129:rs63019465}

rs2255243;dbsnp.129

MISSENSE

dbsnp.111:rs4777035

rs4777035

NM_001004439.1

integrin alpha 11. frequent genotype. SIFT via orthologues says tolerated, but via homologues it says damaging. No further lit on this SNP, not in a particular domain, not modified.

MISSENSE

dbsnp.121:rs12907196

rs12907196

NADPH oxidase that generates superoxide that may play role in apoptosis and cell growth. TT is rather rare genotype, and SIFT via homologue alignment says damaging. Extracellular location, also in ferric oxidoreductase domain. Not in lit.

MISSENSE

dbsnp.100:rs2415129

rs2415129

myosin 9A. TT is by far most frequent genotype. SIFT says tolerated. No disease correlation in lit.

MISSENSE

dbsnp.88:rs1564782

rs1564782

MISSENSE

dbsnp.100:rs2304899

rs2304899

essential enzyme for biosynthesis of vitamin B5 from CoA. Change is natural variant.

MISSENSE

TMC3 3445734 snp C T D N 15 79411822 1098

ZSCAN2 54993 NM_181877.3 3449288 snp G C S T 15 82965001 190

SLC28A1 9154 NM_004213.3 3449710 snp C A Q K 15 83249878 236

ACAN rs938608 176 NM_013227.2 3456373 snp G T S I 15 87199608 929

ACAN rs938609 176 NM_013227.2 3456374 snp T A S T 15 87199634 938

ACAN 176 NM_013227.2 3456378 snp A G I V 15 87203054 1964

KIF7 NM_198525.1 3457570 snp C A S I 15 87977076 444

C15orf32 NM_153040.2 3462752 snp G A A T uncharacterized protein 15 90816430 16

FLJ39743 NM_182562.2 3473331 snp A G S P uncharacterized protein 15 96812603 114

8912 NM_021098.2 3482826 snp G A R H 16 1210162 2076

dbsnp.111:rs4417518

rs4417518

342125

NM_001080532.1

transmembrane channel like 3. uncharacterized.

MISSENSE

dbsnp.94:rs2044502

rs2044502

zinc finger with SCAN domain. Role in spermatogenesis.

MISSENSE

dbsnp.123:rs8187758

rs8187758

nucleoside transporter. Natural variant not associated with disease.

MISSENSE

dbsnp.86:rs938608

aggrecan, a proteoglycan family protein in ECM of cartilagenous tissue. Mutations in this gene can cause skeletal dysplasias and short stature. Frequent genotype. SIFT says tolerated. No identical SNPs in OMIM, no lit info.

MISSENSE

dbsnp.86:rs938609

see above. Frequent genotype. SIFT says tolerated.no identical SNPS in OMIM.

MISSENSE

dbsnp.86:rs1042630

rs1042630

see above for function. Frequent genotype, more than the refseq one. SIFT says tolerated. No similar SNPs in OMIM.

MISSENSE

dbsnp.107:rs3803530

rs3803530

374654

kinesin family member 7, regulator of Shh pathway. Not very frequent genotype, but clearly present. SIFT says tolerated. Disease-related SNPs always cause early termination of gene.

MISSENSE

dbsnp.88:rs1455773

rs1455773

145858

MISSENSE

dbsnp.120:rs12101356

rs12101356

283777

MISSENSE

CACNA1H

dbsnp.86:rs1054645

rs1054645

voltage-dependent calcium channel, role in pacemaking functions in central neurons and support calcium signaling in secretory cells. Some mutations in this gene have been associated with susceptibility to epilepsy. Frequent genotype. SIFT says tolerated. no OMIM SNP.

MISSENSE

TPSG1 25823 NM_012467.3 3482829 snp G T F L 16 1211890 287

BAIAP3 8938 NM_003933.3 3483232 snp A C D A 16 1334507 581

2/2 23162 3483684 snp A G T A 16 1754440 746

C16orf68 79091 NM_024109.2 3500099 snp G A A T 16 8645999 365

ABAT 18 NM_020686.4 3500591 snp A G Q R 16 8747454 55

CIITA 4261 NM_000246.3 3505740 snp A G Q R 16 10910427 899

ABCC6 368 NM_001171.3 3514568 snp C T R Q 16 16159099 1267

dbsnp.86:rs1004041

rs1004041

tryptase, enzymatically only active as heparin-stabilized tetramers. Implicated in asthma and other allergic disorders. Frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.86:rs1132356

rs1132356

p53 target gene, brain specific angiogenesis inhibitor. No disease correlation in OMIM. CC is by far the most frequent genotype. SIFT tolerated.

MISSENSE

MAPK8IP3

dbsnp.100:rs2294619

rs2294619

NM_001040439.1

rare genotype. Aa747/1336 (or 753 for splice variant). Protein ivolved in JNK signaling, poss role in regulation of vesicle transport. No disease-related SNPs. This residue is not part of the coiled coil regions, nor of the modified AA, nor the conserved hydrophobic core, nor the TM region (but just at the border though). SIFT says tolerated.

MISSENSE

dbsnp.89:rs1731000

rs1731000

methyltransferase-like 22 (by similarity). Not much info on genotype frequency. SIFT says tolerated. No OMIM entry.

MISSENSE

dbsnp.89:rs1731017

rs1731017

responsible enzyme for GABA synthesis, the inhibitory neurotransmitter in the CNS. Not an OMIM SNP. Frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.116:rs7197779

rs7197779

class II MHC transactivator, the master control factor for the expression of MHC II. Mutations have been associated with immunodeficiencies and MS. Not an OMIM SNP, GG is by far the most frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.98:rs2238472

rs2238472

ABC-type transporter, here involved in mutli-drug resistance. Lots of natural variants known. This SNP is well-known and associated with lower plasma triglycerides and higher HDL cholesterol.

MISSENSE

ABCC6 368 NM_001171.3 3514628 snp T C M V 16 16178857 847

ABCC6 368 NM_001171.3 3514645 snp G T H Q 16 16186363 631

ABCC6 368 NM_001171.3 3514657 snp A G V A same as above. 16 16188507 613

VWA3A NM_173615.2 3521911 snp T C F L 16 22068636 811

GGA2 23062 NM_015044.3 3523209 snp C G A P 16 23397211 423

EARS2 3523281 snp T C S G 16 23444184 456

23247 NM_015202.1 3530407 snp G A E K uncharacterized protein 16 27691997 1425

rs40832 55911 NM_018690.2 3531396 snp T C V A 16 28416216 775

SULT1A1 6817 NM_177534.1 3531456 snp C T V M 16 28524985 222

ZNF646 9726 NM_014699.2 3533793 snp G A G D uncharacterized protein 16 30999575 1476

dbsnp.116:rs6416668

rs6416668

see above for function. CC genotype is by far the most frequent one Interestingly, though SIFT predicts tolerated, in dbSNP this is marked as a pathogenic allele, but Val is the non-pathogenic one, so refseq is the odd one out.

MISSENSE

dbsnp.116:rs8058694

rs8058694

TT is the rare genotype, btu this allele is clearly annotated as a nonpathogenic allele.

MISSENSE

dbsnp.121:rs12931472

rs12931472

MISSENSE

dbsnp.92:rs1991020

rs1991020

146177

von willebrand factor A domain containing 3A. No OMIM entry. CC is by far the most frequent genotype. SIFT says tolerated. No lit info.

MISSENSE

dbsnp.86:rs1135045

rs1135045

golgi-associated arf-binding protein, a coat protein regulating traffic between the TGN and lysosome. Rather rare genotype, SIFT says tolerated, no OMIM SNP, no lit.

MISSENSE

dbsnp.116:rs6497671

rs6497671

124454

NM_001083614.1

Most frequent genotype. AA457/523. No disease-related SNPs. Is an aminoacyl-tRNA synthetase for the mitochondrial genome.

MISSENSE

KIAA0556

MISSENSE

APOB48R

dbsnp.76:rs40832

aka the apoB receptor on macrophage? Get foam cell formation when overwhelmed with triglycerides. CC is by far most frequent genotype. SIFT says tolerated. No add lit.

MISSENSE

{dbsnp.89:rs1801030;dbsnp.127:rs45543439}

rs1801030;dbsnp.127

By far most common genotype. AA223/295. Is a sulfotransferase (to catecholamines/drugs).

MISSENSE

dbsnp.116:rs7196726

rs7196726

MISSENSE

POL3S 3533799 snp G C P A 16 31003664 405

MLCK 1/1 91807 NM_182493.2 3539885 snp C A V L 16 45331499 179

SALL1 6299 NM_002968.2 3543650 snp C T V I 16 49728675 1274

CHD9 80205 NM_025134.4 3547178 snp T G D E 16 51899248 2311

CES7 2/3 NM_145024.1 3551771 snp C T R Q 16 54465311 70

MT1A 4489 NM_005946.2 3552875 snp C A T N 16 55230727 26

CCL22 6367 NM_002990.3 3554161 snp A C D A 16 55950233 1

dbsnp.116:rs7199949

rs7199949

339105

NM_001039503.2

serin protease 3. can degrade fibrinogen and tPA. This SNP is far from the active site. CC is not very frequent but clearly present. Tolerated by SIFT.

MISSENSE

dbsnp.125:rs28407821

rs28407821

aka MYLK3. Mysosin light chain kinase, involved in muscle contraction and neurotransmitter release. Only SNPs causing early termination cause diseas (aortic aneurysms). Genotype no so frequent.

MISSENSE

dbsnp.111:rs4614723

rs4614723

sal1-like: a Znf-repressor TF probably part of the HDAC complex, important role in development. This is not a SNP but in fact an error in the refseq sequence.

MISSENSE

dbsnp.116:rs6499548

rs6499548

transcriptional coactivator for PPARa and others, proposed role in chromatin remodeling. GG is by far the most frequent genotype. SIFT says tolerated change.

MISSENSE

dbsnp.100:rs2397965

rs2397965

221223

carboxylesterase. Role in hydrolysis/transesterification of xenobiotics, fatty acil and cholesterol ester metabolism. Has no OMIM entry, but SIFT says this change is damaging, so does polyphen, and LS-SNP says the change affects a buried charge, and someone from PolyDoms has marked this as validated. The SNP is not in the active site. TT genotype is not really frequent but there. Cannot find more info about this SNP nor its effect.

MISSENSE

dbsnp.120:rs11640851

rs11640851

metallothionein, binds heavy metals. No genotype frequency info, not an OMIM SNP. Not modified as far as has been reported.

MISSENSE

dbsnp.111:rs4359426

rs4359426

one of several Cys-Cys cytokine genes on the q-arm of chr16. chemotactic activity for various immune cells. CC is most frequent genotype, tolerated according to SIFT.

MISSENSE

CNGB1 1258 NM_001297.3 3555177 snp C T R H 16 56554460 99

GOT2 rs30842 2806 NM_002080.2 3556486 snp A C V G 16 57300954 345

CDH3 1001 NM_001793.3 3568724 snp G C Q H 16 67279033 562

COG4 25839 NM_015386.2 3570947 snp G A T I 16 69105797 161

ZNF23 7571 NM_145911.1 3574431 snp T C S G 16 70044706 27

HPR rs12646 3250 NM_020995.3 3575459 snp C G H D 16 70668448 338

PKD1L2 NM_052892.3 3594438 snp A C S R 16 79708622 2208

dbsnp.121:rs13336595

rs13336595

cyclic nucleotide gated channel beta 1. it's a photoreceptor cation channel, causing retinitis pigmntosa in some cases, not relevant.

MISSENSE

dbsnp.76:rs30842

mitochondrial glutamic-oxaloacetic transaminase. Role in amino acid metabolism and TCA cycle. SIFT predicts the Val to be damaging, but only when aligning homologues iso orthologues. Confidence is low though. Frequent genotype, not an OMIM SNP.

MISSENSE

dbsnp.86:rs1126933

rs1126933

P-cadherin. Cell-cell adhesion in placenta. Aberrant expression has been associated with cervical adenocarcinoma's. Not an OMIM SNP. Natural variant. Frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.108:rs3931036

rs3931036

component of golgi complex, required for normal golgi function, role in SNARE-pin assembly and Golgi-ER retrograde transport. Defects in this gene can cause congenital glycosylation disorders. AA is most frequent genotype by far. Interestingly, SIFT predicts the Tyr to be damaging. SNP is located outside functional domains.

MISSENSE

dbsnp.96:rs2070832

rs2070832

ZNF TF, role in development. Frequent genotype, sift says tolerated. Nothing else known.

MISSENSE

dbsnp.52:rs12646

hemoglobin-binding protein. Well-known variant. No genotype info though. Sift says His is damaging, but with low confidence and only based on homologue-alignment.

MISSENSE

dbsnp.111:rs4889238

rs4889238

114780

polycystic-kidney disease-like, could function as component of cation channel pores. Known variant, not much genotype info. SIFT say tolerated. Not modified.

MISSENSE

PKD1L2 NM_052892.3 3594948 snp G A P L same as above 16 79789775 511

PKD1L2 NM_052892.3 3594949 snp T G K Q same as above 16 79790064 415

PKD1L2 NM_052892.3 3595119 snp T A Q L same as above 16 79807454 119

PKD1L2 NM_052892.3 3595141 snp A G V A same as above 16 79811417 19

OSGIN1 29948 NM_013370.3 3602411 snp C T P L 16 82540571 5

TAF1C 2/6 9013 NM_139353.1 3602876 snp C T C Y 16 82774562 23

C16orf85 3613948 snp T G E D uncharacterized protein 16 87147695 144

ACSF3 NM_174917.1 3615239 snp G A V M 16 87708383 371

ZNF778 NM_182531.2 3615439 snp A C K T 16 87820771 163

ZNF778 NM_182531.2 3615442 snp T C I T same as abov 16 87821881 533

ZNF778 NM_182531.2 3615443 snp G T Q H same as above 16 87821939 552

dbsnp.116:rs7205673

rs7205673

114780

MISSENSE

dbsnp.116:rs7194871

rs7194871

114780

MISSENSE

dbsnp.116:rs7191351

rs7191351

114780

MISSENSE

dbsnp.119:rs9924530

rs9924530

114780

MISSENSE

dbsnp.111:rs4782865

rs4782865

oxidative stress induced growth inhibitor, regulates the differentiation and proliferation of normal cells through the regulation of cell death. According to OMIM its pregnancy-induced. Known natural variant, frequent genotype. SIFT says tolerated. No lit info on this.

MISSENSE

dbsnp.111:rs4782591

rs4782591

By far most frequent genotype. TATA box binding protein associated factor for RNA polI. No disease info.

MISSENSE

dbsnp.101:rs2879897

rs2879897

400555

NM_001001682.1

MISSENSE

dbsnp.107:rs3743979

rs3743979

197322

acyl-CoA synthetase family member 3. known variant.

MISSENSE

dbsnp.125:rs28417933

rs28417933

197320

candidate gene for autism. No genotype info. Sift says tolerated. Outside ZNF region.

MISSENSE

dbsnp.125:rs28415940

rs28415940

197320

MISSENSE

dbsnp.119:rs9921361

rs9921361

197320

MISSENSE

29123 NM_013275.4 3615557 snp G A A V 16 87877538 970

PRDM7 11105 3617008 snp A C D E 16 88668855 89

GEMIN4 50628 NM_015721.2 3618352 snp G C Q E 17 596684 449

SCARF1 2/2 8578 NM_145352.2 3620608 snp C T G S 17 1485295 580

WDR81 NM_152348.2 3620713 snp A G M V uncharacterized protein. 17 1583683 483

OR3A4 rs231678 3623503 snp T G S A uninteresting gene. 17 3160930 192

TRPV3 rs322965 NM_145068.2 3624000 snp T C I V 17 3404821 24

ITGAE 3682 NM_002208.4 3624642 snp C T R Q 17 3603907 481

ITGAE rs220479 3682 NM_002208.4 3624643 snp T C I V same as above. 17 3603923 476

MINK1 5/5 50488 NM_015716.3 3627204 snp T C V A 17 4737049 733

rs346822 55065 NM_017986.3 3627497 snp T C Q R riboflavin transporter. 17 4878298 69

ANKRD11

dbsnp.100:rs2279348

rs2279348

ankyrin repeat domain 11. May recruit HDACs to p160 coactivators to inhibit ligand-dependent activation of transcription. This SNP is in a Lys-rich region. Frequent genoype. SIFT says tolerated.

MISSENSE

dbsnp.121:rs12925933

rs12925933

NM_001098173.1

PR-domain TF. Other members are known to be involved with tumorigenesis. Frequent genotype.

MISSENSE

dbsnp.100:rs2740348

rs2740348

role in spliceosome assembly. Frequent genotype. Sift says tolerated.

MISSENSE

dbsnp.111:rs4790250

rs4790250

Not frequent genotype.Gene scavenges acetylated LDL from blood. Also suggested role as adhesion protein. AA580/830.

MISSENSE

dbsnp.107:rs3809870

rs3809870

124997

MISSENSE

dbsnp.79:rs231678

390756

NM_001005334.1

MISSENSE

dbsnp.79:rs322965

162514

cation channel involved in temperature sensation. Frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.100:rs2272606

rs2272606

binding integrin for E-cadherin, mediates formation of epithelial cell layers. Expressed weakly in a lot of tissues, but stronger in intestinal lymphocytes. SIFT predicts toelrated, frequent genotype.

MISSENSE

dbsnp.79:rs220479

MISSENSE

dbsnp.120:rs11556634

rs11556634

Not a lot of dbSNP info, but 100% genotype in nigeria. Allele is relatively frequent. No disease correlation info. Activates JNK and p38 pathways, esp during mouse brain development.

MISSENSE

GPR172B

dbsnp.79:rs346822

MISSENSE

USP6 9098 NM_004505.2 3627795 snp T C W R 17 4983617 474

TNK1 2/2 8711 NM_003985.3 3632088 snp G A V M 17 7232830 592

CNTROB 3632931 snp C A P Q 17 7788679 577

PFAS 5198 NM_012393.1 3633617 snp C T P S 17 8098034 18

rs871841 22899 NM_173728.2 3633719 snp T C L P 17 8157192 276

dbsnp.116:rs8073787

rs8073787

ubiquitin specific peptidase, it promotes plasma membrane localization of ARF6 and thereby regulates selectively ARF6-dependent endocytic protein trafficking. It is also able to initiate tumourigenesis by inducing the production of MMPs following NFkB activation. CC is the most frequent genotype. SIFT says tolerated. Expression is normally testis-specific. INterestingly, this transcript is often detected in a variety of human cancer cells regardless or their lineage of origin, but not in human cells from normal tissue. Copy number is the same (4) in all cell lines).

MISSENSE

dbsnp.116:rs6503018

rs6503018

AA592 of 666. Frequent genotype. Nonreceptor Tyrosine kinase, involved in negative regulation of cell growth, neg regulation of Ras-MAPK pathway, often used during fetal development. No disease info.

MISSENSE

dbsnp.120:rs11650083

rs11650083

116840

NM_001037144.3

centrosomal BRCA2 interacting protein, required for centriole dulication and cytokinesis. Widely expressed. This SNP is in a region required for centrosome localization and is Pro-rich. Frequent genotype. SIFT says tolerated though. Gene has not been found to be significantly amplified or deleted in a set of 3000 tumours.

MISSENSE

dbsnp.119:rs9891699

rs9891699

phosphoribsoylformylglycinamide synthase, catalyzes fourth step of the IMP biosynthesis step, the de novo pathway of purine biosynthesis. Known natural variant, not in a functional domain. SIFT: tolerated. TT is the most frequent genotype.

MISSENSE

ARHGEF15

dbsnp.86:rs871841

Rho GTPase, role in RhoA ADP for ATP exchange. Known natural variant, frequent genotype, SIFT: tolerated.

MISSENSE

22899 NM_173728.2 3633732 snp T C S P same as above. Not modified. 17 8165000 830

GLP2R 9340 NM_004246.1 3636809 snp G A D N 17 9733492 469

MYH3 4621 NM_002470.2 3638090 snp C T A T 17 10482239 1191

DNAH9 1770 NM_001372.3 3639977 snp A G Q R 17 11463806 444

TEKT3 rs230898 64518 NM_031898.1 3648026 snp C G G A 17 15158161 281

M-RIP 23164 NM_201274.2 3650552 snp C A P Q 17 16986748 326

PEMT rs897453 10400 NM_148173.1 3651157 snp C T V I 17 17366355 57

rs887241 218 NM_000691.3 3653681 snp A C S A 17 19586529 133

SLFN11 91607 NM_152270.3 3669029 snp T C N D uncharacterized protein. 17 30714038 300

SLFN12L XM_496206.3 3669243 snp T C Y C uncharacterized protein 17 30829262 411

CCL15 rs854625 6359 NM_032965.2 3669840 snp A G I T 17 31352573 23

DDX52 11056 NM_007010.2 3671808 snp T C M V 17 33058522 402

ARHGEF15

dbsnp.107:rs3744647

rs3744647

MISSENSE

dbsnp.123:rs17681684

rs17681684

glucagon-like peptide 2 receptor. Stimulates intestinal growth. SIFT says tolerated, natural variant.

MISSENSE

dbsnp.100:rs2285477

rs2285477

myosin heavy chain 3. known natural variant.

MISSENSE

dbsnp.119:rs9892256

rs9892256

dynein heavy chain. Known natural variant. Most frequent genotype by far.

MISSENSE

dbsnp.79:rs230898

exact function of this protein is not known, but it belongs to a family of proteins coassambled with tubulins to form ciliary and flagellar microtubules.

MISSENSE

dbsnp.107:rs3744137

rs3744137

myosin phosphatase Rho-interacting protein. Role in stress fiber formation. Known natural variant.

MISSENSE

dbsnp.86:rs897453

phosphatidylethanolamiine N-methylatransferase. Catalyzes PE--> PC. SIFT says tolerated, known natural variant.

MISSENSE

ALDH3A1

dbsnp.86:rs887241

ALDH in cytoplasm, preference for aromatic and medium-chain aldehyde substrates. Promotes resistance to UV in the cornea. Known natural variant.

MISSENSE

dbsnp.111:rs4796077

rs4796077

MISSENSE

dbsnp.100:rs2304968

rs2304968

342615

MISSENSE

dbsnp.86:rs854625

chemotactic Cys-Cys cytokine for T-cells and monocytes. Acts via CCR1. known natural variant.

MISSENSE

dbsnp.116:rs7216445

rs7216445

DEAD box polypeptide 52. Probable RNA helicase, known natural variant.

MISSENSE

KRT24 NM_019016.1 3675749 snp T C K E keratin, not really interesting 17 36109297 428

KRT37 8688 NM_003770.4 3677326 snp T A S C keratin, not really interesting 17 36834084 72

KRT37 8688 NM_003770.4 3677327 snp T C T A keratin, not really interesting 17 36834087 71

KRT37 8688 NM_003770.4 3677328 snp T C N S keratin, not really interesting 17 36834185 38

KRT38 rs897416 8687 NM_006771.3 3677376 snp A G S P keratin, not really interesting 17 36847293 422

KRT32 3882 NM_002278.3 3677528 snp G T S Y keratin, not really interesting 17 36875593 221

NAGLU rs86312 4669 NM_000263.3 3678937 snp C G R G 17 37949758 736

TUBG2 27175 NM_016437.1 3679166 snp A G M V 17 38072224 412

BRCA1 5/6 672 NM_007295.2 3679663 snp T C S G 17 38476619 1612

dbsnp.100:rs2462961

rs2462961

192666

MISSENSE

dbsnp.119:rs9916475

rs9916475

MISSENSE

dbsnp.119:rs9916484

rs9916484

MISSENSE

dbsnp.119:rs9916724

rs9916724

MISSENSE

dbsnp.86:rs897416

MISSENSE

dbsnp.96:rs2071561

rs2071561

MISSENSE

dbsnp.83:rs86312

N-acetyl glucosaminidase alpha. Degrades heparan sulfate. SIFT says tolerated. Known natural variant.

MISSENSE

dbsnp.86:rs1046097

rs1046097

Tubulin gamma. Is found at the MTOC such as spindle poles of the centrosome. Regulates centrosome duplication and splindle formation. Not much known on frequency distribution of genotypes for this SNP, though marked as known natural variant. SIFT says tolerated. Literature suggests this is a non-damaging mutation.

MISSENSE

dbsnp.89:rs1799966

rs1799966

Very important DNA repair protein, well-known for corr in breast cancer, critical for genome stability maintenance and cell cycle control. Lots of pathogenic associated mutations. Actually, rather rare genotype according to dbSNP but common according to UniProt, not associated with cancer susceptibility. AA1612/1863. Not a modified residue. Outside annotated special domains. SIFT says damaging but with low confidence.

MISSENSE

BRCA1 rs799917 672 NM_007295.2 3679719 snp G A P L 17 38498461 870

ASB16 92591 NM_080863.4 3681597 snp A T Q H 17 39603871 62

C17orf57 NM_152347.3 3685210 snp G A V I uncharacterized protein 17 42806892 311

HOXB1 3211 NM_002144.3 3686512 snp T C E G 17 43962019 264

HOXB7 3217 NM_004502.3 3686648 snp T C T A 17 44043254 8

84073 NM_032133.3 3689491 snp C G S R 17 45961535 909

SPATA20 3/4 64847 NM_022827.2 3689551 snp A G K R 17 45984456 624

KIF2B 84643 NM_032559.4 3694453 snp C G R G 17 49256701 436

ANKFN1 NM_153228.2 3697974 snp G A V I uncharacterized protein. 17 51889632 444

3/6 (others: intron/UTR)

dbsnp.86:rs799917

See above. AA870/1863. Also common polymorphism, unrelated to disease, not in specifically important region.

MISSENSE

dbsnp.116:rs7218599

rs7218599

possible part of an E3 ubiquitin-protein ligase complex. No OMIM entry. Turns out not to be a SNP but a downright sequence conflict with refseq.

MISSENSE

dbsnp.111:rs4968318

rs4968318

124989

MISSENSE

dbsnp.116:rs7226137

rs7226137

homeobox B1. according to SIFT the refseq E is damaging.

MISSENSE

dbsnp.116:rs7406910

rs7406910

homeobox B7. Involved in cell proliferation and differentiation, with an increased expression in some cases of melanoma and ovarian carcinoma. Known natural variant, tolerated says SIFT.

MISSENSE

MYCBPAP

dbsnp.86:rs1133818

rs1133818

unclear role, most likely in spermatogenesis

MISSENSE

dbsnp.116:rs8065903

rs8065903

Most common genotype, unassociated with disease. Secreted protein with role in spermatogenisis.

MISSENSE

dbsnp.111:rs4561519

rs4561519

kinesin family member 2B. Plus-end directed microtubulue-dependent motor protein required for spindle assembly and chromosome movement. No OMIM entry. Most frequent genotype. SIFT says the Gly is tolerated, the Arg not (but with low confidence and only when using homologues in the alignment).

MISSENSE

dbsnp.120:rs10852985

rs10852985

162282

MISSENSE

CUEDC1 1/1 NM_017949.1 3700504 snp C T R H 17 53306035 168

HSF5 3701125 snp T G N T 17 53899278 328

BCAS3 54828 3702855 snp A G N S 17 56141406 86

SCN4A 6329 NM_000334.4 3706617 snp T C S G 17 59394799 523

PECAM1 5175 NM_000442.3 3707021 snp T C R G 17 59781520 669

C17orf58 NM_181655.2 3713433 snp T C I V uncharacterized protein. 17 63418510 91

WIPI1 rs883541 55062 NM_017983.5 3713979 snp G A T I 17 63960716 30

ABCA9 10350 NM_080283.3 3714886 snp C T R H 17 64543051 352

dbsnp.123:rs17762338

rs17762338

404093

Very rare genotype (though present in dbSNP). Unknown function, no known related disease. SNP is not in special region.

MISSENSE

dbsnp.86:rs1017089

rs1017089

124535

NM_001080439.1

heat shock transcription factor family 5. Unknown specifics.

MISSENSE

dbsnp.100:rs2643103

rs2643103

NM_001099432.1

Breast Carcinoma Amplified 3. Unknown role, but sometimes amplified or translocated in cancer. Known natural variant, very high genotype frequency, SIFT says tolerated. No specific amplification visible from CNV data.

MISSENSE

dbsnp.116:rs6504191

rs6504191

voltage gated sodium channel. Uninteresting

MISSENSE

dbsnp.86:rs1131012

rs1131012

platelet/endothelium cell adhesion molecule. Known natural variant, frequent genotype.Lots of studies have been done on PECAM1 SNPs, and the GG genotype showed higher Tyr phosphorylation and transendothelial migration following TNFa stimulation. I do not think this is very relevant for our cells.

MISSENSE

dbsnp.119:rs9891146

rs9891146

284018

MISSENSE

dbsnp.86:rs883541

Protein with probable role in autophagy and trafficking of proteins involved in the mannose-6-phosphate receptor recycling pathway. Is upregulated in a variety of tumour tissues. Very frequent genotype. SIFT says the refseq Thr is damaging.

MISSENSE

dbsnp.92:rs1860447

rs1860447

ABC transporter involved in lipid homeostasis, known natural vairant

MISSENSE

ABCA6 23460 NM_080284.2 3714985 snp T C N S 17 64593424 1321

ABCA10 10349 NM_080282.3 3715184 snp G A P S see above 17 64724017 202

54868 NM_017728.3 3724887 snp G A V M see above 17 70296526 57

OTOP3 NM_178233.1 3725053 snp T C S P uncharacterized protein 17 70449694 198

TSEN54 NM_207346.2 3726108 snp G C K N 17 71029797 346

LLGL2 3993 3726187 snp G A R H 17 71063779 44

ITGB4 rs871443 3691 3726516 snp T C L P 17 71265097 1708

dbsnp.100:rs2302134

rs2302134

same function as above. SIFT says this mutation is damaging. Frequency of genotype is high though. There is a paper on the accuracy of prediction algorithms of ABCA genes, and this SNP is in that paper, but it is not reported whether for this SNP the prediction was accurate.

MISSENSE

dbsnp.119:rs9909216

rs9909216

MISSENSE

TMEM104

dbsnp.92:rs2016126

rs2016126

MISSENSE

dbsnp.88:rs1542752

rs1542752

347741

MISSENSE

dbsnp.119:rs9911502

rs9911502

283989

tRNA splicing endonuclease, catalyzes removal of introns from precursor tRNA's. Frequent genotype, SIFT predicts it to be tolerated.

MISSENSE

dbsnp.89:rs1671036

rs1671036

NM_001015002.1

Protein is a homolog of a fly protein that plays a role in asymmetric cell division and cell migration, and whose KO causes lethal giant larvae. In human it interacts with aPKC complexes and is localized cortically in mitotic cells. May insure the correct organization and orientation of biolar spindles for normal cell division. OE inhibits tigh junctions formation. This SNP is a known natural variant, tolerated in SIFT, frequent genotype. NO additional SNP info in lit.One paper says than in contrast to the fly protein, gene is not a tumour suppressor gene.

MISSENSE

dbsnp.86:rs871443

NM_001005731.1

Integrin, receptor for laminins. Often associated with cancer but more in terms of invasiveness. Critical role in desmosomes of epithelial cells. Frequent genotype. SIFT predicts it to be damaging but only when using orthologues, and with low confidence.

MISSENSE

ACOX1 51 NM_007292.4 3726603 snp G C I M 17 71461134 311

RHBDF2 79651 NM_024599.3 3727085 snp G A P L 17 71986618 207

SEC14L1 rs673918 6397 NM_003003.2 3728833 snp A C T P 17 72702440 187

DNAH17 8632 NM_173628.2 3731163 snp T C T A 17 74015187 1506

AZI1 22994 NM_014984.2 3736949 snp T C T A 17 76788815 271

3737022 snp G C A G 17 76834818 830

BAHCC1 57597 3737250 snp G A A T uncharacterized protein 17 77023783 393

BAHCC1 57597 3737261 snp A G T A uncharacterized protein 17 77028901 1258

CCDC57 NM_198082.2 3738363 snp A G M T 17 77678921 832

dbsnp.86:rs1135640

rs1135640

The protein encoded by this gene is the first enzyme of the fatty acid beta-oxidation pathway, which catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs. Frequent genotype, SIFT says tolerated. Known as polymorphism.

MISSENSE

dbsnp.107:rs3744045

rs3744045

Rhomboid protease-like protein which has no protease activity but regulates the secretion of several ligands of the epidermal growth factor receptor. Indirectly activates the epidermal growth factor receptor signaling pathway and may thereby regulate sleep, cell survival, proliferation and migration (By similarity). Barely genotype info, SIFT says it's damaging but only when using homologues for the alignment, and the confidence is low. Uniprot says this is a known natural variant.

MISSENSE

dbsnp.83:rs673918

Possible role in intracellular transport system. Most frequent genotype by far, SIFT says tolerated. No extra lit.

MISSENSE

dbsnp.119:rs9896398

rs9896398

Dynein heavy chain, associated with axonemal dyneins.

MISSENSE

dbsnp.100:rs2466773

rs2466773

5' azacytidine induced, probable role in spermatogenesis.

MISSENSE

MGC15523

dbsnp.100:rs2725405

rs2725405

124565

NM_001037984.1

solute carrier family 38, member 10, putative NA-dependent aa/proton antiporter

MISSENSE

dbsnp.121:rs12952981

rs12952981

NM_001080519.1

MISSENSE

dbsnp.116:rs7213444

rs7213444

NM_001080519.1

MISSENSE

dbsnp.120:rs11077969

rs11077969

284001

coiled coil domain containing 57 - uncharacterized protein

MISSENSE

CCDC57 NM_198082.2 3738368 snp C T A T 17 77679674 776

CCDC57 NM_198082.2 3738369 snp C T D N 17 77679677 775

CCDC57 NM_198082.2 3738370 snp T C R G 17 77679683 773

METTL4 64863 NM_022840.3 3745935 snp C G V L probable methyltransferase 18 2529015 467

XM_292717.8 3763465 snp G A E K 18 12105508 391

CEP192 55125 NM_032142.2 3765258 snp C T L F 18 13059781 1104

C18orf45 85019 NM_032933.4 3772738 snp G A L F uncaracterized protein 18 19207717 130

CABYR 26256 NM_012189.2 3773835 snp T G S A 18 19990930 489

DSG3 1830 NM_001944.2 3784927 snp A G T A 18 27309954 911

DSG2 1829 NM_001943.2 3784956 snp A G I V 18 27358711 292

dbsnp.116:rs7406162

rs7406162

284001


MISSENSE

dbsnp.116:rs7406163

rs7406163

284001


MISSENSE

dbsnp.111:rs4625783

rs4625783

284001


MISSENSE

dbsnp.116:rs8084295

rs8084295

MISSENSE

DKFZp779B1634

dbsnp.111:rs4519391

rs4519391

342850

ankyrin repeat domain 62, uncharacterized protein

MISSENSE

dbsnp.116:rs6505780

rs6505780

centrosomal protein 192kDa. Required for mitotic centrosome and spindle assembly. Appears to be a major regulator of pericentriolar material recruitment, centrosome maturation, and centriole duplication. No OMIM record though. Known natural variant in Uniprot. TT is very frequent genotype. SIFT says tolerated. Literature says the status of this SNP is non-damaging.

MISSENSE

dbsnp.116:rs8099409

rs8099409

MISSENSE

dbsnp.86:rs1049683

rs1049683

calcium binding Tyr-phosphorylation regulated. Plays role in capacitation process of spermatozoa.

MISSENSE

dbsnp.88:rs1380866

rs1380866

desmoglein 3. TM glycoprotein of desmosomes in epithelial cells. Known natural variant. SIFT says tolerated.

MISSENSE

dbsnp.98:rs2230234

rs2230234

desmoglein 2. Also part of desmosomes in epithelial cells. Known natural variant, but genotype GG is very rare apparently. SIFT says tolerated however. Literature says this SNP is classified 'no known pathogenecity'.

MISSENSE

MEP1B rs616114 4225 NM_005925.2 3785806 snp C T P L 18 28051918 694

MOCOS rs623053 55034 NM_017947.2 3789849 snp C T T I 18 32033852 169

MOCOS rs540967 55034 NM_017947.2 3789850 snp A G S G see above 18 32033893 183

MOCOS rs623558 55034 NM_017947.2 3789851 snp A G H R see above 18 32034017 224

FHOD3 80206 NM_025135.2 3790630 snp G A V I 18 32578088 1150

MYO5B 4645 3808382 snp T C T A 18 45817296 125

C18orf24 3809213 snp G A V I 18 46162553 90

MAPK4 5596 NM_002747.3 3809772 snp G A V M 18 46444437 37

dbsnp.83:rs616114

meprin A, beta. Zinc metalloprotease highly expressed in kidney and leukocytes and certain cancer cells. Known natural variant in Uniprot. TT is rather rare as genotype. SIFT says tolerated. Lit gives nothing.

MISSENSE

dbsnp.83:rs623053

molybdenum cofactor sulfarase. Sulfates cofactor of xanthine DH and aldehyde oxidase. Known natural, non-disease associated SNP.

MISSENSE

dbsnp.83:rs540967

MISSENSE

dbsnp.83:rs623558

MISSENSE

dbsnp.100:rs2303510

rs2303510

formin homology 2 domain 3. Role in regulation of actin cytoskeleton. SNP is in FH2 domain. Genotype is not really frequent but there, SIFT says tolerated. Nothing in lit.

MISSENSE

dbsnp.92:rs1815930

rs1815930

NM_001080467.1

myosin VB. May be involved in vesicular trafficking as is associated with CART, essential for transferrin receptor recycling. Known natural variant.

MISSENSE

dbsnp.116:rs6507992

rs6507992

220134

NM_001039535.2

aka SKA1, spindle and kinetochore associated complex SU1. the SKA1 complex is essential for proper chromosome segregation of chromosomes. Known natural variant. By far most frequent genotype. SIFT says toelrated. Nothing relevatn in lit.

MISSENSE

dbsnp.107:rs3752087

rs3752087

Mitogen-activated protein kinase 4, phosphorylates MAP2 and may promote entry in the cell cycle. Known natural variant, SIFT says damaging in homologue alignment but with low confidence; frequent genotype.

MISSENSE

DCC 1630 NM_005215.2 3812182 snp T C F L 18 48121221 22

C18orf26 NM_173629.1 3816596 snp A C T P uncharacterized protein 18 50416305 188

ALPK2 NM_052947.3 3822064 snp C A A S 18 54353747 1550

ALPK2 NM_052947.3 3822066 snp G A P S 18 54354053 1448

ALPK2 NM_052947.3 3822072 snp A C L V 18 54355229 1056

ALPK2 NM_052947.3 3822074 snp A T N K 18 54355650 915

ALPK2 NM_052947.3 3822079 snp C T G S 18 54355970 809

ALPK2 NM_052947.3 3822080 snp A C H Q 18 54356241 718

5271 NM_198833.1 3831331 snp A G H R 18 59805442 358

dbsnp.119:rs9951523

rs9951523

detected in colorectal cancer. A netrin receptor; mediates axon attraction cytoplasmic tail interacts with Tyr kinases Src and FAK. Protein functions as a tumor supressor gene (often LOH) , frequently mutated in colorectal cancer and esophageal carcinoma. It also acts as a dependence receptor required for apoptosis induction. Known natural variant, CC is by far the most frequent genotype. SIFT says tolerated. There might however be something strange going on with the number of copies: this gene is just on the border of a CNV in Flp. A line has 3 copies, rest 2, except Flp: it has 2 but 2 breakpoints without any data.

MISSENSE

dbsnp.119:rs9947055

rs9947055

284254

MISSENSE

dbsnp.107:rs3809983

rs3809983

115701

alpha kinase 2, not well-characterized.

MISSENSE

dbsnp.107:rs3809982

rs3809982

115701


MISSENSE

dbsnp.107:rs3809976

rs3809976

115701


MISSENSE

dbsnp.111:rs4940404

rs4940404

115701


MISSENSE

dbsnp.107:rs3809970

rs3809970

115701


MISSENSE

dbsnp.120:rs12103986

rs12103986

115701


MISSENSE

SERPINB8

dbsnp.107:rs3826616

rs3826616

serpin peptidase inhibitor clade B member 8. HMW serin proteinase inhibitor. Known natural variant.

MISSENSE

DSEL 92126 NM_032160.2 3838175 snp G A P S 18 63330808 682

RTTN 25914 NM_173630.3 3843598 snp A C S A 18 66022322 125

CNDP2 55748 NM_018235.1 3852397 snp T C Y H 18 70327062 125

ZNF236 rs608433 7776 NM_007345.3 3856829 snp A G I V uncharacterized. 18 72740114 612

MUM1 84939 NM_032853.2 3867588 snp G A G R 19 1311574 219

AMH 268 NM_000479.3 3868989 snp G T S I 19 2200476 48

GNA15 rs310680 2769 NM_002068.2 3871003 snp A G Y C 19 3101237 146

dbsnp.100:rs2279269

rs2279269

dermatan sulfate epimerase-like. Uncharacterized.

MISSENSE

dbsnp.108:rs3911730

rs3911730

rotatin, involved in the genetic cascade governing left-right specification.

MISSENSE

dbsnp.100:rs2278161

rs2278161

cndp dipeptidase 2. non-specific dipeptidase. One isoform may play a role in hepatocellular carcinoma, but is exactly lacks that region of the protein where this SNP is in. Rare gnotype however, and interestingly SIFT predicts it to be damaging. The homologue alignment prediction is of low confidence however. no relevant lit.

MISSENSE

dbsnp.83:rs608433

MISSENSE

dbsnp.107:rs3826942

rs3826942

Melanoma-associated antigen mutated. Involved in the DNA damage response pathway by contributing to maintenance of chromosome architecture. Required for efficient DNA repair and cell survival following DNA damage. No OMIM record though. Most frequent genotype. SIFT says tolerated. no relevant lit on this mutation. copy number is 4 in all lines, except endoT where 3. Interestingly the locus where MUM1 is has LOH (see Joke SNP data) in lines T, S, SG and SGendoT, but it does not in A and Flp, and it fits because there are a few (synonymous) SNPs that are heterozygous in A and Flp but homo in the rest. No inactivating mutations though.

MISSENSE

dbsnp.119:rs10407022

rs10407022

anti-Mullerian hormone, TGFb gene mediating male sexual differentiation. Known natural variant.

MISSENSE

dbsnp.79:rs310680

G protein alpha 15. Known natural variant. Unknown role of protein.

MISSENSE

23217 NM_015174.1 3872216 snp C A V L 19 3782524 209

NM_133475.1 3872893 snp G A E K uncharacterized protein 19 4167909 584

rs353693 NM_133475.1 3872894 snp T G S A uncaracterized protein 19 4168206 683

STAP2 55620 NM_017720.2 3873107 snp C T D N 19 4284710 92

PTPRS 5802 NM_130854.2 3874539 snp A G C R 19 5165696 1418

EMR1 rs373533 2015 NM_001974.3 3877139 snp A C K Q 19 6870623 495

EMR1 rs461645 2015 NM_001974.3 3877140 snp A G I V see above 19 6870752 538

MUC16 94025 NM_024690.2 3881753 snp C G V L mucin 19 8822980 14465

MUC16 94025 NM_024690.2 3882008 snp T A K N see above 19 8948614 1399

COL5A3 50509 NM_015719.3 3884037 snp T C R G 19 9973345 321

DOCK6 57572 NM_020812.2 3885742 snp G A P L 19 11219798 249

KIAA1086

dbsnp.98:rs2240233

rs2240233

Zinc finger RNA binding. Uncharacterzied.

MISSENSE

ANKRD24

dbsnp.119:rs10413818

rs10413818

170961

MISSENSE

ANKRD24

dbsnp.79:rs353693

170961

MISSENSE

dbsnp.116:rs7247504

rs7247504

signal transducing adaptor famaliy member 2. Is the substrate of a breast tumour kinase - a Src-type non-receptor tyrosine kinase. Known natural non-disease-related variant. SIFT says tolerated.

MISSENSE

dbsnp.111:rs4807697

rs4807697

protein tyrosine phosphatase, receptor type S. Likely to play a role in cell-cell interactions and axon guidance, as indicated by mice studies. SNP is in Tyr phosphatasr domain 1, but is not thé active site residue. Genotype suggests this is the normal genotype, by far most frequent one. A allele has less than 0.5 percent frequency. Indeed, Cys (refseq) is noted as damaging in SIFT, but only with orthologues in the alignment.

MISSENSE

dbsnp.80:rs373533

C term of this protein is 7TM hormone-receptor-like, N term is mucin-like. Role unclear.

MISSENSE

dbsnp.80:rs461645

MISSENSE

dbsnp.86:rs1035442

rs1035442

MISSENSE

dbsnp.88:rs1596798

rs1596798

MISSENSE

dbsnp.100:rs2287803

rs2287803

alpha chain for the low-abundance fibrillar collagens. Known natural variant, not a mutation.

MISSENSE

dbsnp.121:rs12978266

rs12978266

dedicator of cytokinesis 6. Potential GEF. Known natural variant.

MISSENSE

MAN2B1 1/1 4125 NM_000528.2 3887553 snp G A T I 19 12633164 311

EMR3 84658 NM_032571.3 3890309 snp C T R Q 19 14613324 384

OR7C1 26664 NM_198944.1 3890629 snp C T V I OR protein, not relevant 19 14771572 125

OR1I1 3891535 snp C G P R idem 19 15059291 138

OR1I1 3891537 snp T C F L idem 19 15059506 210

PGLYRP2 rs892145 NM_052890.3 3892035 snp A T M K 19 15447671 269

PGLYRP2 rs733731 NM_052890.3 3892036 snp C T R Q see above 19 15448184 98

PGLYRP2 NM_052890.3 3892037 snp T C T A see above 19 15448344 45

CIB3 NM_054113.2 3894329 snp C T G E 19 16136654 138

CPAMD8 rs706761 27151 NM_015692.2 3895445 snp G A T I 19 16886291 1314

CPAMD8 27151 NM_015692.2 3895524 snp A G M T same as above. 19 16972296 311

NM_152363.3 3896047 snp T G L W uncharacterized protein. 19 17255123 172

dbsnp.86:rs1054487

rs1054487

aa311/1011 (processed in 3 peptides). Rel common genotype. Not one of the mutations related to alpha-mannosidosis. Lysosomal hydrolase that removes mannoses from mannosides after deglycosylation.

MISSENSE

{dbsnp.116:rs8102646;dbsnp.127:rs45508602}

rs8102646;dbsnp.127

same as EMR1, but role in inflammation.

MISSENSE

dbsnp.119:rs10415562

rs10415562

MISSENSE

dbsnp.116:rs8104843

rs8104843

126370

NM_001004713.1

MISSENSE

dbsnp.116:rs8108721

rs8108721

126370

NM_001004713.1

MISSENSE

dbsnp.86:rs892145

114770

peptidoglycan recognition protein. Known natural variant.

MISSENSE

dbsnp.86:rs733731

114770

MISSENSE

dbsnp.107:rs3813135

rs3813135

114770

MISSENSE

dbsnp.116:rs6512087

rs6512087

117286

calcium and integrin binding family member 3. Exact function unknown.

MISSENSE

dbsnp.86:rs706761

Part of complement protein family of alpha-2-macroglobuli and C3. frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.111:rs4808551

rs4808551

MISSENSE

ANKRD41

dbsnp.100:rs2363956

rs2363956

126549

MISSENSE

UNC13A 23025 3896797 snp A G L P 19 17607946 1121

ZNF708 7562 NM_021269.2 3902894 snp T C K E uncharacterized protein 19 21269270 112

ZNF708 rs547516 7562 NM_021269.2 3902911 snp G A A V uncharacterized protein 19 21283901 70

ZNF208 7757 NM_007153.2 3904918 snp A T L H uncharacterized protein 19 21945334 1164

ZNF91 rs403356 7644 NM_003430.2 3907170 snp C T A T uncharacterized protein 19 23336464 385

ZNF675 NM_138330.2 3907843 snp A G V A 19 23628984 196

ZNF675 NM_138330.2 3907844 snp A C L V same as above 19 23629204 123

rs565791 NM_152481.1 3923819 snp A G C R uncharacterized protein 19 40410945 159

rs892055 NM_170604.2 3928173 snp A G I T 19 43604603 17

PRX rs268671 57716 NM_181882.2 3930734 snp A G V A 19 45593453 881

dbsnp.111:rs4239634

rs4239634

NM_001080421.1

diacyglycerola nd phorbol ester receptor of unc13 family. May play role in vesicle priming in synapse. Genotype GG has an almost absolute frequency. L in refseq is predicted to be damaging but with low confidence and only with homolog alignment in SIFT.

MISSENSE

dbsnp.89:rs1781873

rs1781873

MISSENSE

dbsnp.83:rs547516

MISSENSE

dbsnp.100:rs2359812

rs2359812

MISSENSE

dbsnp.80:rs403356

MISSENSE

dbsnp.120:rs11671053

rs11671053

171392

ZNF with role in osteoclast differentiation

MISSENSE

dbsnp.111:rs4380159

rs4380159

171392

MISSENSE

TMEM162

dbsnp.83:rs565791

148109

MISSENSE

RASGRP4

dbsnp.86:rs892055

115727

ras guanyl releasing protein. Activates endogenous Ras in a cation-dependent manner, expression in myeloid lines was found to be correlated with elevated levels of activated Ras. May also play role in mast cell differentiation. SNP is known natural vairant, frequent genotype, SIFT says tolerated. I do not think it is mutated, but copy number is different in the different lines: 7 in Flp, 5 in A, 4 is T, S, Sg, 3 in EndoT. S, T and Sg also are LOH for this part of the chromosome.

MISSENSE

dbsnp.79:rs268671

periaxin, involved in peripheral nerve myelin upkeep.

MISSENSE

LTBP4 8425 NM_003573.2 3931036 snp A G T A 19 45809708 749

1087 NM_006890.2 3932880 snp A T F I 19 46882698 119

PSG2 5670 NM_031246.2 3934376 snp C G V L 19 48278503 19

ZNF235 9310 NM_004234.3 3936390 snp T G H P uncharacterized protein. 19 49484540 295

ZNF228 7771 NM_013380.3 3936428 snp C G E Q uncharacterized protein 19 49524831 439

ZNF229 7772 NM_014518.2 3936701 snp G A R C uncharacterized protein 19 49625786 336

ZNF229 7772 NM_014518.2 3936702 snp G A S F uncharacterized protein. 19 49626328 155

CARD8 1/1* 22900 NM_014959.1 3942705 snp A T C * 19 53429517 9

KCNA7 3743 NM_031886.2 3944506 snp A G M T 19 54265249 417

KCNA7 3743 NM_031886.2 3944508 snp G C P R 19 54265936 188

PIH1D1 rs13394 55011 NM_017916.1 3945222 snp C T V I uncharacterized protein. 19 54642109 223

dbsnp.86:rs1131620

rs1131620

latent TGFbeta binding protein. May play critical roles in controlling and directing the activity of TGFB1. frequent genotype. SIFT says tolerated. No other lit on this SNP.

MISSENSE

CEACAM7

dbsnp.116:rs8102488

rs8102488

carcinoembryonic antigen-related cell adhesion molecule. Uncharacterized.

MISSENSE

dbsnp.108:rs3887660

rs3887660

pregnancy-specific beta-&-glcoprotein, in fact member of the carcinoembryonic family (see above). Known varaint.

MISSENSE

dbsnp.96:rs2125579

rs2125579

MISSENSE

dbsnp.100:rs2722723

rs2722723

MISSENSE

dbsnp.120:rs12151338

rs12151338

MISSENSE

dbsnp.100:rs2571174

rs2571174

MISSENSE

dbsnp.94:rs2043211

rs2043211

Protein is component of the inflammasome, and plays role in apoptosis and NFkB mediated inflammation. The mutation causes premature stop of translation. Genotype is not very common, roughly 10% of world population, but gene function is only barely affected --> recently discovered new splice variants downstream that produce functional CARD8 protein.

NONSENSE

dbsnp.86:rs1017219

rs1017219

voltage-gated ion channel. Known natural variant, but rather rare genotype. SIFT says tolerated.

MISSENSE

dbsnp.89:rs1611775

rs1611775

see above, but more frequent genotype.

MISSENSE

dbsnp.52:rs13394

MISSENSE

PIH1D1 55011 NM_017916.1 3945235 snp C T G E uncharacterzied protein. 19 54646614 9

PIH1D1 55011 NM_017916.1 3945236 snp T G M L uncharacterized protein. 19 54646618 8

KLK4 9622 NM_004917.3 3947017 snp G T H Q 19 56103447 196

CD33 945 NM_001772.3 3947642 snp G A G R 19 56430728 303

3948010 snp T A L H uncharacterized protein 19 56676536 220

3948015 snp A G H R uncharacterized protein 19 56678358 377

ZNF614 80110 NM_025040.2 3949168 snp C T G R uncharacterized protein. 19 57212418 81

ZNF614 80110 NM_025040.2 3949172 snp G A T I uncharacterized protein 19 57213107 67

ZNF534 XM_496320.4 3950007 snp A C E A uncharacterized protein 19 57633429 314

ZNF578 rs161931 3950391 snp G A E K uncharacterized protein. 19 57706157 237

ZNF83 55769 3950673 snp C T S N uncharacterized protein 19 57809342 95

ZNF28 7576 NM_006969.2 3951395 snp A G M T uncharacterized protein. 19 57995338 470

dbsnp.100:rs2293013

rs2293013

MISSENSE

dbsnp.100:rs2293012

rs2293012

MISSENSE

dbsnp.100:rs2569527

rs2569527

kallikrein-related peptidase 4. Expressed in prostate. Defects in this gene cause enamel formation deficiencies. SIFT says tolerated. Known natural variant.

MISSENSE

dbsnp.126:rs35112940

rs35112940

putative adhesion molecule mediating sialic-acid binding to cells, preferentially alpha-2,6-linked SA. Induces apoptosis in acute myeloid leukemia in vitro. Althoug not many genotyped populations, seems very frequent. Knoxn natural variant, not a mutation. SIFT says tolerated.

MISSENSE

CEACAM18

dbsnp.116:rs8106673

rs8106673

729767

NM_001080405.1

MISSENSE

CEACAM18

dbsnp.119:rs10426247

rs10426247

729767

NM_001080405.1

MISSENSE

dbsnp.129:rs61574510

rs61574510

MISSENSE

dbsnp.119:rs9636139

rs9636139

MISSENSE

dbsnp.88:rs1366258

rs1366258

147658

MISSENSE

dbsnp.79:rs161931

147660

NM_001099694.1

MISSENSE

dbsnp.86:rs1056185

rs1056185

NM_001105551.1

MISSENSE

dbsnp.116:rs8107444

rs8107444

MISSENSE

ZNF816A 1/1 3951887 ins ACT S 19 58146287 184 INSERT

ZNF665 79788 NM_024733.3 3952394 snp T C H R uncharacterized protein. 19 58361084 156

ZNF761 3953366 snp T G I S uncharacterized protein. 19 58649937 67

ZNF761 3953367 snp G A V I uncharacterized protein 19 58650074 113

TMC4 rs641738 NM_144686.1 3954903 snp C T G E uncharacterized channel 19 59368574 16

LENG9 94059 NM_198988.1 3955723 snp C G R P uncharacterized protein 19 59665091 476

NLRP8 2/2 rs306457 NM_176811.2 3959287 snp G C * Y 19 61191090 1048

ZNF470 3960589 snp C T T I uncharacterized protein 19 61780861 417

ZNF543 NM_213598.1 3962231 snp A G Q R uncharacterized protein. 19 62530961 106

ZNF419 79744 3962576 snp A G I V uncharacterized protein. 19 62696742 290

A1BG rs893184 1 NM_130786.2 3964251 snp T C H R 19 63556290 51

dbsnp.126:rs33949217

rs33949217

125893

NM_001031665.1

unknown zinc finger-family protein. Insertion is in frame, and relatively frequent in population.

dbsnp.111:rs4801959

rs4801959

MISSENSE

dbsnp.100:rs2708743

rs2708743

388561

NM_001008401.2

MISSENSE

{dbsnp.92:rs1984432;dbsnp.127:rs41390249}

rs1984432;dbsnp.127

388561

NM_001008401.2

MISSENSE

dbsnp.83:rs641738

147798

MISSENSE

dbsnp.119:rs10423424

rs10423424

MISSENSE

dbsnp.79:rs306457

126205

protein plays role in activation of proinflammatory caspases. Mutation increases protein length by 10 AA(YAVQSSFSGA), of both isoforms. Relatively common genotype , but no evidence of correlation with any disease.

NONSTOP

dbsnp.111:rs4801177

rs4801177

388566

NM_001001668.3

MISSENSE

dbsnp.116:rs8100491

rs8100491

125919

MISSENSE

{dbsnp.96:rs2074077;dbsnp.129:rs61731277}

rs2074077;dbsnp.129

NM_001098495.1

MISSENSE

dbsnp.86:rs893184

alpha-1-B-Glycoprotein. Unknown function, but present in plasma.

MISSENSE

DEFB128 3964823 snp T A K N 20 116727 26

PSMF1 9491 NM_178578.2 3966631 snp T G F C 20 1047522 35

SIRPB1 10326 3967298 snp C G A P 20 1494910 145

TGM6 NM_198994.2 3968877 snp A G M V 20 2323261 57

ADAM33 80332 NM_025220.2 3970482 snp A G M T 20 3598233 763

BMP2 rs235768 650 NM_001200.2 3976718 snp A T R S 20 6707114 189

SPTLC3 rs243887 55304 NM_018327.2 3987550 snp T G L V 20 13001017 139

RRBP1 6238 3995150 snp C A R L 20 17544154 890

GINS1 9837 NM_021067.3 4006139 snp G A V I 20 25346789 96

SPAG4L NM_080675.3 4008949 snp C A E D 20 31054346 38

dbsnp.111:rs4813043

rs4813043

245939

NM_001037732.1

defensin beta 128. Potential antibacterial activity, by similarity, but nohting more is known.

MISSENSE

dbsnp.89:rs1803415

rs1803415

proteasome inhibitor subunit1. Most frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.100:rs2243603

rs2243603

NM_001083910.1

Negative regulator of receptor Tyr-kinase coupled signalling. Not damaging acc to SIFT, frequent genotype (most)

MISSENSE

dbsnp.96:rs2076405

rs2076405

343641

transglutaminase 6. catalyzes corss-linking of proteins and conjugation of polyamines to proteins, but by similarity, furthermore not yet tested. Known natural variant.

MISSENSE

dbsnp.100:rs2280091

rs2280091

ADAM metalloprotease. Implicated in asthma and bronchial hyperresponsiveness. Very rare genotype, but SIFT says tolerated. Cannot find anything of relevance in lit.

MISSENSE

dbsnp.79:rs235768

Bone Morphogenetic protein 2, part of TGFb family. Role in negative regulation of cell cycle. This SNP is in the propeptide, which is cleaved off for activation. Very frequent genotype.

MISSENSE

dbsnp.79:rs243887

serine palmitoyltransferase, third subunit. Catalyzed rate-limiting step of sphingolipid synthesis. Known natural variant, frequent genotype.

MISSENSE

dbsnp.86:rs1132274

rs1132274

NM_001042576.1

ribosome binding protein homolog 1. Probably mediates binding of ribosomes to ER. Rather rare genotype, but SIFT says tolerated.

MISSENSE

dbsnp.114:rs6076347

rs6076347

GINS complex plays an essential role in intitiation of DNA replication and progression of DNA replication forks. Essential for function. Known natural variant, rare genotype, SIFT says tolerated.

MISSENSE

dbsnp.86:rs1133358

rs1133358

140732

aka SUN5. Role in spermatogenesis, but no additional info on this gene.

MISSENSE

C20orf71 NM_178466.3 4009268 snp G A V I uncharacterized protein with BPI fold. 20 31276583 135

MYH7B 57644 NM_020884.2 4011522 snp A G K E slow-twitch type myosin. 20 33046991 1006

PLCG1 rs753381 5335 NM_002660.2 4018258 snp T C I T 20 39230878 812

WFDC3 NM_080614.1 4025035 snp G C H D 20 43851081 35

ZSWIM3 NM_080752.2 4025234 snp T C V A 20 43939379 258

ZNF335 63925 NM_022095.3 4025358 snp C G S T 20 44029613 293

MMP9 4318 NM_004994.2 4025405 snp G C R P 20 44075812 573

BCAS1 rs394732 8537 NM_003657.1 4038102 snp G T Q K 20 52108594 23

dbsnp.107:rs3818222

rs3818222

128861

MISSENSE

dbsnp.100:rs2425015

rs2425015

MISSENSE

dbsnp.86:rs753381

phospholipase C gamma 1. Role in actin reorganization and cell migration. Well-known natural variant. Very frequent genotype.

MISSENSE

dbsnp.114:rs6032538

rs6032538

140686

WAP four-disulfide core domain 3. protease inhibitor. No OMIM entry. Known natural variant, most frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.101:rs2903808

rs2903808

140831

znf with SWIM domain, uncharacterized.

MISSENSE

dbsnp.114:rs6032606

rs6032606

ZNF phosphorylated upon DNA damage by ATM/ATR probably. Enhances activation by ligand-boudn nuclear hormone receptors. Frequent genotype, SIFT says toleraed.

MISSENSE

dbsnp.100:rs2250889

rs2250889

matrix metalloprotease 9. Degrades type V and IV collagens. Role in tumour-associated tissue remodeling. SNP is in hemopexin-like domain 2. Known natural variant, most frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.80:rs394732

Breast Carcinoma Amplified 1. Unknown role, sometimes found highly expressed in breast cancer cell lines or breast tumours, but not consistently in all breast cancer cell lines. Candidate oncogene. Known natural variant, frequent genotype, SIFT says tolerated. Gene is in a region where there are 4 copies in A and T, and 3 in the other lines, though it does not exactly seems to fit the SNP-allelic array from Joke's pdf file.

MISSENSE

AURKA 6790 NM_003600.2 4042743 snp T C I V 20 54394869 56

C20orf86 rs584855 4046368 snp G A R C uncharacterized protein. 20 56227111 350

LAMA5 3911 NM_005560.3 4052893 snp T C K E 20 60338247 1366

LAMA5 3911 NM_005560.3 4052939 snp T C T A same as above. 20 60355037 400

NM_152757.1 4053302 snp T C I V uncharacterized protein 20 60553931 120

PRIC285 rs438363 85441 NM_033405.3 4055497 snp C T S N 20 61668791 218

RBM11 rs409782 54033 NM_144770.2 4063340 snp T G L V uncharacterized protein 21 14518642 1

dbsnp.86:rs1047972

rs1047972

aurora kinase A. Cell cycle-regulated kinase that appears to be involved in microtubule formation and/or stabilization at the spindle pole during chromosome segregation. May play a role in tumour formation and progression. Uniprot file mentions that centrosome amplification can occur when the cycles are uncoupled, and this amplification is associated with cancer and with an increase in the levels of chromosomal instability. AURKA can phosphorylate p53, leading to its UQ and proteasomal degradation. Lit shows that its role in chromosomal stability and relation to aneuploidy is well-established. Very well-studied protein, but unfortunately this SNP is not causal for a LOF. Genotype is very frequent, SIFT says tolerated;

MISSENSE

dbsnp.83:rs584855

140731

XM_001134442.2

MISSENSE

dbsnp.100:rs2427286

rs2427286

laminin alpha5. Major component of basement membranes. Known natural variant, CC is by far the most frequent genotype, refseq is odd one out here. SIFT says both are tolerated though.

MISSENSE

dbsnp.111:rs4925229

rs4925229

MISSENSE

C20orf200

dbsnp.108:rs3934574

rs3934574

253868

MISSENSE

dbsnp.80:rs438363

PPAR alpha interacting complex 285. A nuclear transcriptional coactivator for PPARalpha and gama, as well as a variety of other nuclear receptors. Known natural variant, very frequent genotype, sift says tolerated.

MISSENSE

dbsnp.80:rs409782

MISSENSE

N6AMT1 29104 NM_182749.2 4092513 snp T C K R 21 29172485 117

N6AMT1 29104 NM_182749.2 4092536 snp T C N D same as above. 21 29179438 33

rs198915 NM_181620.1 4095133 snp T A L H 21 30895386 25

GART rs8788 2618 NM_000819.3 4099808 snp C T V I 21 33818982 420

BRWD1 54014 NM_018963.3 4109249 snp A G L P 21 39493115 1698

RIPK4 54101 NM_020639.2 4114707 snp T C M V 21 42034425 665

PRDM15 63977 4114748 snp A G S P uncharacterized protein 21 42094551 1151

RRP1B 23076 NM_015056.2 4118738 snp T C L P uncharacterized protein 21 43931989 435

CCT8L2 NM_014406.4 4125614 snp A G W R 22 15452482 319

dbsnp.96:rs2205447

rs2205447

Interestingly, though called DNA methyltransferase, has been shown to actually be a protein methyltransferase. CC is by far the most frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.92:rs1997607

rs1997607

MISSENSE

KRTAP22-1

dbsnp.79:rs198915

337979

keratin-associated protein 22-1. important for hair shaft strength.

MISSENSE

dbsnp.52:rs8788

trifunctional polypeptide, with enzymatic functions required for de novo purine biosynthesis. Highly conserved in vertebrates. Known natural variant, indeed I is the only accepted AA here (V is damaging according to SIFT), and TT is by far most frequent genotype.

MISSENSE

dbsnp.86:rs1041439

rs1041439

Has bromo and WD domain. In mouse it encodes a gene with a polyQ-region that is a transcriptional activation domain, associates with SWI/SNF and probably involved in chromatin remodeling. Known natural varaint, GG is the most frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.107:rs3746891

rs3746891

Receptor-interacting Ser-Thr kinase 4, interacts with PKCdelta. Can activate NFkB and is required for keratinocyte differentiation. Proteolytically cleaved during Fas-induced apoptosis. CC is by far the most frequent genotype. SIFT says tolerated. No additional info on this SNP in the lit.

MISSENSE

dbsnp.108:rs3850706

rs3850706

NM_001040424.1

MISSENSE

dbsnp.119:rs9306160

rs9306160

MISSENSE

dbsnp.98:rs2236639

rs2236639

150160

possible molecular chaperone, but could be the product of a pseudogene too. Known natural varaint.

MISSENSE

GNB1L 54584 NM_053004.2 4130771 snp C T R H 22 18188768 36

ARVCF rs165815 421 NM_001670.1 4131081 snp C T R Q 22 18339472 905

ZNF280B NM_080764.2 4135361 snp T G E A uncharacterized protein 22 21172956 255

MYO18B 84700 NM_032608.5 4140871 snp G C W C 22 24496899 546

HPS4 89781 NM_152841.1 4142138 snp C A Q H 22 25183904 619

HPS4 89781 NM_152841.1 4142140 snp G A H Y same as above 22 25184440 600

HPS4 rs713998 89781 NM_152841.1 4142154 snp T C E G same as above 22 25192211 223

NEFH rs165602 4744 NM_021076.2 4146663 snp A C E A neurofilament heavy polypeptide. 22 28216042 804

PLA2G3 50487 NM_015715.3 4148930 snp A C S A 22 29866132 69

dbsnp.114:rs5748449

rs5748449

G protein beta 1-like. Is highly expressed in the heart and the region is deleted in DiGeorge syndrome and trisomic in der22 syndrome, and tetrasomic in cat-eye syndrome. Known natural variant, but very rare genotype. SIFT says tolerated though.

MISSENSE

dbsnp.79:rs165815

member of catenin family, role in cell adhesion. Deleted in velo-cardio-facial syndrome. Natural variant.

MISSENSE

dbsnp.98:rs2236729

rs2236729

140883

MISSENSE

dbsnp.108:rs3859866

rs3859866

myosin 18b, may be involved in control of tumour development and progession and mutations/deletions/hypermethylations in this gene are associated with lung cancer. Unfortunately, though the various mutations found in lung cancers have well been described, this one is a natural variant. Very frequent genotype, GG is almost not existing, and the W in refseq is predicted to be damaging by SIFT.

MISSENSE

dbsnp.92:rs1894704

rs1894704

Gene that appears to be important in organelle biogenesis, deletions cause Hermansky Pudlak syndrome where the symptoms result from defects in lysosomes, and melanosomes and platelet dense granules. Most frequent genotype. SIFT says tolerated.

MISSENSE

dbsnp.92:rs1894706

rs1894706

MISSENSE

dbsnp.86:rs713998

MISSENSE

dbsnp.79:rs165602

MISSENSE

dbsnp.98:rs2232176

rs2232176

phospholipase A2 group3. role in ciliogenesis. Known natural variant.

MISSENSE

SFI1 9814 4149499 snp T C Y H 22 30301257 321

APOL2 rs132760 23780 NM_030882.2 4157964 snp T C I V 22 34953676 244

APOL1 8542 NM_003661.2 4158032 snp G A E K 22 34991275 149

APOL1 rs136175 8542 NM_003661.2 4158034 snp G A M I see above 22 34991511 227

rs855791 NM_153609.2 4159437 snp A G V A 22 35792881 735

NM_153609.2 4159488 snp T C K E 22 35815669 252

TRIOBP 11078 4160835 snp T C W R 22 36460417 1376

9582 NM_004900.3 4162764 snp C A T K 22 37712024 145

MCHR1 rs133072 2847 NM_005297.3 4164824 snp A G N D 22 39405488 31

TSPO rs6971 706 NM_000714.4 4169273 snp A G T A 22 41888869 146

dbsnp.114:rs5753700

rs5753700

NM_001007467.1

protein with a role in the dynamic structure of centrosome-attached contractile fibers via its interaction with CETN2. CC is most frequent genotype, SIFT says tolerated.

MISSENSE

dbsnp.78:rs132760

cytoplasmic lipoprotein., may affect movement of lipids or binding of lipids to organelles. Known natural variant. Almost absolute genotype.

MISSENSE

dbsnp.98:rs2239785

rs2239785

role in lipid exchange throughout the body.

MISSENSE

dbsnp.78:rs136175

MISSENSE

TMPRSS6

dbsnp.86:rs855791

164656

serine proteinase attached to the cell surface. Required to sense iron deficiency. Known natural variant, frequent genotype. SIFT says tolerated.

MISSENSE

TMPRSS6

dbsnp.98:rs2235324

rs2235324

164656

see above for function. Genotype is not so frequent, but it is a known natural variant in Uniprot. SIFT says tolerated.

MISSENSE

dbsnp.116:rs8140958

rs8140958

NM_001039141.1

TRIO and F-actin binding protein. Known natural variant.

MISSENSE

APOBEC3B

dbsnp.114:rs5995649

rs5995649

it is though that this gene is an mRNA editing enzyme and may play a role in cell cycle control or cell growth. Known natural variant.

MISSENSE

dbsnp.78:rs133072

melanin-concentrating hormone receptor. SNP has been studied and found to make no functional difference.

MISSENSE

dbsnp.52:rs6971

translocator protein. Key factor in lfow of cholesterol into mitochondria to permit steroid hormone synthesis. May also play role in transport of heme and porphyrins. Known natural variant. Most frequent genotype. SIFT says the refseq Thr is damaging.

MISSENSE

PNPLA3 80339 NM_025225.2 4170717 snp A G K E 22 42673448 433

IL17REL 4184413 snp A G L P IL17-receptor E-like. Uncharacterized. 22 48777606 332

MAGEB3 4114 NM_002365.3 4220100 snp T C I T X 30164296 111

WASF4 NA rs723119 4234450 snp C T Q * untranscribed pseudogene X 47542989 42

WASF4 rs909713 4234452 snp T G V G see above X 47547915 220

SSX5 6758 NM_021015.3 4234861 snp C G E Q X 47939683 18

PAGE2 NM_207339.2 4239075 snp C G L V X 55133190 4

PAGE3 4239295 snp T C N D uncharacterized protein X 55306498 34

FOXR2 NM_198451.1 4239726 snp T C V A uncharacterized protein X 55667725 285

POF1B rs363774 79983 NM_024921.2 4263176 snp T A M L X 84449790 348

CPXCR1 53336 NM_033048.4 4268084 snp A C Y S uncharacterized protein X 87895078 2

ARL13A 4281805 snp G T M I uncharacterized protein X 1E+08 278

dbsnp.100:rs2294918

rs2294918

patatin-like phospholipase domain containing 3. Triacylglycerol lipase. Membrane bound, role in energy balance in adipocytes. Known natural variant, most frequent genotype, sift says tolerated.

MISSENSE

dbsnp.114:rs5771069

rs5771069

400935

NM_001001694.1

MISSENSE

dbsnp.96:rs2071309

rs2071309

melanoma-antigen family B 3.No clear functional role. This SNP is just a known natural variant though. Most frequent genotype. SIFT says toelrated.

MISSENSE

dbsnp.86:rs723119

644739

NM_001102604.1

NONSENSE

dbsnp.87:rs909713

644739

NM_001102604.1

MISSENSE

dbsnp.111:rs4824675

rs4824675

synovial sarcoma, X breakpoint 5. It is homologuous to SSX genes, often involved in a translocation t(X; 18) characteristically found in synovial sarcomas - but this gene isn't. No known function besides transcriptional regulation. Known natural variant.

MISSENSE

dbsnp.92:rs1845444

rs1845444

203569

P-antigen family, member 2 - uncharacterzied.

MISSENSE

dbsnp.111:rs4826381

rs4826381

139793

NM_001017931.1

MISSENSE

dbsnp.100:rs2375465

rs2375465

139628

MISSENSE

dbsnp.79:rs363774

premature ovarian failure 1B. Role unclear, but known to bind actin. Known natural variant.

MISSENSE

dbsnp.114:rs5940915

rs5940915

MISSENSE

dbsnp.108:rs3934462

rs3934462

392509

NM_001012990.2

MISSENSE

MORC4 79710 NM_024657.3 4286334 snp G A T I uncharacterized MORC-type ZNF. X 106086857 472

GPC4 2239 NM_001448.2 4311014 snp G A A V X 132265002 441

PNMA3 29944 NM_013364.4 4330925 snp T C V A X 151977197 376

IRAK1 3654 NM_001569.3 4332043 snp A G F S X 152937385 195

dbsnp.116:rs6622126

rs6622126

MISSENSE

dbsnp.86:rs1048369

rs1048369

glypican 4. cell surface proteoglycan that bears heparan sulfate. Known natural variant.

MISSENSE

dbsnp.116:rs6526155

rs6526155

paraneoplastic antigen MA3. Has homology to retroviral Gag proteins. Highly expressed in a range of tumours. This SNP has been recognized as a sequence error (the V).

MISSENSE

dbsnp.86:rs1059702

rs1059702

IL1-receptor associated kinase 1. Role in IL1-induced upregulation of NFkB. Well-studied protein. Frequent genotype. SIFT says tolerated. Known natural variant. Not involved in any functional role.

MISSENSE

rs67437266}

rs3734727}

42924;dbsnp.111

rs4645434}

rs63253663}

rs62873663}

rs17099476}

rs12912744}

rs2229659;dbsnp.130

rs74011346}

rs63019465}

rs45543439}

rs45508602}

rs41390249}

rs61731277}

a.chromos a.begin a.end a.type a.ref a.alt a.A_locus a.A_allele

HEK293

19 63571776 63571777 snp A G 16336247 G8 145071608 145071609 snp C T 9593592 T11 1083709 1083710 snp C G 11195164 G19 60363148 60363149 snp C T 16319955 T18 63716849 63716850 snp A C 15919495 C

3 164402022 164402023 snp C T 3783115 T14 100487947 100487948 del G 1406944316 1055843 1055847 del GGCA 1466751716 85148391 85148392 snp A T 15159665 T22 25392698 25392698 ins G 16954169 G

293T

5 140534372 140534373 snp G C 6045806 C7 117022290 117022291 snp T G 7803399 G

13 95440301 95440302 snp T A 12862629 A5 140539503 140539504 snp G A 6045844 A7 5973061 5973062 snp G C 7170587 C7 156161893 156161894 snp C G 8015477 G1 246291376 246291377 snp T C 1226575 C6 3209485 3209486 snp T C 6279445 C1 144961133 144961134 snp T C 687887 C

15 22885062 22885063 snp C T 13611605 T6 2967302 2967303 snp T C 6278065 C7 62390629 62390630 snp T C 7488637 C

293FTM

1 246045164 246045167 del AGG 18876853 155440980 155440984 del CAGT 68136826 167710042 167710043 snp C T 13133351 T4 54661675 54661676 snp T C 8082294 C

12 107480604 107480604 ins G 21729293 G13 23366328 23366329 snp A G 21957232 G

9 128211580 128211581 del T 18022568

293S

19 54249383 54249384 snp T C 25328216 C20 42178000 42178001 snp G C 25877857 C

5 140561403 140561404 snp C A 9556186 A10 127387427 127387428 snp A C 17034752 C14 56466102 56466106 del TTCT 2137690012 9355072 9355073 snp T C 18505874 C14 61191065 61191065 ins T 21418926 T19 7850348 7850349 del C 25021962

4 120547097 120547098 snp A G 7327371 G

293SG

10 47429195 47429196 snp A G 16339913 G17 263820 263821 snp A G 22813333 G

8 48968369 48968369 ins G 13736010 G19 7844306 7844306 ins G 24476003 G20 61186681 61186723 del CCTGGAGGCTCTGACG25391660

1 85516171 85516172 snp C A 574473 A16 33870000 33870001 snp T C 22319145 C19 56368496 56368496 ins A 24783451 A

293SGGD

18 58342407 58342408 snp G A 24124013 A4 88754808 88754809 snp C T 6797544 T7 6787574 6787575 snp T C 11631976 C1 246151086 246151087 snp T C 1779339 C

11 67545869 67545869 ins C 17841625 C

293SGGD

12 100943939 100943939 ins G 19424253 G6 31903927 31903928 snp T C 10552036 C

15 19003960 19003961 snp A G 21395988 G6 32904630 32904631 snp C A 10557788 A6 32904662 32904663 snp A G 10557790 G

12 11311641 11311642 snp G A 18523759 A10 38712149 38712150 snp A C 16287354 C10 81435118 81435119 snp A G 16625567 G

6 88164767 88164770 del GAT 110107041 147644857 147644866 del TCTAACCAG 908267

12 97403768 97403769 del A 1939417320 26137716 26137791 sub AAGCCCCCCAGGCCCC25242574 CAGGCCCC

7 39798929 39798930 snp T C 11967434 C8 39300896 39300896 ins T 13657797 T

a.A_allele a.A_totalS a.A_totalS a.A_refsco a.A_coveraa.A_refcona.A_cluste a.A_seque a.xRefG 118 93 -419 26 v dbsnp.116T 117 24 -367 19 v dbsnp.129G 113 113 -486 68 v dbsnp.116T 149 86 -365 19 v dbsnp.86:C 50 213 -423 23 v dbsnp.83:rs653115T 120 120 -267 18 v dbsnp.88:

21 113 -542 25 v dbsnp.12030 138 0 6 v dbsnp.126

T 26 187 -352 31 v dbsnp.116G 119 119 -3351 87 v dbsnp.130C 45 180 -520 28 v dbsnp.111G 34 176 -332 15 v dbsnp.86:A 27 121 -679 39 vA 51 351 -696 37 v dbsnp.123C 87 138 -184 2 v dbsnp.100G 122 122 -356 22 v dbsnp.100C 181 181 -377 16 v dbsnp.129C 43 268 -701 47 cl v dbsnp.111C 145 145 -646 86 v dbsnp.120T 30 142 -295 16 vC 54 296 -640 44 v dbsnp.92:C 45 125 -119 2 v dbsnp.83:

23 127 12 7 v dbsnp.12627 171 -925 12 v dbsnp.130

T 35 91 -144 2 v dbsnp.100C 117 117 -200 9 v dbsnp.86:G 35 82 -754 27 v dbsnp.120G 39 125 -406 14 v dbsnp.108

57 120 -1024 46 v dbsnp.130C 94 94 -424 23 v dbsnp.86:C 26 120 -128 8 vA 175 175 -435 12 v dbsnp.86:C 47 106 -288 18 v dbsnp.129:rs55833808;dbsnp.130:rs66933719;dbsnp.120:rs11455430

33 97 4 8 vC 99 99 -298 1 v dbsnp.120T 34 81 -855 22 v dbsnp.126

120 20 -814 16 v dbsnp.129G 77 77 -92 17 vG 76 76 -124 1 v dbsnp.100G 75 32 -339 8 v dbsnp.119G 50 141 -1041 38 v dbsnp.120G 41 121 -770 41 v dbsnp.129

53 123 97 58 v dbsnp.130:rs66910319A 42 112 -427 30 v dbsnp.107C 93 93 -208 933 cl vA 55 97 -938 21 v dbsnp.129A 116 116 -321 17 v dbsnp.116:rs7229802T 51 100 -293 9 vC 94 94 -721 11 v dbsnp.111C 22 107 -371 16 v dbsnp.120C 40 100 -634 23 v dbsnp.129

G 23 124 -454 7 v dbsnp.129C 20 179 -802 16 v dbsnp.125G 98 98 -65 0 v dbsnp.101A 103 47 -398 24 cl v dbsnp.79:G 31 189 -411 27 cl v dbsnp.79:A 38 91 -1186 21 v dbsnp.120C 34 135 -411 17 v dbsnp.102:rs3087759;dbsnp.130:rs72639555G 89 89 -64 0 v dbsnp.101:rs2983794

23 120 31 23 v dbsnp.130:rs72597035;dbsnp.126:rs3507013122 86 -24 1 v dbsnp.13041 120 -164 25 v dbsnp.130

CAGGCCCC 61 143 22 51 cl vC 35 107 -200 20 v dbsnp.121T 27 129 -635 12 v dbsnp.130

a.geneId a.mrnaAcc a.proteinA a.symbol a.orientati a.componea.componea.hasCodi a.impact116412 XM_37566XP_375665LOC11641 - CDS 2 Y COMPATIB5339 NM_20138NP_958786PLEC1 - CDS 30 Y COMPATIB4583 NM_00245NP_002448MUC2 + CDS 29 Y NO-CHANG7137 NM_00036NP_000354TNNI3 - TSS-UPST 0 Y UNKNOWN-

dbsnp.83:rs653115 0647109 XM_93012XP_935219LOC64710 - CDS 2 Y MISSENSE767578 NR_003194.1 SNORD114+ UTR 0 N UNKNOWN-146336 XR_040908.1 FLJ32252 - UTR 0 N UNKNOWN-64779 NM_02276NP_073601MTHFSD - TSS-UPST 0 Y UNKNOWN-440823 NR_003491.1 MIAT + UTR 2 N UNKNOWN-

56129 NM_01894NP_061763PCDHB7 + CDS 0 Y COMPATIB1080 NM_00049NP_000483CFTR + CDS 14 Y COMPATIB

55757 NM_02012NP_064506UGCGL2 - CDS 7 Y MISSENSE56128 NM_01912NP_061993PCDHB8 + CDS 0 Y MISSENSE

222967 NM_17356NP_775836RSPH10B - CDS 2 Y MISSENSE140545 NM_03093NP_112198RNF32 + CDS 8 Y MISSENSE284521 NM_17591NP_787107OR2L13 + INTRON 0 Y UNKNOWN-389362 XR_017905.1 C6orf86 + UTR 3 N UNKNOWN-728989 XM_00112XP_001129LOC72898 - CDS 3 Y COMPATIB

63968 NR_003106.1 PWCR1 + UTR 0 N UNKNOWN-401233 XR_040703.1 LOC40123 - UTR 2 N UNKNOWN-643955 NR_003952.1 LOC64395 - UTR 2 N UNKNOWN-284532 NM_00100NP_001001OR5AT1 - CDS 0 Y DELETE

26084 NM_01559NP_056410SGEF + CDS 11 Y FRAMESHI6953 NM_00461NP_004601TCP10 - CDS 4 Y MISSENSE

170825 NM_13326NP_573574GSX2 + CDS 0 Y NO-CHANG9733 NM_01470NP_055521SART3 - TSS-UPST 0 Y UNKNOWN-4285 NM_00593NP_005923MIPEP - TSS-UPST 0 Y UNKNOWN-

89853 NM_03344NP_258257FAM125B + INTRON 5 Y UNKNOWN-94027 NM_03314NP_149133CGB7 - CDS 2 Y COMPATIB57158 NM_02043NP_065166JPH2 - CDS 3 Y COMPATIB56125 NM_01893NP_061754PCDHB11 + CDS 0 Y MISSENSE

dbsnp.129:rs55833808;dbsnp.130:rs66933719;dbsnp.120:rs11455430 00

642846 XR_017754.2 LOC64284 + UTR 21 N UNKNOWN-400221 XM_37846XP_378462FLJ22447 + UTR3 2 Y UNKNOWN-

80164 XM_00171XP_001719FLJ22184 - TSS-UPST 0 Y UNKNOWN-100128460 XR_037866.1 LOC10012 - UTR 0 N UNKNOWN-

55747 NM_01823NP_060702FAM21B + CDS 9 Y MISSENSE400566 NM_00101NP_001013LOC40056 + CDS 1 Y MISSENSE

5591 NM_00108NP_001075PRKDC - CDS 30 Y NO-CHANG80164 XM_00171XP_001719FLJ22184 - INTRON 5 Y UNKNOWN-

dbsnp.130:rs66910319 08915 NM_00392NP_003912BCL10 - TSS-UPST 0 Y UNKNOWN-

649159 XR_041241.1 TOP - UTR 0 N UNKNOWN-284367 NR_002804.1 SIGLECP3 + UTR 3 N UNKNOWN-

dbsnp.116:rs7229802 01834 NM_01420NP_055023DSPP + CDS 4 Y COMPATIB

728194 NM_00109NP_001093LOC72819 + CDS 14 Y COMPATIB343172 NM_00100NP_001005OR2T8 + CDS 0 Y MISSENSE

221 NM_00069NP_000685ALDH3B1 + CDS 6 Y NO-CHANG

51019 NM_01605NP_057137CCDC53 - CDS 5 Y NO-CHANG3304 NM_00534NP_005337HSPA1B + CDS 0 Y NO-CHANG

727832 XR_037552.1 LOC72783 - UTR 2 N UNKNOWN-6891 NM_01883NP_061313TAP2 - INTRON 10 Y UNKNOWN-6891 NM_01883NP_061313TAP2 - INTRON 10 Y UNKNOWN-5544 NM_00624NP_006240PRB3 - CDS 3 Y MISSENSE

dbsnp.102:rs3087759;dbsnp.130:rs72639555 0dbsnp.101:rs2983794 0dbsnp.130:rs72597035;dbsnp.126:rs35070131 0

100132417 XR_039082.1 LOC10013 + UTR 5 N UNKNOWN-121456 XR_016411.1 LOC12145 - TSS-UPST 0 N UNKNOWN-284801 XM_37897XP_378973LOC28480 - TSS-UPST 0 Y UNKNOWN-349114 XR_040230.1 LOC34911 + UTR 3 N UNKNOWN-255926 NR_001448.1 ADAM5P + UTR 5 N UNKNOWN-

a.nucleoti a.proteinP a.annotat a.sampleS a.genomeRa.pfam a.knownGea.knownGea.knownGea.chainSelf1057 244 S S S CDSsilent Q96EG3 -uc002qsm.14604 1491 A A A CDSsilent NP_958786-uc003zab.1

12641 4204 P P P CDSsilent NP_00244 +uc001lsx. 10 0 CDSsilent Q8N9W5-4-uc002qjh. 10 0

282 94 V M V intron;RNA +uc003feg.2:intron4:2 0 RNA +uc001yis. 1

503 0 CDSFRAME -uc002cko.10 0

1496 0 RNA +uc003adb.1:exon3:11946 590 A A A CDSsilent Q9Y5E2 +uc003lit. 12693 853 T T T CDSsilent P13569 +uc003vjd.1:exon15:

927 285 N I N CDSsilent; NP_064506-uc001vmt.1:exon8:261890 568 G S G CDSMIS NP_06199 +uc003liu. 1

482 70 T S T CDSsilent NP_77583 -uc003sph. 11054 290 H Q H CDSsilent; Q9H0A6;Q+uc003wmo.1:exon9:2

0 0 intron;CDSQ8N349;Q +uc001ids. 1603 0 W R W intron;UTR;Q5JS55;N +uc003mvi.1:intron1:562 162 A A A intron -uc009wjd 1

1162 0 intron;intron;intron; +uc001yxh. 11952 0 1

240 0 UTR5 -uc003tsp. 1487 162 S S PFAM:PF00CDSDEL Q8NHC5 -uc001idm. 1

2388 741 SH TS SH CDSDELSPLNP_056410+uc003ezv.1:exon12:768 185 G E G CDSsilent NP_004601-uc003qvu. 1721 135 H H H intron;CDSNP_00619 +uc003haa. 1

0 0 UTR5;ESPLQ9H1K1-2;+uc001tnc. 10 0 CDSMIS ;B2RNN3; -uc001uoz. 10 0 PFAM:PF1 intron Q9H7P6;Q +uc004bqh.1:intron6

838 157 S S S intron;CDSP01233;NP-uc002pmc 12600 575 P P P CDSsilent Q9BR39 -uc002xli.1:exon4:431872 624 R S R CDSMIS Q9Y5F2 +uc003liy. 1

0 0 RNA;intron +uc001lil.2:exon5:190 0 UTR3 +uc001xcr.1:exon4:75

2530 0 RNA +uc001qvp 11193 0 intron +uc001xfp.2:intron3

0 0 11381 0 downstream;upstrea +uc003icx. 1

759 253 T A T CDSMIS Q5SNT6 +uc009xni. 1886 290 T A T CDSsilent; NP_001013+uc002frh. 1

3786 1243 L L F CDSFRAMENP_008835-uc003xqi.1:exon32:00 0 RNA -uc002mip. 10 0 RNAEND +uc002yec.1:exon4:0-0 0 intron +uc001dla.1:intron2:3 0 1

2066 0 UTR3 ;Q8IW38; +uc002pvy. 10 0 CDSMIS;R Q9C0B9; +uc002lip. 1

2090 656 S S S CDSsilent A8MUI0 +uc003hqu.1:exon5:81971 566 S S S CDSsilent; B2RXJ0;NP+uc003sqw. 1

144 48 W R W PFAM:PF00CDSMIS A6NH00 +uc001idr. 1976 300 GR GR GV RNA;CDSF ;NP_00068+uc001omx 1

601 147 P P Q PFAM:PF1 ESPLICE;R NP_057137-uc001tiy.2:intron6:0425 73 I I I CDSMIS P08107 +uc003nxk 1435 0 upstream +uc001ytm 1

0 0 intron;UT Q9UP03;Q -uc003ocb. 10 0 intron;CDSQ9UP03;Q -uc003ocb. 1

719 227 P S P intron NP_002714-uc001qzf. 10 0 RNA -uc009xmd 10 0 intron A6NNL0-2 +uc009xsc 10 0 RNA +uc003plt.1:exon3:88

1268 0 UTR3 NP_00112 +uc009wkx 10 0 UTR3 -uc001tff.1:exon4:120 0 RNAEND -uc002wvk. 1

1692 0 RNA +uc003thf. 1398 0 RNA +uc010lws.1:exon4:53

a.cytoBan a.dgv a.genomic a.homopola.homopol a.1000gCE a.1000gCH a.1000gYRIa.snp130_q13.43 1 0.942 0.925 0.881 rs7255489q24.3 1 0.425 0.083 - rs5564658p15.5 1 0.800 - 0.983 rs7944723q13.42 0.992 1.000 1.000 rs890872q22.1 0.983 1.000 0.992 rs653115q26.1 1 0.658 0.850 0.576 rs1492171q32.31 - - - rs1071387p13.3 1 - - - -q24.1 1 0.658 0.400 0.339 rs7197427q12.1 - - - -q31.3 1 1 - - - rs4912601q31.2 0.442 0.358 0.763 rs1042077q32.1 - - - -q31.3 1 1 - - - rs1784449p22.1 1 1 - - - rs2711191q36.3 0.45 0.45 0.525 rs2302147q44 1 - - - rs5589392p25.2 0.883 0.675 0.203 rs4959786q21.1 1 1 0.308 0.067 0.119 rs1158559q11.2 1 - - - -p25.2 - - - rs1963161q11.21 1 1 - - - rs574717q44 1 - - - rs3597923q25.2 - - - rs7168499q27 1 1 C 6 - - - rs2345794q12 0.633 0.833 0.356 rs1132998q23.3 - - - -q12.12 1 1 - - 0.169 rs4067961q33.3 - - - rs3544597q13.33 1 1 - - - rs1059308q13.12 0.092 - 0.203 -q31.3 1 1 - - - rs799833;q26.13 0.85 0.867 0.831 rs5583380q23.1 1 - - - -p13.31 1 1 - - - rs1077151q23.1 - - - rs3436712p13.2 1 - - - -q26 1 1 0.208 - - -q11.22 1 1 - - - rs2669647p13.3 1 - - - rs9891763q11.21 1 - - - rs1141151p13.2 - - - -q13.33 1 - - - -p22.3 1 - - - rs3768233p11.2 1 1 - - - -q13.33 - - - -q21.33 1 0.783 0.733 0.669 rs7229802q22.1 0.208 0.15 0.008 -p22.1 1 1 - - - rs4724762q44 1 - - - rs1120456q13.2 1 1 - - - -

q23.2 - - - -p21.32 1 1 - - - rs2849194q11.2 1 1 - - - rs2934040p21.32 0.3 0.358 0.136 rs241449p21.32 0.3 0.358 0.229 rs241448p13.2 1 0.967 0.733 0.559 rs1105420p11.21 1 - - - rs3087759q22.3 1 1 - - - rs2983794q15 1 - - - -q21.1 1 1 - - - -q23.1 - - - rs6768186p11.1 1 1 C 11 - - - -p14.1 1 1 - - - rs1323693p11.23 1 - - - rs7258036

a.snp130_fa.fannot_i a.genomena.g_combinb.annovar b.locus_anb.fannot_i c.fannot_i c.sift_scor0 3964281 1 0 exonic ZNF837 39642810 2269953 1 0 exonic PLEC 22699530.404166 2622561 1 0 exonic MUC2 2622561 2622561 0.160 3957750 1 0 exonic C19orf51 39577500 3838964 1 0 ncRNA_exoLOC64354 38389640.389007 961881 1 0 ncRNA_exoLOC64710 9618810 3352560 1 0 ncRNA_exoSNORD114 3352560- 3482548 1 0 ncRNA_exoLOC14633 34825480 3609036 1 0 ncRNA_exoFLJ30679 3609036- 4142493 1 0 ncRNA_exoMIAT 4142493

0 1455855 1 0 exonic PCDHB7 14558550.499949 1975297 1 0 exonic CFTR 1975297 1975297 0.78

- 3190586 1 0 exonic UGGT2 31905860 1455863 1 0 exonic PCDHB8 1455863 1455863 0.060 1806121 1 0 exonic RSPH10B, 1806121

0.499974 2037639 1 0 exonic RNF32 2037639 2037639 0.410 346907 1 0 exonic OR2L3 346907

0.491567 1523127 1 0 exonic PSMG4 15231270.21444 185437 1 0 ncRNA_exoLOC72898 185437

- 3372855 1 0 ncRNA_exoSNORD116 33728550 1522662 1 0 ncRNA_exoLOC40123 15226620 1900553 1 0 ncRNA_exoLOC64395 19005530 346458 1 0 exonic OR14A16 3464580 950005 1 0 exonic ARHGEF26 950005

0.2822 1786233 1 0 exonic TCP10 17862330.360004 1080618 1 0 exonic GSX2 1080618 1080618 0.12

- 3010532 1 0 exonic ISCU 30105320 3065508 1 0 exonic C1QTNF9B 3065508 3065508 0.260 2433121 1 0 ncRNA_exoNRON 2433121

0.451754 3944462 1 0 exonic CGB7 3944462- 4022531 1 0 exonic JPH2 4022531

0 1455912 1 0 exonic PCDHB11 14559120 2606245 1 0 ncRNA_exoLOC28303 2606245

- 3285308 1 0 ncRNA_exoOTX2OS1 32853080 2860193 1 0 ncRNA_exoLOC64284 28601930 3292381 1 0 ncRNA_exoFLJ22447 3292381

- 3879827 1 0 ncRNA_exoLOC38849 3879827- 1157503 1 0 ncRNA_exoFLJ14186 1157503

0 2515624 1 0 exonic FAM21B 25156240 3617850 1 0 exonic C17orf97 36178500 2134541 1 0 exonic PRKDC 2134541

- 3879822 1 0 exonic;spli FLJ22184; 3879822- 4054448 1 0 ncRNA_exoLOC63930 4054448

0 126736 1 0 ncRNA_exoLOC64662 126736- 3538054 1 0 ncRNA_exoLINC00273 3538054- 3947603 1 0 ncRNA_exoSIGLECP3 3947603

0.40521 3829342 1 0 exonic ZCCHC2 3829342- 1123352 1 0 exonic DSPP 1123352

0 1807825 1 0 exonic RSPH10B, 1807825 1807825 0.210 346681 1 0 exonic OR2T8 346681

- 2737615 1 0 exonic ALDH3B1 2737615

- 3000400 1 0 exonic CCDC53 30004000.156157 1573346 1 0 exonic HSPA1B 1573346

0 3365300 1 0 exonic GOLGA6L6 33653000.491942 1573998 1 0 exonic TAP2 15739980.415121 1573999 1 0 exonic TAP2 1573999 1573999 0.860.365103 2865809 1 0 intronic PRB3 2865809 2865809 0.08

0 2508996 1 0 ncRNA_exoSEPT7L 2508996 2508996 0.970 2554997 1 0 ncRNA_exoLOC65062 2554997

- 1667746 1 0 ncRNA_exoC6orf164 1667746- 188552 1 0 ncRNA_exoFCGR1C 188552

0 2995961 1 0 ncRNA_exoLOC64377 2995961- 4006708 1 0 ncRNA_exoLOC28480 4006708

0 1867398 1 0 ncRNA_exoLINC00265 18673980 2125521 1 0 ncRNA_exoADAM5P 2125521

Full name/Notes/RemSplice variantsSilent SNPSilent SNP

mucin 2, o Silent SNPhypotheticSNP in 3' UTRhypothetical proteinhypotheti CG: A: Homo, others: no call; RTG: A, T: homo, S, SGendoT: like refseq, others (G, Flp) no call

hypothetical proteinhypotheticSNP in 3' UTRmyocardial CG: other no calls; RTG: all homo inserting G 2 nt downstream. Misalignment CG, not unique for A, but novel common to all 6. Illumina: 5 2nt downstream, 2 identical to this SNP.

Silent SNPSilent SNP

UDP-glucoseOthers: no -Others also Homo or Hetero(as called by RTG, no calls CG): low coverage region: T: 27 reads: 26A,1G; A:27 reads: 24A, 3G; Flp: 15 reads: 14A, 1G; S: 12 reads: 12A, 0G; SG: 13 reads: 12A, 1G; SGendoT: 27 reads: 26A,1G.

radial spo RTG: no SNP, CG: others no call. T: 20 reads:100%C; A:39 reads: 51% C, 49% G; Flp, SG: no reads; S: 7 reads: 100%G, SGendoT: 3 reads: 100% G. CG: others no call, RTG: A, S, T: homo, SG: Hetero; SGendoT, Flp: no call. A: 4 reads, all G, Illumina 4 reads G. Flp, S: no reads; SG: 10 reads: 1 C, 9 G; Sgendo T: 2 reads, both G; T: 13 reads: 100% G.

olfactory r CG: others no call, RTG: A,T: homo; S, SGendoT,Flp: hetero, SG: no callothers: no iso 1 is affected, other 2 variants not.

phosphodieCG: others no call, RTG: all homo (RTG is right)

HIV-1 Tat specific factor 1 pseudogene zinc finger protein 479 pseudogene olfactory receptor, family 14, subfamily A, member 16.Rho guaninOthers: no call at this SNP and A, SG, SGT, T: del GTCA 2 nt upstream for this SNP S and Flp: no call.t-complex others hetero?, so probably not unique, low coverage region: Others: no call, for A (47 reads:47% C, 53% T), S (38 reads: 37% C, 63% T): probably Hetero ((Flp: low coverage region: 10) T(1 of 9 are T)GS homeobNot unique, low coverage region: others: no call (A: 3 reads: 100% C; S: 3 reads: 100% C; T: 6 reads: 100% C; Flp: 8 reads: 100%)iron-sulfur Others: no CDS variant 2 (aa 25), 3'UTR splice variant 1 C1q and tuOthers no c-non-proteinOthers: HeNACGB7, ChorNot unique to S, no calls in other lines realignment looks the same.Silent mutation.JPH2, Junc Probably not unique to S, Snp is in a CpG island, with shallow coverage in general. CG called everything as a no call, except in S line.Silent mutationPCDHB11, PNot unique to S, no calls in other lines, realignment looks the same. Missense R to S.Not in a geNot unique to S. Due to a stretch of C's and a missense A to C base some hassle with the calling. Mutation present in all linesThe mutatioNot unique to S. It's a 4 bp deletion that's homozygous in the S lineage, since this line is LOH in Chr 14. It's HET in Flp, T and A. LOC642846.Not unique to S. It's a no call in all other lines, but the realignment files look the same, seems to be a homozygous snp in all lines. It's a T to C (L21P). Not in a geNot unique to S. It's an insertion of a T base in a stretch of 4 T's. The same mutation is present in all other lines, but called differently.LOC388499,Not unique to S. It's a deletion of a single C in a CC context. The same mutation is present in all other lines. It's a frameshift mutation.Not in a geNot unique to S. It's a Homozygous A to G in all lines. According to refseq it's not in a gene.WASH complNot unique to SG. No calls in the other lines, but the realignments look the same. Shallow realignment coverage.C17orf97, Not unique to SG. No calls in the other lines, but the realignments look the same. It's homozygous in all lines. A to G (T281A) of C17orf97, an uncharacterized protein.PRKDC the Not unique to SG. It's a snp according to refseq, but actually the "mutant" sequence is the WT, that gives the correct protein sequence!Not a geneNot unique to SG. It's a G insertion at a stretch of 2 G's and differently called in SG. It's not in a gene according to refseq.Not a geneNot unique to SG. It's in a tandem repeat region, so miscalled. Homozygous and present in all lines. It's not in a gene.BCL10 promNot unique to SG. It's a 2bp deletion at the edge of a stretch of A's. No call in other lines, but realignment file points to the same mutation. It's just before the very beginning of the 5' UTR of the BCL10 gene,and doesn't change anything to the annotated sequence. Might have a promotor effect??Not in a g Not unique to SG. It's a snp that has some dubious reads, might be homozygous in SG, but not sure. Other lines show comparable results at the same base but give a no call. It's not in a gene according to refseq.SIGLEC3, PuNot unique to SG. It's an insertion of an extra A, mapped either before or after an already present A. It's at the endo of the 3' UTR of the SIGLEC3 gene. ZCCHC2, ZiNot unique to SGendoT. Shallow realignment coverage causes no calls in other lines, probably because it's in a CpG island. It's a homozygous G to A, silent mutation in the first exon of ZCCHC2.DSPP, DentiNot unique to SGendoT. This is a C to T snp in all lines. It's not clear whether it's HOM or HET due to low realignment coverage, but the same mutant is seen in all lines, and called as a no call. It causes a silent mutation in exon 5 of DSPP. RSPH10B2, Not unique to SGendoT, a clear homozygous mutation in all lines. T to C, silent S in the RSPH10B2 gene.olfactory Not unique to SGendoT, seems to be HET snp. In all lines. T to C, W49R. It's in an olfactory receptor: OR2T8.ALDH3B1, wNot unique to SGendoT, an insertion of C before or after an existing C causes miscalling. The 1bp insertion is present in all lines, and homozygous, it cuases a frameshift mutation.

small nucleolar RNA, C/D box 114-2

protocadherin beta 8. Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain

ring finger protein 32. May play a role in sperm formation.

proteasome (prosome, macropain) assembly chaperone 4. Chaperone protein which promotes assembly of the 20S proteasome.

small nucleolar RNA, C/D box 116-21

CCDC53, WANot unique to SGendoT, an insertion of G before or after an existing G causes miscalling. This 1 bp insertion is present in all lines and homozygous. It causes a framshift mutation in CCDC53 at V147. Actually, this framshift mutation "restores" the wild type protein sequence, because the reference sequence prematurely terminates at Q148.HSPA1B, HeNot unique to SGendoT. The same realignment pattern of heterozygous A and G is seen in the other lines, but results in no calls there. It's a silent I74 in HSPA1B exon 1.GOLGA6L6, Not unique to SGendoT. Snp caller seems to make a mistake here, since the only available read from the realignment states that the sequence is refseq, and there is another read that is of low quality. There is a HET snp in the other lines, that is called as a no call. It's a silent mutation.TAP2, AntigNot unique 1 of 2TAP2, AntigNot unique 1 of 2PRB3, BasicNot unique to SGendoT. It seems to be a HOM snp in all lines, G to A and it's in an intron.CDC10L, unNot unique to SGendoT. This seems to be a HET snp in all lines. It's a A to C in the 3' UTR.LOC650623 Not unique to SGendoT. This seems to be a HOM snp A to G in the 5' UTR of LOC650623 of all 6 lines.C6orf164, iNot unique to SGendoT. The other lines have a deletion around the same position that results in an identical mutation (3bp deletion). The mutation is in the 3' UTR.FCGR1C is Not unique to SGendoT. The other lines have the same 9 bp deletion, but it's a no call. Reason?? It's in the 3' UTR of FCGR1C. No gene inNot unique to SGendoT. It's a 1bp deletion (A) in a stretch of 12 A's, mapped to the beginning or the ending of the stretch. It's present in all lines. No gene inNot unique to SGendoT. This mutation is inside a CpG island and in a very high coverage region (at least 500x raw coverage) This indicates that it might be a repeat sequence. It's not in a gene according to refseq.LOC349114 Not unique in SGendoT. It's a snp present in all lines, HET in 293A and 293T and HOM in the others. It's in the last exon. According to refseq, no coding exons.ADAM5P, PuNot unique in SGendoT. It's an insertion of a T base before or after an existing T. The mutation is in exon 5, but refseq has only non coding exons annotated. The status of the protein in Uniprot is "existence uncertain.

CG: other no calls; RTG: all homo inserting G 2 nt downstream. Misalignment CG, not unique for A, but novel common to all 6. Illumina: 5 2nt downstream, 2 identical to this SNP.

Others also Homo or Hetero(as called by RTG, no calls CG): low coverage region: T: 27 reads: 26A,1G; A:27 reads: 24A, 3G; Flp: 15 reads: 14A, 1G; S: 12 reads: 12A, 0G; SG: 13 reads: 12A, 1G; SGendoT: 27 reads: 26A,1G.RTG: no SNP, CG: others no call. T: 20 reads:100%C; A:39 reads: 51% C, 49% G; Flp, SG: no reads; S: 7 reads: 100%G, SGendoT: 3 reads: 100% G. CG: others no call, RTG: A, S, T: homo, SG: Hetero; SGendoT, Flp: no call. A: 4 reads, all G, Illumina 4 reads G. Flp, S: no reads; SG: 10 reads: 1 C, 9 G; Sgendo T: 2 reads, both G; T: 13 reads: 100% G.

Others: no call at this SNP and A, SG, SGT, T: del GTCA 2 nt upstream for this SNP S and Flp: no call.others hetero?, so probably not unique, low coverage region: Others: no call, for A (47 reads:47% C, 53% T), S (38 reads: 37% C, 63% T): probably Hetero ((Flp: low coverage region: 10) T(1 of 9 are T)Not unique, low coverage region: others: no call (A: 3 reads: 100% C; S: 3 reads: 100% C; T: 6 reads: 100% C; Flp: 8 reads: 100%)

Probably not unique to S, Snp is in a CpG island, with shallow coverage in general. CG called everything as a no call, except in S line.Silent mutation

Not unique to S. Due to a stretch of C's and a missense A to C base some hassle with the calling. Mutation present in all linesNot unique to S. It's a 4 bp deletion that's homozygous in the S lineage, since this line is LOH in Chr 14. It's HET in Flp, T and A. Not unique to S. It's a no call in all other lines, but the realignment files look the same, seems to be a homozygous snp in all lines. It's a T to C (L21P). Not unique to S. It's an insertion of a T base in a stretch of 4 T's. The same mutation is present in all other lines, but called differently.Not unique to S. It's a deletion of a single C in a CC context. The same mutation is present in all other lines. It's a frameshift mutation.

Not unique to SG. No calls in the other lines, but the realignments look the same. Shallow realignment coverage.Not unique to SG. No calls in the other lines, but the realignments look the same. It's homozygous in all lines. A to G (T281A) of C17orf97, an uncharacterized protein.Not unique to SG. It's a snp according to refseq, but actually the "mutant" sequence is the WT, that gives the correct protein sequence!Not unique to SG. It's a G insertion at a stretch of 2 G's and differently called in SG. It's not in a gene according to refseq.Not unique to SG. It's in a tandem repeat region, so miscalled. Homozygous and present in all lines. It's not in a gene.Not unique to SG. It's a 2bp deletion at the edge of a stretch of A's. No call in other lines, but realignment file points to the same mutation. It's just before the very beginning of the 5' UTR of the BCL10 gene,and doesn't change anything to the annotated sequence. Might have a promotor effect??Not unique to SG. It's a snp that has some dubious reads, might be homozygous in SG, but not sure. Other lines show comparable results at the same base but give a no call. It's not in a gene according to refseq.Not unique to SG. It's an insertion of an extra A, mapped either before or after an already present A. It's at the endo of the 3' UTR of the SIGLEC3 gene. Not unique to SGendoT. Shallow realignment coverage causes no calls in other lines, probably because it's in a CpG island. It's a homozygous G to A, silent mutation in the first exon of ZCCHC2.Not unique to SGendoT. This is a C to T snp in all lines. It's not clear whether it's HOM or HET due to low realignment coverage, but the same mutant is seen in all lines, and called as a no call. It causes a silent mutation in exon 5 of DSPP. Not unique to SGendoT, a clear homozygous mutation in all lines. T to C, silent S in the RSPH10B2 gene.Not unique to SGendoT, seems to be HET snp. In all lines. T to C, W49R. It's in an olfactory receptor: OR2T8.Not unique to SGendoT, an insertion of C before or after an existing C causes miscalling. The 1bp insertion is present in all lines, and homozygous, it cuases a frameshift mutation.

Not unique to SGendoT, an insertion of G before or after an existing G causes miscalling. This 1 bp insertion is present in all lines and homozygous. It causes a framshift mutation in CCDC53 at V147. Actually, this framshift mutation "restores" the wild type protein sequence, because the reference sequence prematurely terminates at Q148.Not unique to SGendoT. The same realignment pattern of heterozygous A and G is seen in the other lines, but results in no calls there. It's a silent I74 in HSPA1B exon 1.Not unique to SGendoT. Snp caller seems to make a mistake here, since the only available read from the realignment states that the sequence is refseq, and there is another read that is of low quality. There is a HET snp in the other lines, that is called as a no call. It's a silent mutation.

Not unique to SGendoT. This seems to be a HOM snp A to G in the 5' UTR of LOC650623 of all 6 lines.Not unique to SGendoT. The other lines have a deletion around the same position that results in an identical mutation (3bp deletion). The mutation is in the 3' UTR.Not unique to SGendoT. The other lines have the same 9 bp deletion, but it's a no call. Reason?? It's in the 3' UTR of FCGR1C. Not unique to SGendoT. It's a 1bp deletion (A) in a stretch of 12 A's, mapped to the beginning or the ending of the stretch. It's present in all lines. Not unique to SGendoT. This mutation is inside a CpG island and in a very high coverage region (at least 500x raw coverage) This indicates that it might be a repeat sequence. It's not in a gene according to refseq.Not unique in SGendoT. It's a snp present in all lines, HET in 293A and 293T and HOM in the others. It's in the last exon. According to refseq, no coding exons.Not unique in SGendoT. It's an insertion of a T base before or after an existing T. The mutation is in exon 5, but refseq has only non coding exons annotated. The status of the protein in Uniprot is "existence uncertain.

Others also Homo or Hetero(as called by RTG, no calls CG): low coverage region: T: 27 reads: 26A,1G; A:27 reads: 24A, 3G; Flp: 15 reads: 14A, 1G; S: 12 reads: 12A, 0G; SG: 13 reads: 12A, 1G; SGendoT: 27 reads: 26A,1G.

Not unique to SG. It's a 2bp deletion at the edge of a stretch of A's. No call in other lines, but realignment file points to the same mutation. It's just before the very beginning of the 5' UTR of the BCL10 gene,and doesn't change anything to the annotated sequence. Might have a promotor effect??Not unique to SG. It's a snp that has some dubious reads, might be homozygous in SG, but not sure. Other lines show comparable results at the same base but give a no call. It's not in a gene according to refseq.

Not unique to SGendoT. This is a C to T snp in all lines. It's not clear whether it's HOM or HET due to low realignment coverage, but the same mutant is seen in all lines, and called as a no call. It causes a silent mutation in exon 5 of DSPP.

Not unique to SGendoT, an insertion of G before or after an existing G causes miscalling. This 1 bp insertion is present in all lines and homozygous. It causes a framshift mutation in CCDC53 at V147. Actually, this framshift mutation "restores" the wild type protein sequence, because the reference sequence prematurely terminates at Q148.

Not unique to SGendoT. Snp caller seems to make a mistake here, since the only available read from the realignment states that the sequence is refseq, and there is another read that is of low quality. There is a HET snp in the other lines, that is called as a no call. It's a silent mutation.

Not unique to SGendoT. This mutation is inside a CpG island and in a very high coverage region (at least 500x raw coverage) This indicates that it might be a repeat sequence. It's not in a gene according to refseq.

Not unique in SGendoT. It's an insertion of a T base before or after an existing T. The mutation is in exon 5, but refseq has only non coding exons annotated. The status of the protein in Uniprot is "existence uncertain.

Not unique to SGendoT, an insertion of G before or after an existing G causes miscalling. This 1 bp insertion is present in all lines and homozygous. It causes a framshift mutation in CCDC53 at V147. Actually, this framshift mutation "restores" the wild type protein sequence, because the reference sequence prematurely terminates at Q148.

Symbol Name

AKT2 v-akt murine thymoma viral oncogene homolog 2APC adenomatous polyposis of the colon gene

homozygous in all lines, but dbSNP says its a non-pathogenic allele, though it is flanked by two regions often mutated in cancer. Unclear.ASXL1 additional sex combs like 1

No noted relation to cancer (not in omim/cosmic), though in an exon where quite a few mutations are. However, genotype in world population is almost 100%.ATM ataxia telangiectasia mutated

Reference and HEK genomes say K, but cosmic data says one cancer was detected with a N>K change. SNP not in dbSNP, so unclear whether this is a common variant or not, and whether or not related to cancer.Different from refseq genome. Heterozygous in all lines, this heterogenous genotype is rather rare (so is the A allele) or at least not frequent. This missense has been detected 9 times in breast cancers but zygosity is unknown (I suspect homo). Reports say tDifferent from refseq genome but not in cosmic as known mutation. Homozygous in all lines (no call in Flp but realignment suggest also homoz). This genotype is almost the exclusive genotype, so refseq was an exception here. According to SIFT both aa are

ATRX alpha thalassemia/mental retardation syndrome X-linkedDifferent from refseq genome but not in cosmic as known mutation. Heterozygous in all lines. Relatively common genotype.SIFT says both are tolerated.Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Interestingly, both the heterozygous A/G genotype as the G/G homozygous genotype are very rare (GG not even visible in dbSNP). Also dbSNP says allele is probably pathog

BCL6 B-cell CLL/lymphoma 6Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Heterozygous genotype is relatively frequent. SIFT prediction tolerated, polyphen says benign.

BHD folliculin, Birt-Hogg-Dube syndromeDifferent from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Heterozygous genotype rather frequent, and AA is at end of protein (343aa). SIFT says tolerated, polyphen does not know this sequence (?)

BLM Bloom SyndromeDifferent from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. The T allele is very rare, so heterozygous genotype is rather rare, homozygous TT almost inexistent, suggesting a mutation. No OMIM record for this one, SIFT SAYS LEDifferent from refseq but not in cosmic. Heterozygous in A,T, SG, SGEndoT (no call in others). Genotype not really frequent. SIFT says tolerated.

BRCA1 familial breast/ovarian cancer gene 1Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. Genotype quite common. SIFT says damaging but confidence is very low. Unclear effect, one sample with cancer had this mutation.Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. Marked as a common polymorphism in UniProt. Genotype rather rare but there.Different from Refseq, only the deletion of this whole K codon is marked in cosmic. According to Uniprot this is a well-known common polymorphism.Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. GG genotype is not really frequent but present. Also marked in UniProt as common polymorphism, not cancer associated.

BRCA2 familial breast/ovarian cancer gene 2Different from refseq but not in cosmic as cancer mutation. Heterozygous in A, SG,SGenodT, T but no call in Flp and S. For Flp because there has not been a realignment, for S its unclear because there is realignment data and it's clearly heterozygous. And raw coverage is OKDifferent from refseq but not in cosmic as cancer mutation. Homozygous in all lines except SG and T, but either because of low coverage or uncertainty of base, I think its homo in all. Also, it appears that the refseqs Val is actually the exception, and this alle

CCNE1 cyclin E1EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene hom

very frequent genotype, heterozygous in Flp, S, SG, SGendoT and no realignment for T, low coverage in A. Arg to Lys not drastic change, I consider this not likely to be important.ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma deriv

Heterozygous in all, well-known natural variant with frequent genotype. This allele has been associated with relatively higher risk of lung cancer in non-smoker and non-drinkers subgroups in a Korean population.ERCC4 excision repair cross-complementing rodent repair deficiency, complementation group

Heterozygous in A, Flp, T only. Interestingly, the G allele (refseq) has almost an absolute frequency, resulting in a very high GG genotype frequency, with rare AG genotype. AA almost undetected. Not present in comsic as cancer mutation. According to SIFT thiERCC5 excision repair cross-complementing rodent repair deficiency, complementation gro

Homozygous in all lines. This is an example where refseq has the 'odd' genotype: CC is almost the exclusive genotype found in all sequences in dbSNP, GG never. Sift says tolerated. No disease association found.Interestingly similar to above. Homozygous in all, refseq is odd one out with the very rare GG phenotype. Nothing known about effect. SIFT says tolerated.Clear C/G heterozygosity in A, SG, SGendoT. S does not have enough coverage in the realignment (no sight of this C allele on 4 reads), T has no realignment at all, and FlpIn is heterozygous but with 3 alleles: G (refseq), C (like SG etc), but also 8% of rea

FANCA Fanconi anemia, complementation group AHeterozygous in A, FlpIn, T. Both this heterozygous genotype as the TT are frequent genotypes. Common polymorphism as stated in Uniprot, not related to FA.

FANCC Fanconi anemia, complementation group CHeterozygous in S and SG (other lines: no realignment). Not in dbSNP, unclear effect.

FBXW7 F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)

FHIT fragile histidine triad geneIKZF1 IKAROS family zinc finger 1JUN jun oncogeneLCP1 lymphocyte cytosolic protein 1 (L-plastin)MADH4 (SMAD4) Homolog of Drosophila Mothers Against Decapentaplegic 4 geneMDM4 Mdm4 p53 binding protein homologMECT1 (CRTC1) mucoepidermoid translocated 1MITF microphthalmia-associated transcription factorMYC v-myc myelocytomatosis viral oncogene homolog (avian)MYCL1 v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)NF1 neurofibromatosis type 1 geneNFIB nuclear factor I/BPAX5 paired box gene 5 (B-cell lineage specific activator protein)PAX8 paired box gene 8

This mutation causes the loss of a splice acceptor, but the only known tumor cuasing mutation with this gene is a fusion gene PAX8/PPARG1. There is no sign for this. PMS2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae)

HOM missense, not known whether this mutation causes cancer. The G/G allele present in our lines is the allele that occurs in most of the human population.HET missense (CG Snp caller seems to be inconclusive) not known whether this mutation causes cancer. The T/C allele in our lines doesn't occur often in the human population, mostly C/C.HET missense I54V in A, S and Flp, not in others. Snp not known in dbsn or COSMIC. Mutation in 1 of 2 isoforms.Only in Flp line, probably a HET mutations. It's known, but no known relation with pathology. K413R or silent.Only in SGendoT, not known in COSMIC or dbSNP. It's Heterozygous. L454SOnly in T, A and SGendoT, Heterozygous novel. K465SHeterozygous, only in T. Low frequency genotype. Not known to be related with disease.Heterozygous, only in A and T. Seems to be also present in SG according to realignment. This exact mutation is novel, but another one is known in dbSNP. It seems to be coupled to the position 5993127 mutation, 2 bases downstream. Not known whether itHET, only in A. May be present in other lines looking at the realignment files. D599NHET in all lines. Known in dbSNP, no frequency data available. Not known to be related with any disease. G857A

PTEN phosphatase and tensin homolog geneRAB5EP (RABEP1) rabaptin, RAB GTPase binding effector protein 1 (RABPT5)

Problematic sequencing in first exon due to CpG island. There is a 26 bp deletion, overlapping with the splice acceptor site of exon 18. This means the junction of exon 17 and 18 is probably impaired. The impact of this is not clear since the last part of exon 17 and completely exon 18 are 3' UTR. The rs56107242

RB1 retinoblastoma geneNO reads in last part of first exon !!! GC rich part…

RECQL4 RecQ protein-like 4NO (good) sequence in 1st and 2nd exon, but in CpG island.S92P missense mutation, homozygous. Snp is known and the allele in our lines (C) occurs much more often than the refseq one (T). R1005Q missense. HOM is S lineage and HET in others. According to Snp Array data, this is due to LOH in S lineage. Genome diploid at this locus for all lines, except T. The most occurring allele in the human population is G/G or A/G, few A/A. In the S lineage

RET ret proto-oncogene No sequencing data first exon, in CpG island.Very low coverage at exon 11, harboring a mutationt site important for cancer and no realignment triggered.

SETD2 SET domain containing 2No sequencing data first exon, in CpG island.Het G-->T, P1962L in exon 12.

SOCS1SOCS1 lies almost completely in a CpG island, with the consequence there is very little to no coverage in most of the single coding exon.In general there seems to be a bad realignment… Not much to say about possible mutations here…

suppressor of cytokine signaling 1

SRGAP3 SLIT-ROBO Rho GTPase activating protein 3TCF1 transcription factor 1, hepatic (HNF1) symbol: HNF1A

There is a homozygous S574G mutation of our lines vs refseq. In this case, refseq is again the "disease causing" sequence. No further mutations.TP53 tumor protein p53

This is a heterozygous snp only present in 293T leading to a nonsynonymous change: R280S. The mutation is known in COSMIC. The mutation is in the E4F1 interacting domain and the affected residue has an important function in DNA binding by p53. ZygositThis is a heterozygous snp in all lines, in 4 of 7 isoforms of p53. P72R. According to Cosmic, the R is the WT allele instead of P. The snp is known (rs1042522). Both GG, GC and CC alleles occur in the population.

TSC1 tuberous sclerosis 1 geneHeterozygous missense present in all lines, HOM in Flp. In all 3 splice variants. M322T. In he human population, the Met genotype is the most frequent one. The mutation is not known to be related to disease.

VHL von Hippel-Lindau syndrome geneProbably a HET mutation of L128H. It's not clear in which lines it's present, because of a very low realignment coverage. Most probable in T, not confirmed in others. It's known in the COSMIC database from a clear cell renal carcinoma (1 sample only).

WRN Werner syndrome (RECQL2)HET L1074F mutation in all lines. Not known to be associated with disease and both alleles occur at a high frequency in the known

XPC xeroderma pigmentosum, complementation group CThree frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.This HOM mutation is not known to be related to disease. No frequency data available. A472RHET mutation certainly present in A, Flp, T and SGendoT. No or almost no realignment data in S and SG. It's not a rare snp.

GeneID Cancer Syndrome

208 yes ovarian, pancreatic E Dom324 yes yes colorectal colorectal Adenomatous polyposis coli; E, M, O Rec

homozygous in all lines, but dbSNP says its a non-pathogenic allele, though it is flanked by two regions often mutated in cancer. Unclear.171023 yes MDS, CMML L Rec

No noted relation to cancer (not in omim/cosmic), though in an exon where quite a few mutations are. However, genotype in world population is almost 100%.472 yes yes T-PLL leukemia, Ataxia-telangiectasia L, O Rec

Reference and HEK genomes say K, but cosmic data says one cancer was detected with a N>K change. SNP not in dbSNP, so unclear whether this is a common variant or not, and whether or not related to cancer.Different from refseq genome. Heterozygous in all lines, this heterogenous genotype is rather rare (so is the A allele) or at least not frequent. This missense has been detected 9 times in breast cancers but zygosity is unknown (I suspect homo). Reports say tDifferent from refseq genome but not in cosmic as known mutation. Homozygous in all lines (no call in Flp but realignment suggest also homoz). This genotype is almost the exclusive genotype, so refseq was an exception here. According to SIFT both aa are

546 yes Pancreatic neuroendocrine tumors E RecDifferent from refseq genome but not in cosmic as known mutation. Heterozygous in all lines. Relatively common genotype.SIFT says both are tolerated.Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Interestingly, both the heterozygous A/G genotype as the G/G homozygous genotype are very rare (GG not even visible in dbSNP). Also dbSNP says allele is probably pathog

604 yes NHL, CLL L DomDifferent from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Heterozygous genotype is relatively frequent. SIFT prediction tolerated, polyphen says benign.

201163 yes renal, fibr Birt-Hogg-Dube syndrome E, M Rec?Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Heterozygous genotype rather frequent, and AA is at end of protein (343aa). SIFT says tolerated, polyphen does not know this sequence (?)

641 yes leukemia, Bloom Syndrome L, E RecDifferent from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. The T allele is very rare, so heterozygous genotype is rather rare, homozygous TT almost inexistent, suggesting a mutation. No OMIM record for this one, SIFT SAYS LEDifferent from refseq but not in cosmic. Heterozygous in A,T, SG, SGEndoT (no call in others). Genotype not really frequent. SIFT says tolerated.

672 yes yes ovarian breast, ov Hereditary breast/ovarian c E RecDifferent from refseq but not in cosmic as cancer mutation. Homozygous in all lines. Genotype quite common. SIFT says damaging but confidence is very low. Unclear effect, one sample with cancer had this mutation.Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. Marked as a common polymorphism in UniProt. Genotype rather rare but there.Different from Refseq, only the deletion of this whole K codon is marked in cosmic. According to Uniprot this is a well-known common polymorphism.Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. GG genotype is not really frequent but present. Also marked in UniProt as common polymorphism, not cancer associated.

675 yes yes breast, ov breast, ov Hereditary breast/ovarian c L, E RecDifferent from refseq but not in cosmic as cancer mutation. Heterozygous in A, SG,SGenodT, T but no call in Flp and S. For Flp because there has not been a realignment, for S its unclear because there is realignment data and it's clearly heterozygous. And raw coverage is OKDifferent from refseq but not in cosmic as cancer mutation. Homozygous in all lines except SG and T, but either because of low coverage or uncertainty of base, I think its homo in all. Also, it appears that the refseqs Val is actually the exception, and this alle

898 yes serous ovarian E Dom1956 yes yes glioma, N NSCLC Familial lung cancer E, O Dom

very frequent genotype, heterozygous in Flp, S, SG, SGendoT and no realignment for T, low coverage in A. Arg to Lys not drastic change, I consider this not likely to be important.2064 yes breast, ovarian, other tumour types, NSCLC, gastri E Dom

Heterozygous in all, well-known natural variant with frequent genotype. This allele has been associated with relatively higher risk of lung cancer in non-smoker and non-drinkers subgroups in a Korean population.2072 yes skin basal Xeroderma pigmentosum (F)E Rec

Heterozygous in A, Flp, T only. Interestingly, the G allele (refseq) has almost an absolute frequency, resulting in a very high GG genotype frequency, with rare AG genotype. AA almost undetected. Not present in comsic as cancer mutation. According to SIFT thi2073 yes skin basal Xeroderma pigmentosum (G)E Rec

Homozygous in all lines. This is an example where refseq has the 'odd' genotype: CC is almost the exclusive genotype found in all sequences in dbSNP, GG never. Sift says tolerated. No disease association found.Interestingly similar to above. Homozygous in all, refseq is odd one out with the very rare GG phenotype. Nothing known about effect. SIFT says tolerated.Clear C/G heterozygosity in A, SG, SGendoT. S does not have enough coverage in the realignment (no sight of this C allele on 4 reads), T has no realignment at all, and FlpIn is heterozygous but with 3 alleles: G (refseq), C (like SG etc), but also 8% of rea

2175 yes AML, leuk Fanconi anaemia A L RecHeterozygous in A, FlpIn, T. Both this heterozygous genotype as the TT are frequent genotypes. Common polymorphism as stated in Uniprot, not related to FA.

2176 yes AML, leuk Fanconi anaemia C L Rec

55294 yes colorectal, endometrial, T-ALL E, L HAPLOINSU

Cancer Somatic Mut

Cancer Germline Mut

Tumour Types (Somatic Mutations)

Tumour Types (Germline Mutations)

Tissue Type

Cancer Molecular Genetics

2272 yes pleomorphic salivary gland adenoma E Dom10320 yes ALL L Rec?

3725 yes sarcoma M Dom3936 yes NHL L Dom4089 yes yes colorectal,gastrointesJuvenile polyposis E Rec4194 yes GBM, bladder, retinoblastoma M Dom

94159 yes salivary gland mucoepidermoid E Dom4286 yes melanoma E Dom4609 yes Burkitt lymphoma, amplified in other cancers, B-CL, E Dom4610 yes small cell lung E Dom4763 yes yes neurofibroneurofibroNeurofibromatosis type 1 O Rec4781 yes adenoid cystic carcinoma, lipoma E Dom5079 yes NHL, ALL, B-ALL L Dom7849 yes follicular thyroid E Dom

This mutation causes the loss of a splice acceptor, but the only known tumor cuasing mutation with this gene is a fusion gene PAX8/PPARG1. There is no sign for this. 5395 yes colorectal Hereditary non-polyposis col E Rec

HOM missense, not known whether this mutation causes cancer. The G/G allele present in our lines is the allele that occurs in most of the human population.HET missense (CG Snp caller seems to be inconclusive) not known whether this mutation causes cancer. The T/C allele in our lines doesn't occur often in the human population, mostly C/C.HET missense I54V in A, S and Flp, not in others. Snp not known in dbsn or COSMIC. Mutation in 1 of 2 isoforms.Only in Flp line, probably a HET mutations. It's known, but no known relation with pathology. K413R or silent.

Heterozygous, only in T. Low frequency genotype. Not known to be related with disease.Heterozygous, only in A and T. Seems to be also present in SG according to realignment. This exact mutation is novel, but another one is known in dbSNP. It seems to be coupled to the position 5993127 mutation, 2 bases downstream. Not known whether it

HET in all lines. Known in dbSNP, no frequency data available. Not known to be related with any disease. G857A5728 yes yes glioma, p harmartomaCowden Syndrome, BannayanL, E, M, O Rec9135 yes CMML L Dom

There is a 26 bp deletion, overlapping with the splice acceptor site of exon 18. This means the junction of exon 17 and 18 is probably impaired. The impact of this is not clear since the last part of exon 17 and completely exon 18 are 3' UTR. The rs561072425925 yes yes retinoblas retinoblas Familial retinoblastoma L, E, M, O Rec

9401 yes osteosarcoRothmund-Thompson Syndr M Rec

S92P missense mutation, homozygous. Snp is known and the allele in our lines (C) occurs much more often than the refseq one (T). R1005Q missense. HOM is S lineage and HET in others. According to Snp Array data, this is due to LOH in S lineage. Genome diploid at this locus for all lines, except T. The most occurring allele in the human population is G/G or A/G, few A/A. In the S lineage

5979 yes yes medullary medullary Multiple endocrine neoplasi E, O Dom

Very low coverage at exon 11, harboring a mutationt site important for cancer and no realignment triggered.29072 yes clear cell renal carcinoma E Rec

yes Hodgkin Lymphoma, PMBL L RecSOCS1 lies almost completely in a CpG island, with the consequence there is very little to no coverage in most of the single coding exon.In general there seems to be a bad realignment… Not much to say about possible mutations here…

8651

9901 yes pilocytic astrocytoma M Dom6927 yes yes hepatic ad hepatic ad Familial Hepatic Adenoma E Rec

There is a homozygous S574G mutation of our lines vs refseq. In this case, refseq is again the "disease causing" sequence. No further mutations.7157 yes yes breast, co breast, sa Li-Fraumeni syndrome L, E, M, O Rec

This is a heterozygous snp only present in 293T leading to a nonsynonymous change: R280S. The mutation is known in COSMIC. The mutation is in the E4F1 interacting domain and the affected residue has an important function in DNA binding by p53. ZygositThis is a heterozygous snp in all lines, in 4 of 7 isoforms of p53. P72R. According to Cosmic, the R is the WT allele instead of P. The snp is known (rs1042522). Both GG, GC and CC alleles occur in the population.

7248 yes hamartoma,Tuberous sclerosis 1 E, O RecHeterozygous missense present in all lines, HOM in Flp. In all 3 splice variants. M322T. In he human population, the Met genotype is the most frequent one. The mutation is not known to be related to disease.

7428 yes yes renal, he renal, he von Hippel-Lindau syndromeE, M, O RecProbably a HET mutation of L128H. It's not clear in which lines it's present, because of a very low realignment coverage. Most probable in T, not confirmed in others. It's known in the COSMIC database from a clear cell renal carcinoma (1 sample only).

7486 yes osteosarc Werner Syndrome L, E, M, O RecHET L1074F mutation in all lines. Not known to be associated with disease and both alleles occur at a high frequency in the known

7508 yes skin basal Xeroderma pigmentosum (C)E RecThree frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.This HOM mutation is not known to be related to disease. No frequency data available. A472RHET mutation certainly present in A, Flp, T and SGendoT. No or almost no realignment data in S and SG. It's not a rare snp.

Chr Chr Band Chr Pos (xxxxx)

A 19 19q13.1-q13.2 D, Mis, N, F, S 5 5q21

chr5:112204655 mis T>AF, N, Mis 20 20q11.1

chr20:30486663 mis T>CD, Mis, N, F, S 11 11q22.3

Reference and HEK genomes say K, but cosmic data says one cancer was detected with a N>K change. SNP not in dbSNP, so unclear whether this is a common variant or not, and whether or not related to cancer. chr11:107632276mis C>GDifferent from refseq genome. Heterozygous in all lines, this heterogenous genotype is rather rare (so is the A allele) or at least not frequent. This missense has been detected 9 times in breast cancers but zygosity is unknown (I suspect homo). Reports say t chr11:107680672mis G>ADifferent from refseq genome but not in cosmic as known mutation. Homozygous in all lines (no call in Flp but realignment suggest also homoz). This genotype is almost the exclusive genotype, so refseq was an exception here. According to SIFT both aa are chr11:107688379mis A>G

Mis, F, N ATR-X (alp yes X Xq21.1 chrX:76824619mis C>G

Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Interestingly, both the heterozygous A/G genotype as the G/G homozygous genotype are very rare (GG not even visible in dbSNP). Also dbSNP says allele is probably pathogchrX:76742766 mis A>GT, Mis IG loci, ZNFN1A1, LCP1, PIM1, 3 3q27

chr3:188928905 mis G>AMis. N, F 17 17p11.2

Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. Heterozygous genotype rather frequent, and AA is at end of protein (343aa). SIFT says tolerated, polyphen does not know this sequence (?) chr17:17065540 mis G>AMis, N, F 15 15q26.1

Different from refseq but not in cosmic as cancer mutation. Heterozygous in all lines. The T allele is very rare, so heterozygous genotype is rather rare, homozygous TT almost inexistent, suggesting a mutation. No OMIM record for this one, SIFT SAYS LE chr15:89127130 mis C>Tchr15:89155525 mis G>A

D, Mis, N, F, S 17 17q21Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. Genotype quite common. SIFT says damaging but confidence is very low. Unclear effect, one sample with cancer had this mutation. chr17:38498517 mis C>T

chr17:38498006 mis A>Gchr17:38497577 mis A>G

Different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. GG genotype is not really frequent but present. Also marked in UniProt as common polymorphism, not cancer associated. chr17:38476627 mis A>GD, Mis, N, F, S 13 13q12 chr13:31812592

Different from refseq but not in cosmic as cancer mutation. Heterozygous in A, SG,SGenodT, T but no call in Flp and S. For Flp because there has not been a realignment, for S its unclear because there is realignment data and it's clearly heterozygous. And raw coverage is OK mis G>TDifferent from refseq but not in cosmic as cancer mutation. Homozygous in all lines except SG and T, but either because of low coverage or uncertainty of base, I think its homo in all. Also, it appears that the refseqs Val is actually the exception, and this alle chr13:31827387 mis T>C

A 19 19q12A, O, Mis 7 7p12.3-p12.1

chr7:55196798 mis G>AA, Mis, O 17 17q21.1

Heterozygous in all, well-known natural variant with frequent genotype. This allele has been associated with relatively higher risk of lung cancer in non-smoker and non-drinkers subgroups in a Korean population. chr17:35137563 mis C>GMis, N, F 16 16p13.3-p13.13

Heterozygous in A, Flp, T only. Interestingly, the G allele (refseq) has almost an absolute frequency, resulting in a very high GG genotype frequency, with rare AG genotype. AA almost undetected. Not present in comsic as cancer mutation. According to SIFT thichr16:13936534 mis G>AMis, N, F 13 13q33

Homozygous in all lines. This is an example where refseq has the 'odd' genotype: CC is almost the exclusive genotype found in all sequences in dbSNP, GG never. Sift says tolerated. No disease association found. chr13:102325851mis G>Cchr13:102325970mis G>C

Clear C/G heterozygosity in A, SG, SGendoT. S does not have enough coverage in the realignment (no sight of this C allele on 4 reads), T has no realignment at all, and FlpIn is heterozygous but with 3 alleles: G (refseq), C (like SG etc), but also 8% of rea chr13:102326008mis G>C or AD, Mis, N, F, S 16 16q24.3

chr16:88376981 mis G>AD, Mis, N, F, S 9 9q22.3

chr9:96974267 mis A>GMis, N, D, F 4 4q31.3 none present

Mutation Type

Translocation Partner

Other Syndrome/Disease

Other Germline Mut

SNP type (mis, del, amp, trans..)

SNP nt change (A>G)

T HMGA2 3 3p14.2 none presentD 7 7p12.2 none presentA 1 1p32-p31T BCL6 13 13q14.1-q14.3 D, Mis, N, F 18 18q21.1 none presentA 1 1q32T MAML2 19 19p13A Waardenbuyes 3 3p14.1A, T IGK@, BCL5, BCL7A , BTG1, TR 8 8q24.12-q24.13 A 1 1p34.3 D, Mis, N, F, S, O 17 17q12 none presentT MYB, HGMA2 9 9p24.1T, Mis, D, FIGH@, ETV6, PML, FOXP1, ZNF5 9 9p13 noneT PPARG Thyroid dyyes 2 2q12-q14

113710803 insertion CMis, N, F 7 7p22

5993301 mis T-->C5993514 mis G-->A6012052 mis T-->C5993684 mis AAA-->AG5993561 mis CTG-->TCG5993528 mis T-->C5993485 mis G-->C

Heterozygous, only in A and T. Seems to be also present in SG according to realignment. This exact mutation is novel, but another one is known in dbSNP. It seems to be coupled to the position 5993127 mutation, 2 bases downstream. Not known whether it 5993124 mis T-->C5993127 mis C-->T5979575 mis G-->C

D, Mis, N, F, S 10 10q23.3 noneT PDGFRB 17 17p13

There is a 26 bp deletion, overlapping with the splice acceptor site of exon 18. This means the junction of exon 17 and 18 is probably impaired. The impact of this is not clear since the last part of exon 17 and completely exon 18 are 3' UTR. The rs56107242 5227610 Del (26 bp)D, Mis, N, F, S 13 13q14 none

N, F, S 8 8q24.3

145713322 MIS A-->GR1005Q missense. HOM is S lineage and HET in others. According to Snp Array data, this is due to LOH in S lineage. Genome diploid at this locus for all lines, except T. The most occurring allele in the human population is G/G or A/G, few A/A. In the S lineage 145708624 MIS G-->T

T, Mis, N, H4, PRKARHirschspruyes 10 10q11.2 none

N, F, S, Mis 3 3p21.31 none

47100389 MIS G-->TF, O 16 16p13.13

T RAF1 3 3p25.3Mis, F Maturity-oyes 12 12q24.2 none

119921765 mis A-->GMis, N, F 17 17p13

This is a heterozygous snp only present in 293T leading to a nonsynonymous change: R280S. The mutation is known in COSMIC. The mutation is in the E4F1 interacting domain and the affected residue has an important function in DNA binding by p53. Zygosit 7517823 Mis A-->TThis is a heterozygous snp in all lines, in 4 of 7 isoforms of p53. P72R. According to Cosmic, the R is the WT allele instead of P. The snp is known (rs1042522). Both GG, GC and CC alleles occur in the population. 7520197 Mis G-->C

D, Mis, N, F, S 9 9q34 Heterozygous missense present in all lines, HOM in Flp. In all 3 splice variants. M322T. In he human population, the Met genotype is the most frequent one. The mutation is not known to be related to disease. 134776725 Mis A-->G

D, Mis, N, F, S 3 3p25Probably a HET mutation of L128H. It's not clear in which lines it's present, because of a very low realignment coverage. Most probable in T, not confirmed in others. It's known in the COSMIC database from a clear cell renal carcinoma (1 sample only). 10163240 Mis T-->A

Mis, N, F, S 8 8p12-p11.231118822 Mis G-->T

Mis, N, F, S 3 3p25Three frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.

14174970 Mis GCT-->GG14162450 Mis G-->T

dbSNP ID

- Has 7 copies in Flp,- -

V1821D rs459552- -

L815P rs6058694- -

N750K -D1835N (orD5rs1801516 ToleratedN1983S (or Nrs659243 Tolerated

- -Q891E (orQ929rs3088074 ToleratedN1822S (or N1rs45439799 Tolerated

No -A493T rs2229362 Tolerated

- -G303R rs3744124 Tolerated

- -P868L rs11852361 DAMAGINGV1321I rs56009845/ Tolerated

- -P824/871Q rs799917 DAMAGING but low confidence.E1038G rs16941 DAMAGING but low confidence.K1183R rs16942 ToleratedS509/1566/1rs1799966 all DAMAGING but low confidence.

- -R2034C rs1799954 DAMAGINGV2466A rs169547 Tolerated

- Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. CCNE1 Has not been detected as significantly OE in TvsA exon array, log2FC is only 0.2 (so 2^(0.2)=1.14) in the 293T line. In Flp line, again not 2 fold change DE (but 1,4 compared to A). - 2 or 3 copies in all l

R521K rs2227983 Tolerated- 293T 2 copies, Flp 3

P1140/1170 rs161552325 rs number not known by SIFT.- -

R415Q rs1800067 DAMAGING- -

G1053R rs9514066 ToleratedG1080R rs9514067 ToleratedD1104H/N rs17655 DAMAGING, but low confidence from paralogues.

- -G501S rs2239359 Tolerated

- -R126G NA

none present - -

Protein change (delaa xx-xx)

SIFT prediction for SNP

Evidence for fusion genes in SV files? (AvsNA19238 and all lines vsA)

Evidence for amplification of gene (Snp array or CG CNV data)

none present No, but some deletions -none present - -

- 3 copies in Flp and Fused to ADARB1 in Flp -

none present - -- 5 copies in 293S, 4 Not with MAML2, but the-- 2 copies in Flp, 4 inNo 5 copies in 293S, 2 i- 3 copies in 293A, 4

none present - -Not with any of these t -No -No -

splice site a -- -

K-->E rs2228006 toleratedP-->S rs1805321 toleratedI-->V - toleratedK silent or K- rs63751313 toleratedL-->S - toleratedK-->R - toleratedH-->Q rs63750685 toleratedM-->V (rs63750100) toleratedD-->N toleratedG-->A rs1802683 tolerated

- -No -

splice site a rs56107242 -- -No -- -

S-->P rs2721190 toleratedR-->Q rs4251691 tolerated

No -

- -

P-->L rs4082155 tolerated- -

Not with RAF1, but in 2-- -

S-->G rs1169305 tolerated- -

R-->S - DAMAGINGP-->R rs1042522 tolerated

- -M-->T rs1073123 tolerated

- -L-->H - DAMAGING

- -L-->F rs1801195 tolerated

- -

A-->R rs55819243 DAMAGINGQ-->K rs2228001 tolerated

-No, has at least 3 copies in all lines.

-

No, 2 copies in Flp and 3 in others.

-

-

-

-

Only 2 copies in 293T according to snp array data. Not confirmed by CG CNV (3 copies), 3 or 4 in others.

Only 2 copies in 293A and 293Flp, 3 or 4 in other lines.

Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. CCNE1 Has not been detected as significantly OE in TvsA exon array, log2FC is only 0.2 (so 2^(0.2)=1.14) in the 293T line. In Flp line, again not 2 fold change DE (but 1,4 compared to A). -

-

-

-

Only 2 copies in 293S and 293Flp, 3 or 4 in others.

2 copies in Flp, 3 in others.

2 copies in 293A and Flp, 3 in others.

Evidence for deletion of gene or part of gene (Snp array or CG CNV data)

-2 copies in 293Flp, 293SG and 293SgendoT, 3 copies in others, no data in a large part of intron 3 of IKZF1. Is this a deletion??--3 copies in A, 4 copies in Flp, only 2 copies in other lines.-----Only 2 copies in 293T, at least 3 in all others.

Only 2 copies in 293S, at least 3 in all others.-

-

Only 2 copies in 293SG and SGendoT, 3 in others.-

1 or 2 copies in 293S, 2 in 293A. Seems to be 3 in others--

-

-

-

--

-

At least 3 copies in all lines.

At least 3 copies in all lines.

-

-

Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. CCNE1 Has not been detected as significantly OE in TvsA exon array, log2FC is only 0.2 (so 2^(0.2)=1.14) in the 293T line. In Flp line, again not 2 fold change DE (but 1,4 compared to A).

2 copies in 293Flp, 293SG and 293SgendoT, 3 copies in others, no data in a large part of intron 3 of IKZF1. Is this a deletion??

Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. CCNE1 Has not been detected as significantly OE in TvsA exon array, log2FC is only 0.2 (so 2^(0.2)=1.14) in the 293T line. In Flp line, again not 2 fold change DE (but 1,4 compared to A).

Gene symbol and name Splice variant dbSNP ID refseq base alt baseANAPC1; anaphase promoting compl-

rs2306009 G Trs2612906 C G- G A- G A- T C- A Grs34148650 T C- G A- C G- C T

G AANAPC11; anaphase promoting comp 7

6 of 7ATM; ataxia telangiectasia mutated (EC:2.7.11.1) [KO:K04728] [EC:2.7.11.1]

- C Grs1801516 G Ars659243 A G

ATR; ataxia telangiectasia and Rad3 -rs2227928 A G

BUB1B; budding uninhibited by benzimidazoles 1 homolog beta (yeast) (EC:2.7.11.1) [KO:K06637] [EC:2.7.11.1]G A

CCNA2; cyclin A2 [KO:K06627] -rs769242 T C

CCND1; cyclin D1 [KO:K04503]

CCND3; cyclin D3 [KO:K10152]rs1051130 A G

CCNE1; cyclin E1 [KO:K06626]- - -

CDC14B; CDC14 cell division cycle 14 32 of 3

CDKN2D; cyclin-dependent kinase inh 21 of 2

CHEK1; CHK1 checkpoint homolog (S. 33 of 3 rs506504 A G

CHEK2; CHK2 checkpoint homolog (S. pombe) (EC:2.7.11.1) [KO:K06641] [EC:2.7.11.1]

CUL4A; cullin 4A [KO:K10609] 2all 2

DNTT; deoxynucleotidyltransferase, 2all 2 rs6584066 A G

E2F1; E2F transcription factor 1 [KO -

E2F2; E2F transcription factor 2 [KO -rs2075995 C A

E2F5; E2F transcription factor 5, p 3all 3

ERCC4; excision repair cross-complementing rodent repair deficiency, complementation group 4 [KO:K10848] [EC:3.1.-.-]rs1800067 G A

ERCC5; excision repair cross-complementing rodent repair deficiency, complementation group 5 [KO:K10846]rs9514066 G Crs9514067 G C

rs72936240

rs17655 G C or AERCC6; excision repair cross-compl -

rs2228526 T Crs2228527 G Crs2228529 T C

ESPL1; extra spindle pole bodies hom-rs6580942 C Ars1318648 C A- T Grs1110719 A Trs1056685 G A

EXO1; exonuclease 1 [KO:K10746] [EC 3all 3 rs735943 A Gall 3 rs1047840 G Aall 3 rs1635498 C T

FZR1; fizzy/cell division cycle 20 re 3

HMGB1; high mobility group box 1 -

- C T- A T

LIG1; ligase I, DNA, ATP-dependent (-- C T

LIG3; ligase III, DNA, ATP-dependent 2all 2 - G A

MAD1L1; MAD1 mitotic arrest deficie 3all 3 - C Tall 3 - T A

MAD2L1; MAD2 mitotic arrest deficie-- T C

MAD2L2; MAD2 mitotic arrest deficie 21 of 2

MBD4; methyl-CpG binding domain pr-- G A

MCM2; minichromosome maintenance-- G A

MCM4; minichromosome maintenance 2all 2 rs762679 T A

MCM5; minichromosome maintenance-rs2307340 C G

MCM7; minichromosome maintenance 21 of 2 rs2070215 T C

MLH3; mutL homolog 3 (E. coli) [KO 2all 2 rs175081 T Call 2 - G Call 2 rs28756982 C T

MNAT1; menage a trois homolog 1, c-- C T

MSH3; mutS homolog 3 (E. coli) [KO -

rs184967 A Grs26279 G A

NEIL3; nei endonuclease VIII-like 3 ( -rs13112358 C Trs13112390 A Crs1876268 G A

OGG1; 8-oxoguanine DNA glycosylase 81of 8 rs1052133 C G1of 8 rs1052133 C G2/8 rs1052133 C G

PARP4; poly (ADP-ribose) polymerase family, member 4 (EC:2.4.2.30) [KO:K10798] [EC:2.4.2.30]1/1 rs9578751 G A1/1 rs9318600 T A

rs7140044 G A1/1 rs4770684 T C

rs9581043 G APMS2; PMS2 postmeiotic segregation increased 2 (S. cerevisiae) [KO:K10858]

rs2228006 T Crs1805321 G A- T Crs63751313 AAA AGG, AGA, - CTG TCG- T Crs63750685 G C(rs63750100) T C- C Trs1802683 G C

POLD1; polymerase (DNA directed), delta 1, catalytic subunit 125kDa (EC:2.7.7.7) [KO:K02327] [EC:2.7.7.7]1/1 G T

POLE; polymerase (DNA directed), epsilon (EC:2.7.7.7) [KO:K02324] [EC:2.7.7.7]1/1 A G

PRKDC; protein kinase, DNA-activated, catalytic polypeptide (EC:2.7.11.1) [KO:K06642] [EC:2.7.11.1]- C

PTTG2; pituitary tumor-transforming 2 [KO:K06635]G C

RAD23A; RAD23 homolog A (S. cerevisiae) [KO:K10839]1/1 rs11558955 A G

RBL2; retinoblastoma-like 2 (p130) [KO:K04681]1/1 rs17800727 A G

RPA4; replication protein A4, 30kDa [KO:K10741]1/1 rs2642219 G A

SMC1B; structural maintenance of chromosomes 1B [KO:K06636]1/1 acc to refseq (but 3/3 acc to uniproC T

TDG; thymine-DNA glycosylase (EC:3.2.2.29) [KO:K03649] [EC:3.2.2.-]1/1 G T1/1 rs2888805 G A

TP53; tumor protein p53 [KO:K04451]- A Trs1042522 G C

XPC; xeroderma pigmentosum, complementation group C [KO:K10838]

rs55819243 GCT GGTrs2228001 G T

XRCC1; X-ray repair complementing defective repair in Chinese hamster cells 1 [KO:K10803]1/1 rs25487 A G1/1 rs2682557 A T

XRCC6; X-ray repair complementing defective repair in Chinese hamster cells 6 [KO:K10884]1/1 G A

refseq aa alt aa notesComponent of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated

A D HET missense A1632D in all lines. dbSNP reports few frequency data, but the homozygous T/T allele doesA P HET missense A1524P in 293T, possibly in 293A. Very low realignment coverage in all lines.dbSNP reportsL F HET mutation only in 293A. Some evidence in realignment that it's possibly also present in 293S and 293H Y HET mutation only in 293A and 293Flp. No evidence in realignment of other lines. H1184Y. Novel, not caM V HET mutation only in 293SGendoT. No evidence in realignment of other lines. M1177V. Novel.V A HET mutation in 293A, 293SG and 293SGendoT. No evidence in other lines. V1037A. Novel, not called byD G HET mutation in all lines except 293T. D1036G.dbSNP reports few frequency data (only 2).S F HET mutation only in Flp. No evidence in other lines. Not called by CG. Novel.V L HET mutation only in Flp. No evidence in other lines. Not called by CG. Novel.M I HET mutation only in Flp. No evidence in other lines. Not called by CG. Novel.Q * HET in all lines except 293A, but there is some evidence in 293A realignment. Very little frequency data

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulatedNo data for first exon, due to CpG island. But this is 5' UTR.ATM is a kinase that is essential for p53 activity. It's responsible for detecting and cor

N K Reference and HEK genomes say K, but cosmic data says one cancer was detected with a N>K change. SNP D N Different from refseq genome. Heterozygous in all lines, this heterogenous genotype is rather rare (so isN S Different from refseq genome but not in cosmic as known mutation. Homozygous in all lines (no call in F

Serine/threonine protein kinase which activates checkpoint signaling upon genotoxic streM T HOM mutation in all lines, according to dbSNP it's not a rare snp.

BUB1B; budding uninhibited by benzimidazoles 1 homolog beta (yeast) (EC:2.7.11.1) [KO:K06637] [EC:2.7.11.1]R Q different from refseq but not in cosmic as cancer mutation. Homozygous in all lines. The

Essential for the control of the cell cycle at the G1/S (start) and the G2/M (mitosis) transI V HOM mutation in all lines. According to dbSNP, the allele present in the 293 lines is the common one and

No coverage in part of second exon. For the rest OK.

S P HET snp in 293A, not present in 293T, and HOM SNP in all others.

- - In T line only there seems to be an amplification of a region comprising this cyclinE gen

Very little sequence information on first exon, due to CpG island.

First exon lies inside a CpG island and has little coverage, but seems to be OK.Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle a

I V HOM snp in all lines, known. The refseq is rare acoording to dbSNP, the base in the 293 lines is not rare

There is a very high raw coverage region spanning the last four exons and further downstream of CHEK2 (500-1000x and about 24 kb). The realignment coverage is also around 100, with peaks to about 250, in all lines. Repetitive elements (LINE, SINE, LTR,…) satellite DNA and simple repeats do not seem to be much different than in the surrounding area. There are 4 alleles in 293A, and this is the case in the whole region, so this cannot explain the observation. When looking at the fraction of called vs not called bases from 69 cell lines (published by CG) it's clear that there are problems in this region, since the fraction of called bases goes down in that region. It will not be attempted to interpret the SNP's in this area, since they cannot be trusted, and are almost never called anyway. Core component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes wVery little or no sequence information on first and second exon, due to CpG island.Template-independent DNA polymerase which catalyzes the random addition of deoxynucleo

R G HOM snp in all lines, known. The refseq is rare acoording to dbSNP, the base in the 293 lines is not rareTranscription activator that binds DNA cooperatively with dp proteins through the E2 reNo sequence information on first and second exon, due to CpG island.Transcription activator that binds DNA cooperatively with DP proteins through the E2 re

Q H HOM snp in all lines, known. It's not very common, but not rare either. Not known to be related to a disTranscriptional activator that binds to E2F sites, these sites are present in the promoterNo/very little sequence info first exon (5' UTR) due to CpG island.

ERCC4; excision repair cross-complementing rodent repair deficiency, complementation group 4 [KO:K10848] [EC:3.1.-.-]R Q Heterozygous in A, Flp, T only. Interestingly, the G allele (refseq) has almost an absol

ERCC5; excision repair cross-complementing rodent repair deficiency, complementation group 5 [KO:K10846]G R Homozygous in all lines. This is an example where refseq has the 'odd' genotype: CC is almost the exclusG R Interestingly similar to above. Homozygous in all, refseq is odd one out with the very rare GG phenotype

D H or N Clear C/G heterozygosity in A, SG, SGendoT. S does not have enough coverage in the realignment (no sightEssential factor involved in transcription-coupled nucleotide excision repair which allHomo sapiens piggyBac transposable element derived 3 (PGBD3), mRNA in exon 5. This is known and not specific for our cell line. Chr10:50.410.959 homozygous G to C, silent, novel snp. Chr10:50.348.801 homozygous T to G, Met to Val, novel snp. Chr10:50.348.450, T to C homozygous, novel snp, Arg to Gly. Chr10:50.337.149 homozygous T to G, Glu to Arg, novel snp.

M V HOM snp in all lines. Known snp, it's not very rare and not known to be connected to disease.R Q HOM snp in all lines. Known snp, it's not very rare and not known to be connected to disease.Q G HOM snp in all lines. Known snp, it's not rare and not known to be connected to disease.

Caspase-like protease, which plays a central role in the chromosome segregation by cleA D HOM snp in all lines. Known snp, it's not very rare. S R HOM snp in all lines. Known snp, it's not rare and not known to be connected to disease.V G HET snp in all lines, novel.K M HOM snp in all lines, not known to be related to disease. It's not very rare.R H HOM snp in all lines, not known to be related to disease. It's the most common snp according to dbSNP

5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' doubleH R HET snp in all lines. According to dbSNP this is the most common allele.E K HOM snp in all lines. According to dbSNP it's the most common allele. R C HOM snp in all lines. According to dbSNP it's the most common allele.

Key regulator of ligase activity of the anaphase promoting complex/cyclosome (APC/C), No sequence info first exon (5' UTR) due to CpG island.DNA binding proteins that associates with chromatin and has the ability to bend DNA. BNo sequence info first exon (5' UTR) due to CpG island.Same phenomenon as cdc27, high raw coverage, but only exons! According to Nucl. As. Res. (1989) 17 (3):1197-1214, there are many HMG pseudogenes in the human genome. Overexpression of HMGB1 is correlated with cancer.

R Q HET in 293 Flp, A and T, possibly in S. No data in SG and SgendoT that support this snp. But is it for theD E HET snp only in 293T. Novel. But is it for the real gene or a pseudogene???

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recomG R HET snp, novel, in all lines except Flp and A. No realignment triggered here.

Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repV M HET snp, novel, unique to SGendoT, no realignment in other lines.

Component of the spindle-assembly checkpoint that prevents the onset of anaphase untiE K HET snp, novel, unique to SG and SGendoTK M HET snp, novel, unique to 293T

Component of the spindle-assembly checkpoint that prevents the onset of anaphase untiE G HET snp, novel, unique to S lineage (S, SG, SGendoT)

Adapter protein able to interact with different proteins and involved in different bioNo sequence info first exon (5' UTR) due to CpG island.Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase act

P S HET snp, novel, unique to SG and SGendoT.Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative h

E K HET snp, novel, unique to SGendoT, no realignment in other lines.Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative

L M HOM snp in all lines, a bit rare, according to dbSNP. Not known to be related to a disease.Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative

T S HET in all lines, except in 293T, No sign of the snp here. 293T seems to have a LOH genotype in this regiActs as component of the MCM2-7 complex (MCM complex) which is the putative replicative

N S HET in all lines, except in 293T, No sign of the snp here. Snp is not rare.Probably involved in the repair of mismatches in DNA. Defects in MLH3 are the cause o

N D HOM snp in all lines. 293 snp is actually the most common allele. F L HET snp, unique to 293T; Novel. V I HET in 293A, Flp and T. HOM snp in S lineage. HET is not common, the HOM version is never observed in

Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) H Y HET snp, unique to SG and SGendoT. No realignment triggered in other lines.

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes No sequence info first exon (5' UTR and coding) due to CpG island.

Q R HOM snp, presumably present in all lines, but not called in S, SGendoT and Flp. G/G is the most commonA T HOM in all lines. A/A is the most common genotype.

Removes damaged bases from DNA, leaving an abasic site. Reports about DNA glycosylase P L HOM T/T in all lines, and this is also the most common version of the allele. Not known to be related to Q H HOM in all lines. Quite common snp.G R HOM snp, presumably present in all lines, but not called in Flp and A. A/A, present in our lines, is the

DNA NER repair enzyme that incises DNA at 8-oxoG residues (result of ROS damage). ES C HET snp in all lines except 293T, although some evidence in the realignment. Snp is not rare.P A HET snp in all lines except 293T, although some evidence in the realignment. Same as above, but another I/S M/C This SNP is a missense SNP but only for 2 out of 8 splice variants in dbSNP - in 1 it is

Poly-ADP ribosyl transferase-like 1, has the same catalytic domain as poly-ADP ribosyl transferase 1, but no N-terminal DNA binding domain which activates the C-term catalytic domain. Probably PPIs necessary for activity. Role in DNA repair. S N This SNP is a known SNP, found heterozygously in all lines except Flp (no realignment dF Y see above for function. Heterozygous in all lines (though SNP caller says no call for S S N see above for function. Homozygous in all lines. Present in dbSNP: rare genotype. ToleratM T see above for function. Homozygous in all lines (though no call for Flp but I reckon it V I see above for function. The realignments suggest it is heterozygous in all lines except F

Mismatch repair endonuclease PMS2. Component of the post-replicative DNA mismatch reK E HOM missense, not known whether this mutation causes cancer. The G/G allele present in our lines is thP S HET missense (CG Snp caller seems to be inconclusive) not known whether this mutation causes cancer. ThI V HET missense I54V in A, S and Flp, not in others. Snp not known in dbsn or COSMIC. Mutation in 1 of 2 iK K or R Only in Flp line, probably a HET mutations. It's known, but no known relation with pathology. K413R or siL S Only in SGendoT, not known in COSMIC or dbSNP. It's Heterozygous. L454SK R Only in T, A and SGendoT, Heterozygous novel. K465SH Q Heterozygous, only in T. Low frequency genotype. Not known to be related with disease.M V Heterozygous, only in A and T. Seems to be also present in SG according to realignment. This exact mutD N HET, only in A. May be present in other lines looking at the realignment files. D599NG A HET in all lines. Known in dbSNP, no frequency data available. Not known to be related with any diseas

POLD1; polymerase (DNA directed), delta 1, catalytic subunit 125kDa (EC:2.7.7.7) [KO:K02327] [EC:2.7.7.7] Catalytic subunit of polD, the polymerase involved in DNA replication and repair. W L Novel mutation, only present in SG and SGEndoT --> introduced by EMS? Heterozygous though, frequency

Thought to be the main polymerase in eukaryotes for leading strand synthesis.N S Very rare genotype, homozygous in all lines. Snp is known in dbSNP, and SIFT says dama

Case of prob mistake in RefSeq: the refseq sequence, if correct, would end in premature sMember of securin family, but no info can be found on what this gene does.

R P Known SNP, frequent genotype. SIFT says the P is tolerated, the Arg in refseq is supposeInterestingly, seems to have multiple functions: involved in NER, but is also multiubiquitin chain receptor: binds to Lys48 and the proteasome, to deliver substrates to the proteasome probably.

T A Known natural variant, SIFT says tolerated. Genotype is rare, but not a lot of populatiKey regulator of entry in cell division. Also directly involved in heterochromatin formation by stabilizing histone methylation. Potent inhibitor of E2F-mediated trans-activation; associates wit E2F5. May act as tumour suppressor.

Y C Heterozygous SNP found in S, SG, and SGENdoT only. This SNP is the only known naturalcomponent of the alternative replication protein A complex, that probably plays a role in DNA repair (not replication nor cell cycle progression).

A T This SNP is heterozygous in all lines, and a known polymorphism. Genotype is frequent.Role in chromatid cohesion and DNA recombination, but conflicting reports: entrez says it works during meiosis and mitosis, uniprot says it is a meiosis-specific protein.

A V This SNP is heterozygous in SG and SGENdoT only, not present in the other lines. SIFT preCorrects GT mismatches to GC (from hydrolytic deamination of 5-mC to T).

A S heterozygous in T only (not present in the other lines), with 38% of reads bearing the SerV M see abve for function. Heterozygous in all lines (though SNP caller says no call in SG,

Cellular tumor antigen p53. Acts as a tumor suppressor in many tumor types; induces growR S This is a heterozygous snp only present in 293T leading to a nonsynonymous change: R280S. The mutationP R This is a heterozygous snp in all lines, in 4 of 7 isoforms of p53. P72R. According to Cosmic, the R is the

DNA repair protein complementing XP-C cells. nvolved in global genome nucleotide exciThree frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.

A R This HOM mutation is not known to be related to disease. No frequency data available. A472RQ K HET mutation certainly present in A, Flp, T and SGendoT. No or almost no realignment data in S and SG. It'

Necessary for efficient repair of DNA ss breaks by exposure to ionizing radiation and alkylating agents. Q R Homozygous in all lines, known in dbSNP. In fact, this is a case where refseq has the rN Y see above for function. This is a known natural variant, tolerated as SIFT predicts. Homoz

Role in chromosome translocations, in NHEJ and V(D)J recombination. E K This SNP is located in the Ku. Heterozygous mutation in SG and SGendoT only. Novel SN

Chromosome position first base protein position impact (MIS, DEL,…) SIFT prediction2

HET missense A1632D in all lines. dbSNP reports few frequency data, but the homozygous T/T allele does 112259430 1632 MIS DAMAGINGHET missense A1524P in 293T, possibly in 293A. Very low realignment coverage in all lines.dbSNP reports 112266552 1524 MIS DAMAGINGHET mutation only in 293A. Some evidence in realignment that it's possibly also present in 293S and 293 112289444 1191 MIS ToleratedHET mutation only in 293A and 293Flp. No evidence in realignment of other lines. H1184Y. Novel, not ca 112289465 1184 MIS DAMAGINGHET mutation only in 293SGendoT. No evidence in realignment of other lines. M1177V. Novel. 112289486 1177 MIS DAMAGINGHET mutation in 293A, 293SG and 293SGendoT. No evidence in other lines. V1037A. Novel, not called by 112295383 1037 MIS DAMAGINGHET mutation in all lines except 293T. D1036G.dbSNP reports few frequency data (only 2). 112295386 1036 MIS DAMAGING

112321900 555 MIS DAMAGING112321910 552 MIS Tolerated112330713 488 MIS Tolerated

HET in all lines except 293A, but there is some evidence in 293A realignment. Very little frequency data 112330900 465 NONSENSE17

11Reference and HEK genomes say K, but cosmic data says one cancer was detected with a N>K change. SNP chr11:107632276 750 MIS ToleratedDifferent from refseq genome. Heterozygous in all lines, this heterogenous genotype is rather rare (so is chr11:107680672 1835 MIS ToleratedDifferent from refseq genome but not in cosmic as known mutation. Homozygous in all lines (no call in F chr11:107688379 1983 MIS Tolerated

3143764302 211 MIS Tolerated

15 chr15:38265123 349 MIS Tolerated4

HOM mutation in all lines. According to dbSNP, the allele present in the 293 lines is the common one and 122961667 163 MIS Tolerated

6 42011760 178 MIS Tolerated

19 - - - -9

19

11HOM snp in all lines, known. The refseq is rare acoording to dbSNP, the base in the 293 lines is not rare 125030405 471 MIS Tolerated

There is a very high raw coverage region spanning the last four exons and further downstream of CHEK2 (500-1000x and about 24 kb). The realignment coverage is also around 100, with peaks to about 250, in all lines. Repetitive elements (LINE, SINE, LTR,…) satellite DNA and simple repeats do not seem to be much different than in the surrounding area. There are 4 alleles in 293A, and this is the case in the whole region, so this cannot explain the observation. When looking at the fraction of called vs not called bases from 69 cell lines (published by CG) it's clear that there are problems in this region, since the fraction of called bases goes down in that region. It will not be attempted to interpret the SNP's in this area, since they cannot be trusted, and are almost never called anyway. 13

10HOM snp in all lines, known. The refseq is rare acoording to dbSNP, the base in the 293 lines is not rare 98068229 112 MIS Tolerated

20

1HOM snp in all lines, known. It's not very common, but not rare either. Not known to be related to a dis 23720051 226 MIS Tolerated

8

16 chr16:13936534 415 Damaging13

Homozygous in all lines. This is an example where refseq has the 'odd' genotype: CC is almost the exclus chr13:102325851 1053 MIS ToleratedInterestingly similar to above. Homozygous in all, refseq is odd one out with the very rare GG phenotype chr13:102325970 1080 MIS Tolerated

Clear C/G heterozygosity in A, SG, SGendoT. S does not have enough coverage in the realignment (no sightchr13:102326008 1104 MIS Damaging (low confidence for homlogues)10

Homo sapiens piggyBac transposable element derived 3 (PGBD3), mRNA in exon 5. This is known and not specific for our cell line. Chr10:50.410.959 homozygous G to C, silent, novel snp. Chr10:50.348.801 homozygous T to G, Met to Val, novel snp. Chr10:50.348.450, T to C homozygous, novel snp, Arg to Gly. Chr10:50.337.149 homozygous T to G, Glu to Arg, novel snp. HOM snp in all lines. Known snp, it's not very rare and not known to be connected to disease. 50348723 1097 MIS ToleratedHOM snp in all lines. Known snp, it's not very rare and not known to be connected to disease. 50248375 1213 MIS ToleratedHOM snp in all lines. Known snp, it's not rare and not known to be connected to disease. 50337111 1413 MIS Tolerated


HOM snp in all lines. Known snp, it's not rare and not known to be connected to disease. 51956812 614 MIS Tolerated51966278 1164 MIS DAMAGING51968150 1435 MIS DAMAGING

HOM snp in all lines, not known to be related to disease. It's the most common snp according to dbSNP 51972970 2037 MIS Tolerated1

240096774 354 MIS Tolerated240108924 589 MIS Tolerated240111898 723 MIS Tolerated

19

13

Same phenomenon as cdc27, high raw coverage, but only exons! According to Nucl. As. Res. (1989) 17 (3):1197-1214, there are many HMG pseudogenes in the human genome. Overexpression of HMGB1 is correlated with cancer.HET in 293 Flp, A and T, possibly in S. No data in SG and SgendoT that support this snp. But is it for the 29933654 163 MIS DAMAGING

29933527 205 MIS DAMAGING???? D to E in D/E rich sequence stretch.19

53322351 667 MIS DAMAGING17

30353155 865 MIS Tolerated7

1822261 710 MIS DAMAGING2222104 289 MIS DAMAGING


11


3128822363 800 MIS DAMAGING

8HOM snp in all lines, a bit rare, according to dbSNP. Not known to be related to a disease. 49947989 650 MIS Tolerated

22HET in all lines, except in 293T, No sign of the snp here. 293T seems to have a LOH genotype in this regi 34132661 180 MIS Tolerated


1474583636 826 MIS Tolerated74583616 832 MIS Tolerated

HET in 293A, Flp and T. HOM snp in S lineage. HET is not common, the HOM version is never observed in 74584854 420 MIS Tolerated14

60416191 232 MIS Tolerated5

HOM snp, presumably present in all lines, but not called in S, SGendoT and Flp. G/G is the most common 80185737 949 MIS Tolerated80204693 1045 MIS Tolerated

4HOM T/T in all lines, and this is also the most common version of the allele. Not known to be related to 178511744 443 MIS Tolerated

178511829 471 MIS ToleratedHOM snp, presumably present in all lines, but not called in Flp and A. A/A, present in our lines, is the 179518748 520 MIS Tolerated

3HET snp in all lines except 293T, although some evidence in the realignment. Snp is not rare. 9773773 326 MIS Damaging using homologues, not so using orthologues. Low confidence.HET snp in all lines except 293T, although some evidence in the realignment. Same as above, but another 9773773 332 MIS Tolerated

3 9773773 332/326 MIS Tolerated for P>A, but the Cys is damaging according to the homologue alignment only, and with low confidence. Poly-ADP ribosyl transferase-like 1, has the same catalytic domain as poly-ADP ribosyl transferase 1, but no N-terminal DNA binding domain which activates the C-term catalytic domain. Probably PPIs necessary for activity. Role in DNA repair.

13 23972490 122 MIS tolerated13 23966808 215 MIS tolerated13 23927295 873 MIS tolerated 13 23925744 936 MIS tolerated13 23921936 1012 MIS tolerated

7HOM missense, not known whether this mutation causes cancer. The G/G allele present in our lines is th 5993301 541 MIS toleratedHET missense (CG Snp caller seems to be inconclusive) not known whether this mutation causes cancer. Th 5993514 470 MIS toleratedHET missense I54V in A, S and Flp, not in others. Snp not known in dbsn or COSMIC. Mutation in 1 of 2 i 6012052 54 MIS toleratedOnly in Flp line, probably a HET mutations. It's known, but no known relation with pathology. K413R or si 5993684 413 MIS tolerated

5993561 454 MIS tolerated5993528 465 MIS tolerated

Heterozygous, only in T. Low frequency genotype. Not known to be related with disease. 5993485 479 MIS toleratedHeterozygous, only in A and T. Seems to be also present in SG according to realignment. This exact mut 5993124 600 MIS tolerated

5993127 599 MIS toleratedHET in all lines. Known in dbSNP, no frequency data available. Not known to be related with any diseas 5979575 857 MIS tolerated

19Novel mutation, only present in SG and SGEndoT --> introduced by EMS? Heterozygous though, frequency 55593988 23 MIS tolerated

12 131730599 1396 MIS damaging when using orthologues in alignment

8 48968371 1243 INS

4 37638581 44 MIS the refseq R is damaging when using homologues in the alignment, but with low confidenceInterestingly, seems to have multiple functions: involved in NER, but is also multiubiquitin chain receptor: binds to Lys48 and the proteasome, to deliver substrates to the proteasome probably.

19 12920147 131 MIS toleratedKey regulator of entry in cell division. Also directly involved in heterochromatin formation by stabilizing histone methylation. Potent inhibitor of E2F-mediated trans-activation; associates wit E2F5. May act as tumour suppressor.

16 52038511 210 MIS damaging when using homologues in the alignment, but confidence is low.component of the alternative replication protein A complex, that probably plays a role in DNA repair (not replication nor cell cycle progression).

X 96026062 33 MIS Damaging using homologues, tolerated using ortho's, but low confidence.Role in chromatid cohesion and DNA recombination, but conflicting reports: entrez says it works during meiosis and mitosis, uniprot says it is a meiosis-specific protein.

22 44183350 68 MIS damaging

12 102894950 50 MIS tolerated12 102904864 367 MIS tolerated17

This is a heterozygous snp only present in 293T leading to a nonsynonymous change: R280S. The mutation 7517823 280 MIS DAMAGINGThis is a heterozygous snp in all lines, in 4 of 7 isoforms of p53. P72R. According to Cosmic, the R is the 7520197 72 MIS tolerated

3Three frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.This HOM mutation is not known to be related to disease. No frequency data available. A472R 14174970 472 MIS NOT toleratedHET mutation certainly present in A, Flp, T and SGendoT. No or almost no realignment data in S and SG. It' 14162450 940 MIS toleratedNecessary for efficient repair of DNA ss breaks by exposure to ionizing radiation and alkylating agents.

19 48747566 399 MIS refseq q is damaging when using homolog alignment, but low confidence19 48739666 576 MIS tolerated

22 40376708 333 MIS damaging

There is a very high raw coverage region spanning the last four exons and further downstream of CHEK2 (500-1000x and about 24 kb). The realignment coverage is also around 100, with peaks to about 250, in all lines. Repetitive elements (LINE, SINE, LTR,…) satellite DNA and simple repeats do not seem to be much different than in the surrounding area. There are 4 alleles in 293A, and this is the case in the whole region, so this cannot explain the observation. When looking at the fraction of called vs not called bases from 69 cell lines (published by CG) it's clear that there are problems in this region, since the fraction of called bases goes down in that region. It will not be attempted to interpret the SNP's in this area, since they cannot be trusted, and are almost never called anyway.

Damaging (low confidence for homlogues)

Homo sapiens piggyBac transposable element derived 3 (PGBD3), mRNA in exon 5. This is known and not specific for our cell line. Chr10:50.410.959 homozygous G to C, silent, novel snp. Chr10:50.348.801 homozygous T to G, Met to Val, novel snp. Chr10:50.348.450, T to C homozygous, novel snp, Arg to Gly. Chr10:50.337.149 homozygous T to G, Glu to Arg, novel snp.

Same phenomenon as cdc27, high raw coverage, but only exons! According to Nucl. As. Res. (1989) 17 (3):1197-1214, there are many HMG pseudogenes in the human genome. Overexpression of HMGB1 is correlated with cancer.

DAMAGING???? D to E in D/E rich sequence stretch.

Damaging using homologues, not so using orthologues. Low confidence.

Tolerated for P>A, but the Cys is damaging according to the homologue alignment only, and with low confidence. Poly-ADP ribosyl transferase-like 1, has the same catalytic domain as poly-ADP ribosyl transferase 1, but no N-terminal DNA binding domain which activates the C-term catalytic domain. Probably PPIs necessary for activity. Role in DNA repair.

damaging when using orthologues in alignment

the refseq R is damaging when using homologues in the alignment, but with low confidence

Key regulator of entry in cell division. Also directly involved in heterochromatin formation by stabilizing histone methylation. Potent inhibitor of E2F-mediated trans-activation; associates wit E2F5. May act as tumour suppressor. damaging when using homologues in the alignment, but confidence is low.

Damaging using homologues, tolerated using ortho's, but low confidence.

Three frameshift mutations compared to the refseq, over exons 9 and 10. These three taken together, give the correct protein sequence in our lines and a mutant one in refseq. There is one mutation if you take everything together, that's the Ala472Arg one below.

refseq q is damaging when using homolog alignment, but low confidence

Homo sapiens piggyBac transposable element derived 3 (PGBD3), mRNA in exon 5. This is known and not specific for our cell line. Chr10:50.410.959 homozygous G to C, silent, novel snp. Chr10:50.348.801 homozygous T to G, Met to Val, novel snp. Chr10:50.348.450, T to C homozygous, novel snp, Arg to Gly. Chr10:50.337.149 homozygous T to G, Glu to Arg, novel snp.

Abbrevi TermA amplificationAEL acute eosinophilic leukemiaAL acute leukemiaALCL anaplastic large-cell lymphomaALL acute lymphocytic leukemiaAML acute myelogenous leukemiaAML* acute myelogenous leukemia (primarily treatment associated)APL acute promyelocytic leukemiaB-ALL B-cell acute lymphocytic leukaemiaB-CLL B-cell Lymphocytic leukemiaB-NHL B-cell Non-Hodgkin LymphomaCLL chronic lymphatic leukemiaCML chronic myeloid leukemiaCMML chronic myelomonocytic leukemiaCNS central nervous systemD large deletionDFSP dermatofibrosarcoma protuberansDLBCL diffuse large B-cell lymphomaDLCL diffuse large-cell lymphomaDom dominantE epithelialF frameshiftGIST gastrointestinal stromal tumourJMML juvenile myelomonocytic leukemiaL leukaemia/lymphomaM mesenchymalMALT mucosa-associated lymphoid tissue lymphomaMDS myelodysplastic syndromeMis MissenseMLCLS mediastinal large cell lymphoma with sclerosisMM multiple myelomaMPD Myeloproliferative disorderN nonsenseNHL non-Hodgkin lymphomaNK/T natural killer T cellNSCLC non small cell lung cancerO otherPMBL primary mediastinal B-cell lymphomapre-B Al pre-B-cell acute lymphoblastic leukaemiaRec reccesiveS splice siteT translocationT-ALL T-cell acute lymphoblastic leukemiaT-CLL T-cell chronic lymphocytic leukaemiaTGCT testicular germ cell tumourT-PLL T cell prolymphocytic leukaemia

#ASSEMBL GS00370-DNA_A01_1110_36-ASM#SOFTWAR1.11.0.21#GENERATcgatools#GENERAT2011-Dec-06 15:28:13.657622#FORMAT_2.0#GENOME_NCBI build 36#SAMPLE GS00370-DNA_A01#TYPE JUNCTIONS#DBSNP_B dbSNP build 130#GENE_ANNCBI build 36.3#CGATOOL1.5.0

>Id LeftChr LeftPosition Lef LeftLength RightChr RightPosition RigRightLengtDistance4728 chr1 5943284 + 378 chr1 5948663 + 337 53794718 chr1 31171979 + 336 chr1 31172691 + 355 7121578 chr1 32966449 - 474 chr1 32968851 - 524 24021520 chr1 33288920 - 268 chr7 24415236 - 5064179 chr1 187467473 + 356 chr1 187468454 + 227 981

499 chr1 221270911 - 421 chr15 63333071 + 4564915 chr1 239702746 + 440 chr1 243353657 - 484 3650911

636 chr1 239843487 - 339 chr1 239844780 + 430 12934101 chr2 42300411 + 411 chr2 42307151 + 281 67404099 chr2 44337954 + 401 chr2 44345038 + 161 70844092 chr2 53626037 + 402 chr2 53631348 + 352 53114087 chr2 62203991 + 370 chr2 62204784 + 292 7934910 chr2 62465302 + 344 chr2 62468961 - 409 36594051 chr2 119762084 + 331 chr2 119767011 + 439 49273947 chr2 141903703 + 394 chr2 142025961 + 325 1222583896 chr2 208798701 + 582 chr2 208805688 + 369 69873879 chr2 232809146 + 390 chr2 232938046 + 444 1289003876 chr2 237596582 + 423 chr2 237611957 + 496 153753816 chr3 76901816 + 424 chr3 76969495 + 374 676793215 chr6 81112919 + 437 chr6 81114601 + 580 16823199 chr6 113534763 + 351 chr6 113538281 + 360 35183198 chr6 113807653 + 412 chr6 113809812 + 408 21593161 chr6 146250543 + 342 chr6 146255759 + 113 5216

941 chr6 165042624 - 276 chr19 54306117 - 4291197 chr6 168983816 - 85 chr6 168983915 - 89 993016 chr7 143468426 + 388 chr7 143475011 + 426 65853014 chr7 144634401 + 447 chr7 144649787 + 413 153864498 chr8 83347925 + 616 chr8 84877117 - 493 15291922881 chr8 143395366 + 330 chr8 143396564 + 380 11982858 chr9 24135482 + 446 chr9 24140391 + 257 49092857 chr9 24492071 + 352 chr9 24509103 + 396 170322795 chr9 130402343 + 390 chr9 130405306 + 444 29632769 chr10 4402191 + 310 chr10 4408853 + 409 66622761 chr10 6687901 + 511 chr10 6688860 + 239 9592664 chr11 7945362 + 392 chr11 7946397 + 320 10352609 chr11 58388350 + 388 chr11 58393131 + 318 47812603 chr11 67086873 + 461 chr11 67089129 + 172 2256

2516 chr12 51882260 + 285 chr12 51882862 + 212 6021024 chr13 76278236 - 594 chr13 82255600 - 474 59773642062 chr13 83147490 + 433 chr19 9093770 + 4072406 chr13 92042627 + 430 chr13 92044021 + 342 13942403 chr13 96739659 + 372 chr13 96742213 + 406 25542381 chr14 22122064 + 458 chr14 22123393 + 443 1329

968 chr15 99844519 - 386 chr15 100131539 - 381 287020

4416 chr15 99968989 + 502 chr15 99983555 - 392 14566234 chr15 99982424 - 441 chr15 100039685 + 413 57261

2263 chr16 151991 + 477 chr16 160588 + 342 8597964 chr16 29716800 - 397 chr16 30966334 - 568 1249534

861 chr17 65536607 - 317 chr17 65536914 - 326 3071908 chr18 69153643 + 355 chr18 69155235 + 200 15924259 chr19 9101118 + 282 chr19 14088676 - 491 4987558

67 chr19 13126349 - 410 chr19 54305570 + 421 411792214252 chr19 14492663 + 403 chr19 60422800 - 445 45930137

791 chr19 17303753 - 387 chr19 17311557 - 201 78041832 chr19 35039066 + 432 chr19 36520988 + 466 1481922

755 chr19 48220955 - 299 chr19 48548654 - 383 32769963 chr19 57276266 - 397 chr19 63647895 + 274 6371629

1798 chr20 4879297 + 452 chr20 4919975 + 524 406781768 chr20 46808824 + 471 chr20 46811240 + 227 24161759 chr20 58545071 + 375 chr20 58558265 + 391 131941754 chr20 61862533 + 458 chr20 61863075 + 219 5424202 chrX 2957385 + 247 chrX 89432558 - 387 86475173

25 chrX 11490715 - 519 chrX 13753204 + 571 2262489696 chrX 70227303 - 451 chrX 71661517 - 392 1434214

1591 chrX 117905950 + 694 chrX 117907853 + 480 19031150 chr8 58280822 - 181 chr8 58296674 - 210 158523226 chr6 69198887 + 488 chr6 69199830 + 391 9433131 chr7 4047791 + 403 chr7 4048823 + 390 10322598 chr11 69660203 + 260 chr11 69662138 + 417 19352500 chr12 92028424 + 360 chr12 92029510 + 383 10862320 chr15 38609286 + 488 chr15 38610947 + 248 1661

796 chr19 966732 - 272 chr19 966995 - 281 2631696 chr22 23780020 + 283 chr22 23782793 + 340 2773

DiscordantMaFrequencyInB AssembledEventId Type RelatedJunNotes43 0.00 agtcaccca 485 deletion One of three copies affected. In this copy, the NPHP4 gene loses it's exon 6 and most of intron 5. NPHP4 is Nephrocystin-4, Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8 By similarity. Does not seem to be strictly required for ciliogenesis.25 0.00 gaggttga 484 deletion No annotated elements involved.19 0.00 ccatgttg 116 tandem-duplication No annotated elements involved.48 0.00 cctttagag 110 interchromosomal No annotated elements involved on either chromosome.19 0.00 ttttatggc 456 deletion No annotated elements involved.97 0.00 ggacacatc 24 interchromosomal No annotated elements involved on either chromosome.

134 0.00 tgctcagcc 492 probable-inversion see separate word doc82 0.00 ttcaattta 30 probable-inversion see separate word doc10 0.00 gcaggaca 447 deletion Deletion of a part of intron 1 of EML4 gene in 2 of 3 copies of the gene. EML4 may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic.16 0.00 agagagac 446 deletion No annotated elements involved.54 0.00 cgttcctat 445 deletion No annotated elements involved.12 0.00 tttaaaaa 444 deletion Deletion inside intron 2 of COMMD1. Too short to predict how many copies affected. COMMD1 promotes ubiquitination of NF-kappa-B subunit RELA and its subsequent proteasomal degradation. Down-regulates NF-kappa-B activity. Down-regulates SOD1 activity by interfering with its homodimerization. Plays a role in copper ion homeostasis. Can bind one copper ion per monomer. May function to facilitate biliary copper excretion within hepatocytes.66 0.00 ccaccccca 489 probable-inversion No annotated elements involved.41 0.00 agaggggc 438 deletion No annotated elements involved.16 0.00 ctctccttc 436 deletion This deletion affects exon 3 of the tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.19 0.00 ggtggtgg 429 deletion No annotated elements involved.12 0.00 gaatcttaa 425 deletion This deletion affects the 3' end of the DIS3L2 gene, exon 11 through 18 (last one). It's a deletion only present in 293A and Flp, as can be seen from the CG CNV, and with only 1 of 3 (293A) or 1 of 2 (Flp) alleles deleted.95 0.00 ggccaagct 424 deletion No annotated elements involved.60 0.00 aaatgactat 415 deletion No annotated elements involved.

118 0.00 atggttatat 347 deletion No annotated elements involved.12 0.00 ggagagaat 345 deletion No annotated elements involved.75 0.00 tccatttcaa 344 deletion No annotated elements involved.11 0.00 gtctttgg 341 deletion Deletion of probably 1 of 5 copies of SHPRH: large part of intron 28, exon 29 and small part of intron 29. No noticeable CNV breakpoints in any line... SHPRH is an E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. This gene is important for genomic stability through it's interaction with PCNA, and aputative tumor suppressor gene.38 0.00 aatgttgac 6 complex 67 On chr 6,TINAG is involved. TINAG Mediates adhesion of proximal tubule epithelial cells via integrins alpha3-beta1 and alphaV-beta3. This is a non catalytic peptidase C1 family protein. The target location for joining with chr19 does not contain any genes, but heavy rearrangements and duplications took place on this chromosome.10 0.00 catttccct 96 tandem-duplication No annotated elements involved.

102 0.00 tcaatgcta 323 deletion No annotated elements involved.123 0.00 gggctcatt 321 deletion No annotated elements involved.

11 0.00 caaccaaa 467 probable-inversion No annotated elements involved.20 0.00 cgcctctc 310 deletion Deletion inside intron 7 of TSNARE1, t-SNARE domain containing protein 1. A protein with unknown function.20 0.00 aaattttgt 308 deletion No annotated elements involved.87 0.00 gaccattta 307 deletion No annotated elements involved.62 0.00 cttaagtctt 301 deletion Deletion of the largest part of intron 26 and exon 27, and a piece of intron 27 of SPTAN1, a fodrin, which seems to be involved in secretion, interacts with calmodulin in a calcium-dependent manner and is thus candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Not all copies seem to be deleted.46 0.00 agaactgtc 295 deletion No annotated elements involved.55 0.00 cgaccagg 292 deletion No annotated elements involved.20 0.00 ttgacagga 275 deletion No annotated elements involved.37 0.00 ggtctgaaa 265 deletion No annotated elements involved. Lies inside SV Id 4460, non-novel probable inversion.14 0.00 ttgaaatg 263 deletion No annotated elements involved. Lies inside SV Id 4460 AND SV Id 270, both are non-novel probable inversions.

11 0.00 ttcaaaaa 249 deletion No annotated elements involved.16 0.00 attattta 67 tandem-duplication Tandem duplication of ~6000 kb of chr 13. It brings the copy number from 2 to 3 in this area.Several other things going on in this chromosome, also in the other lines.38 0.00 tctttttgc 199 interchromosomal No annotated elements involved.28 0.00 cctagctg 234 deletion GPC5, glypican 5 is involved: 1.3 kb short deletion in intron 7 (this intron is about 700 kb long), the last intron. GPC5 is a cell surface proteoglycan that bears heparan sulfate. It's present in all lines.17 0.00 ccatgaaac 233 deletion Deletion of 2.5 kb of intron 2 of MBNL2. Mediates pre-mRNA alternative splicing regulation. Musclebind-Like 2 Acts either as activator or repressor of splicing on specific pre-mRNA targets.

123 0.00 catgctctc 225 deletion Deletion of 1.3 kb part in intron 1 of DAD1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1, Component of the N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.107 0.00 gttctgtac 57 tandem-duplication Duplication involving the first exon of PCSK6, TM2D3 and TARSL2.

PCSK6 is Proprotein convertase subtilisin/kexin type 6, Likely to represent an endoprotease activity within the constitutive secretory pathway, with unique restricted distribution in both neuroendocrine and non-neuroendocrine tissues and capable of cleavage at the RX(K/R)R consensus motif.TM2D3 is a TM2 domain-containing protein 3, it might be involved in Alzheimer'sTARSL2 is a probable threonyl-tRNA synthetase 2, cytoplasmic

90 0.00 aacaaagtg 462 probable-inversion No annotated elements involved.125 0.00 taaatagtgg 9 probable-inversion Inversion disrupting the TARSL2 gene. TARSL2 is a probable threonyl-tRNA synthetase 2, cytoplasmic

13 0.00 gcatgggcc 214 deletion Deletion involving Hemoglobin subunit mu. At least one or two copies of this protein, maybe all are deleted. 64 0.00 ttttgacc 55 tandem-duplication Duplication of 1300 kb piece of chr 16 containing many genes. Total copy number comes to 4 or 5 depending on the cell line. Relevant genes are shown below, many involved in DNA repair and histone remodelling.

MAZ, Myc associated Zinc Finger: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.SEZ6L2: Seisure-related 6 homolog-like 2. Upregulated in lung cancers, especially in NSCLC.TAOK2: Serine/threonine-protein kinase involved in different processes such as membrane blebbing and apoptotic bodies formation DNA damage response and MAPK14/p38 MAPK stress-activated MAPK cascade. Phosphorylates itself, MBP, activated MAPK8, MAP2K3, MAP2K6 and tubulins. Activates the MAPK14/p38 MAPK signaling pathway through the specific activation and phosphorylation of the upstream MAP2K3 and MAP2K6 kinases. In response to DNA damage, involved in the G2/M transition DNA damage checkpoint by activating the p38/MAPK14 stress-activated MAPK cascade, probably by mediating phosphorylation of upstream MAP2K3 and MAP2K6 kinases. Isoform 1, but not isoform 2, plays a role in apoptotic morphological changes, including cell contraction, membrane blebbing and apoptotic bodies formation. This function, which requires the activation of MAPK8/JNK and nuclear localization of C-terminally truncated isoform 1, may be linked to the mitochondrial CASP9-associated death pathway. Isoform 1 binds to microtubules and affects their organization and stability independently of its kinase activity. Prevents MAP3K7-mediated activation of CHUK, and thus NF-kappa-B activation, but not that of MAPK8/JNK. May play a role in the osmotic stress-MAPK8 pathway. Isoform 2, but not isoform 1, is required for PCDH8 endocytosis. Following homophilic interactions between PCDH8 extracellular domains, isoform 2 phosphorylates and activates MAPK14/p38 MAPK which in turn phosphorylates isoform 2. This process leads to PCDH8 endocytosis and CDH2 cointernalization. Both isoforms are involved in MAPK14 phosphorylation.INO80E: Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.PPP4C: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase By similarity. In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin. MAPK3: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK-1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1. Phosphorylates heat shock factor protein 4 (HSF4). Participates in a signaling cascade initiated by activated KIT and KITLG/SCF. GIYD2: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.BCL7C: B-cell lymphoma 7 protein family member. May play an anti-apoptotic role.

30 0.00 gaaggttga 51 tandem-duplication No annotated elements involved.13 0.00 tctatggc 180 deletion No annotated elements involved.79 0.00 catggggtg 461 probable-inversion Right end of inversion in first intron of PRKACA, left end not in annotated element. PRKACA is cAMP-dependent protein kinase catalytic subunit alpha. Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis. 22 0.00 aaaacttg 6 complex 941 "left end" of this rearrangement is in the 3' UTR of IER2, Immediate early response gene 2 protein. "right end" is not in an annotated element. This SV is connected to SV ç14, a chromosomal translocation between chr6 and 19.16 0.00 catacttg 460 probable-inversion No annotated elements involved in breakpoints. 12 0.00 gtgtggtt 44 tandem-duplication Tandem duplication with right breakpoint in GTBP3 (GTPase involved in the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs) and left breakpoint in ANO8 (Calcium activated Chloride channel)43 0.00 agtacaaag 169 deletion Deletion of 1 of 4 copies. Inside this is c19orf2 (Unconventional prefoldin RPB5 interactor), ZNF536 (unknown function), DKZp566F0947 (ncRNA with unknown function) and on right breakpoint TSHZ3 (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start sites)27 0.00 gtcatgatt 42 tandem-duplication Tandem duplication of the area where the adenoviral has integrated, in the PSG gene cluster. PSG 2, 4, 5 and 9 and PRG1 (ncRNA with unknown function) are inside the duplication. 20 0.00 aaaaaatg 5 probable-inversion Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.42 0.00 acagtgga 159 deletion Deletion of 2 of 3 copies of exon 2 and large pieces of the surrounding introns 1 and 2 of the SLC23A2 gene. It contains only 5' UTR elements. Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na+ for each ascorbate.39 0.00 cggtcaga 153 deletion Small deletion in intron 1 of PREX1 gene. Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol-3,4,5-triphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.32 0.00 agggcgagg 150 deletion No annotated elements involved.40 0.00 gagttata 147 deletion Small deletion in intron 3 of ZBTB46 gene (function unknown).17 0.00 cactccgac 459 probable-inversion Very large inversion, spanning almost the entire p arm of chrX and about 1/3 of the q arm. The left end breakpoint is in the ARSH gene, arylsulfatase H.15 0.00 gtgaatca 3 probable-inversion 2 mb inversion with the left side in intron 1 of the ARHGAP6 gene (Rho GTPase-activating protein 6,Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology.) and the right side in the first intron of the GPM6B gene (poorly characterised protein, may be involved in neuronal transport).10 0.00 taaaaaat 35 tandem-duplication Duplication of about 1,5 mb. CNV from 6 to 7. It involves many genes. The right breakpoint is in HDAC8 (Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. May play a role in smooth muscle cell contractility.)25 0.00 ttgaggtg 119 deletion No annotated elements involved.15 0.05 gtgttcct 87 tandem-duplication No annotated elements involved.

202 0.06 aggcagaaag 350 deletion No annotated elements involved.118 0.06 aaaaccccc 336 deletion Small deletion inside intron 17 of SDK1 gene (Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.)

58 0.06 ccatgacc 261 deletion Small deletion inside intron 11 of ANO1 (Acts as a calcium-activated chloride channel. Required for normal tracheal development. Gene is known to be amplified certain gastrointestinal cancers.72 0.06 taattaact 246 deletion No annotated elements involved.47 0.06 aggatgatc 218 deletion No annotated elements involved.27 0.06 cggccacag 46 tandem-duplication Small duplication inside intron 1 of C19orf6 (mambralin, a poorly characterized protein, potential as a tumor marker).28 0.06 tactaaaat 135 deletion Small deletion inside intron 4 of KIAA1671, a protein with unknown function.

One of three copies affected. In this copy, the NPHP4 gene loses it's exon 6 and most of intron 5. NPHP4 is Nephrocystin-4, Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8 By similarity. Does not seem to be strictly required for ciliogenesis.No annotated elements involved.No annotated elements involved.No annotated elements involved on either chromosome.No annotated elements involved.No annotated elements involved on either chromosome.

Deletion of a part of intron 1 of EML4 gene in 2 of 3 copies of the gene. EML4 may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic.No annotated elements involved.No annotated elements involved.Deletion inside intron 2 of COMMD1. Too short to predict how many copies affected. COMMD1 promotes ubiquitination of NF-kappa-B subunit RELA and its subsequent proteasomal degradation. Down-regulates NF-kappa-B activity. Down-regulates SOD1 activity by interfering with its homodimerization. Plays a role in copper ion homeostasis. Can bind one copper ion per monomer. May function to facilitate biliary copper excretion within hepatocytes.No annotated elements involved.No annotated elements involved.This deletion affects exon 3 of the tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.No annotated elements involved.This deletion affects the 3' end of the DIS3L2 gene, exon 11 through 18 (last one). It's a deletion only present in 293A and Flp, as can be seen from the CG CNV, and with only 1 of 3 (293A) or 1 of 2 (Flp) alleles deleted.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.Deletion of probably 1 of 5 copies of SHPRH: large part of intron 28, exon 29 and small part of intron 29. No noticeable CNV breakpoints in any line... SHPRH is an E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. This gene is important for genomic stability through it's interaction with PCNA, and aputative tumor suppressor gene.On chr 6,TINAG is involved. TINAG Mediates adhesion of proximal tubule epithelial cells via integrins alpha3-beta1 and alphaV-beta3. This is a non catalytic peptidase C1 family protein. The target location for joining with chr19 does not contain any genes, but heavy rearrangements and duplications took place on this chromosome.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.Deletion inside intron 7 of TSNARE1, t-SNARE domain containing protein 1. A protein with unknown function.No annotated elements involved.No annotated elements involved.Deletion of the largest part of intron 26 and exon 27, and a piece of intron 27 of SPTAN1, a fodrin, which seems to be involved in secretion, interacts with calmodulin in a calcium-dependent manner and is thus candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Not all copies seem to be deleted.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved. Lies inside SV Id 4460, non-novel probable inversion.No annotated elements involved. Lies inside SV Id 4460 AND SV Id 270, both are non-novel probable inversions.

No annotated elements involved.Tandem duplication of ~6000 kb of chr 13. It brings the copy number from 2 to 3 in this area.Several other things going on in this chromosome, also in the other lines.No annotated elements involved.GPC5, glypican 5 is involved: 1.3 kb short deletion in intron 7 (this intron is about 700 kb long), the last intron. GPC5 is a cell surface proteoglycan that bears heparan sulfate. It's present in all lines.Deletion of 2.5 kb of intron 2 of MBNL2. Mediates pre-mRNA alternative splicing regulation. Musclebind-Like 2 Acts either as activator or repressor of splicing on specific pre-mRNA targets. Deletion of 1.3 kb part in intron 1 of DAD1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1, Component of the N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.Duplication involving the first exon of PCSK6, TM2D3 and TARSL2. PCSK6 is Proprotein convertase subtilisin/kexin type 6, Likely to represent an endoprotease activity within the constitutive secretory pathway, with unique restricted distribution in both neuroendocrine and non-neuroendocrine tissues and capable of cleavage at the RX(K/R)R consensus motif.TM2D3 is a TM2 domain-containing protein 3, it might be involved in Alzheimer'sTARSL2 is a probable threonyl-tRNA synthetase 2, cytoplasmicNo annotated elements involved.Inversion disrupting the TARSL2 gene. TARSL2 is a probable threonyl-tRNA synthetase 2, cytoplasmicDeletion involving Hemoglobin subunit mu. At least one or two copies of this protein, maybe all are deleted. Duplication of 1300 kb piece of chr 16 containing many genes. Total copy number comes to 4 or 5 depending on the cell line. Relevant genes are shown below, many involved in DNA repair and histone remodelling.MAZ, Myc associated Zinc Finger: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.SEZ6L2: Seisure-related 6 homolog-like 2. Upregulated in lung cancers, especially in NSCLC.TAOK2: Serine/threonine-protein kinase involved in different processes such as membrane blebbing and apoptotic bodies formation DNA damage response and MAPK14/p38 MAPK stress-activated MAPK cascade. Phosphorylates itself, MBP, activated MAPK8, MAP2K3, MAP2K6 and tubulins. Activates the MAPK14/p38 MAPK signaling pathway through the specific activation and phosphorylation of the upstream MAP2K3 and MAP2K6 kinases. In response to DNA damage, involved in the G2/M transition DNA damage checkpoint by activating the p38/MAPK14 stress-activated MAPK cascade, probably by mediating phosphorylation of upstream MAP2K3 and MAP2K6 kinases. Isoform 1, but not isoform 2, plays a role in apoptotic morphological changes, including cell contraction, membrane blebbing and apoptotic bodies formation. This function, which requires the activation of MAPK8/JNK and nuclear localization of C-terminally truncated isoform 1, may be linked to the mitochondrial CASP9-associated death pathway. Isoform 1 binds to microtubules and affects their organization and stability independently of its kinase activity. Prevents MAP3K7-mediated activation of CHUK, and thus NF-kappa-B activation, but not that of MAPK8/JNK. May play a role in the osmotic stress-MAPK8 pathway. Isoform 2, but not isoform 1, is required for PCDH8 endocytosis. Following homophilic interactions between PCDH8 extracellular domains, isoform 2 phosphorylates and activates MAPK14/p38 MAPK which in turn phosphorylates isoform 2. This process leads to PCDH8 endocytosis and CDH2 cointernalization. Both isoforms are involved in MAPK14 phosphorylation.INO80E: Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.PPP4C: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase By similarity. In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin. MAPK3: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK-1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1. Phosphorylates heat shock factor protein 4 (HSF4). Participates in a signaling cascade initiated by activated KIT and KITLG/SCF. GIYD2: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.BCL7C: B-cell lymphoma 7 protein family member. May play an anti-apoptotic role.No annotated elements involved.No annotated elements involved.Right end of inversion in first intron of PRKACA, left end not in annotated element. PRKACA is cAMP-dependent protein kinase catalytic subunit alpha. Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis. "left end" of this rearrangement is in the 3' UTR of IER2, Immediate early response gene 2 protein. "right end" is not in an annotated element. This SV is connected to SV ç14, a chromosomal translocation between chr6 and 19.No annotated elements involved in breakpoints. Tandem duplication with right breakpoint in GTBP3 (GTPase involved in the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs) and left breakpoint in ANO8 (Calcium activated Chloride channel)Deletion of 1 of 4 copies. Inside this is c19orf2 (Unconventional prefoldin RPB5 interactor), ZNF536 (unknown function), DKZp566F0947 (ncRNA with unknown function) and on right breakpoint TSHZ3 (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start sites)Tandem duplication of the area where the adenoviral has integrated, in the PSG gene cluster. PSG 2, 4, 5 and 9 and PRG1 (ncRNA with unknown function) are inside the duplication. Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.Deletion of 2 of 3 copies of exon 2 and large pieces of the surrounding introns 1 and 2 of the SLC23A2 gene. It contains only 5' UTR elements. Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na+ for each ascorbate.Small deletion in intron 1 of PREX1 gene. Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol-3,4,5-triphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.No annotated elements involved.Small deletion in intron 3 of ZBTB46 gene (function unknown).Very large inversion, spanning almost the entire p arm of chrX and about 1/3 of the q arm. The left end breakpoint is in the ARSH gene, arylsulfatase H.2 mb inversion with the left side in intron 1 of the ARHGAP6 gene (Rho GTPase-activating protein 6,Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology.) and the right side in the first intron of the GPM6B gene (poorly characterised protein, may be involved in neuronal transport).Duplication of about 1,5 mb. CNV from 6 to 7. It involves many genes. The right breakpoint is in HDAC8 (Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. May play a role in smooth muscle cell contractility.)No annotated elements involved.No annotated elements involved.No annotated elements involved.Small deletion inside intron 17 of SDK1 gene (Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.)Small deletion inside intron 11 of ANO1 (Acts as a calcium-activated chloride channel. Required for normal tracheal development. Gene is known to be amplified certain gastrointestinal cancers.No annotated elements involved.No annotated elements involved.Small duplication inside intron 1 of C19orf6 (mambralin, a poorly characterized protein, potential as a tumor marker).Small deletion inside intron 4 of KIAA1671, a protein with unknown function.

One of three copies affected. In this copy, the NPHP4 gene loses it's exon 6 and most of intron 5. NPHP4 is Nephrocystin-4, Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8 By similarity. Does not seem to be strictly required for ciliogenesis.

Deletion of a part of intron 1 of EML4 gene in 2 of 3 copies of the gene. EML4 may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic.

Deletion inside intron 2 of COMMD1. Too short to predict how many copies affected. COMMD1 promotes ubiquitination of NF-kappa-B subunit RELA and its subsequent proteasomal degradation. Down-regulates NF-kappa-B activity. Down-regulates SOD1 activity by interfering with its homodimerization. Plays a role in copper ion homeostasis. Can bind one copper ion per monomer. May function to facilitate biliary copper excretion within hepatocytes.

This deletion affects exon 3 of the tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.

This deletion affects the 3' end of the DIS3L2 gene, exon 11 through 18 (last one). It's a deletion only present in 293A and Flp, as can be seen from the CG CNV, and with only 1 of 3 (293A) or 1 of 2 (Flp) alleles deleted.

Deletion of probably 1 of 5 copies of SHPRH: large part of intron 28, exon 29 and small part of intron 29. No noticeable CNV breakpoints in any line... SHPRH is an E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. This gene is important for genomic stability through it's interaction with PCNA, and aputative tumor suppressor gene.On chr 6,TINAG is involved. TINAG Mediates adhesion of proximal tubule epithelial cells via integrins alpha3-beta1 and alphaV-beta3. This is a non catalytic peptidase C1 family protein. The target location for joining with chr19 does not contain any genes, but heavy rearrangements and duplications took place on this chromosome.

Deletion of the largest part of intron 26 and exon 27, and a piece of intron 27 of SPTAN1, a fodrin, which seems to be involved in secretion, interacts with calmodulin in a calcium-dependent manner and is thus candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Not all copies seem to be deleted.

Tandem duplication of ~6000 kb of chr 13. It brings the copy number from 2 to 3 in this area.Several other things going on in this chromosome, also in the other lines.

GPC5, glypican 5 is involved: 1.3 kb short deletion in intron 7 (this intron is about 700 kb long), the last intron. GPC5 is a cell surface proteoglycan that bears heparan sulfate. It's present in all lines.Deletion of 2.5 kb of intron 2 of MBNL2. Mediates pre-mRNA alternative splicing regulation. Musclebind-Like 2 Acts either as activator or repressor of splicing on specific pre-mRNA targets. Deletion of 1.3 kb part in intron 1 of DAD1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1, Component of the N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.

PCSK6 is Proprotein convertase subtilisin/kexin type 6, Likely to represent an endoprotease activity within the constitutive secretory pathway, with unique restricted distribution in both neuroendocrine and non-neuroendocrine tissues and capable of cleavage at the RX(K/R)R consensus motif.

Duplication of 1300 kb piece of chr 16 containing many genes. Total copy number comes to 4 or 5 depending on the cell line. Relevant genes are shown below, many involved in DNA repair and histone remodelling.MAZ, Myc associated Zinc Finger: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

TAOK2: Serine/threonine-protein kinase involved in different processes such as membrane blebbing and apoptotic bodies formation DNA damage response and MAPK14/p38 MAPK stress-activated MAPK cascade. Phosphorylates itself, MBP, activated MAPK8, MAP2K3, MAP2K6 and tubulins. Activates the MAPK14/p38 MAPK signaling pathway through the specific activation and phosphorylation of the upstream MAP2K3 and MAP2K6 kinases. In response to DNA damage, involved in the G2/M transition DNA damage checkpoint by activating the p38/MAPK14 stress-activated MAPK cascade, probably by mediating phosphorylation of upstream MAP2K3 and MAP2K6 kinases. Isoform 1, but not isoform 2, plays a role in apoptotic morphological changes, including cell contraction, membrane blebbing and apoptotic bodies formation. This function, which requires the activation of MAPK8/JNK and nuclear localization of C-terminally truncated isoform 1, may be linked to the mitochondrial CASP9-associated death pathway. Isoform 1 binds to microtubules and affects their organization and stability independently of its kinase activity. Prevents MAP3K7-mediated activation of CHUK, and thus NF-kappa-B activation, but not that of MAPK8/JNK. May play a role in the osmotic stress-MAPK8 pathway. Isoform 2, but not isoform 1, is required for PCDH8 endocytosis. Following homophilic interactions between PCDH8 extracellular domains, isoform 2 phosphorylates and activates MAPK14/p38 MAPK which in turn phosphorylates isoform 2. This process leads to PCDH8 endocytosis and CDH2 cointernalization. Both isoforms are involved in MAPK14 phosphorylation.INO80E: Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.PPP4C: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase By similarity. In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin. MAPK3: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK-1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1. Phosphorylates heat shock factor protein 4 (HSF4). Participates in a signaling cascade initiated by activated KIT and KITLG/SCF. GIYD2: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Right end of inversion in first intron of PRKACA, left end not in annotated element. PRKACA is cAMP-dependent protein kinase catalytic subunit alpha. Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis. "left end" of this rearrangement is in the 3' UTR of IER2, Immediate early response gene 2 protein. "right end" is not in an annotated element. This SV is connected to SV ç14, a chromosomal translocation between chr6 and 19.

Tandem duplication with right breakpoint in GTBP3 (GTPase involved in the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs) and left breakpoint in ANO8 (Calcium activated Chloride channel)Deletion of 1 of 4 copies. Inside this is c19orf2 (Unconventional prefoldin RPB5 interactor), ZNF536 (unknown function), DKZp566F0947 (ncRNA with unknown function) and on right breakpoint TSHZ3 (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start sites)Tandem duplication of the area where the adenoviral has integrated, in the PSG gene cluster. PSG 2, 4, 5 and 9 and PRG1 (ncRNA with unknown function) are inside the duplication. Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.Deletion of 2 of 3 copies of exon 2 and large pieces of the surrounding introns 1 and 2 of the SLC23A2 gene. It contains only 5' UTR elements. Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na+ for each ascorbate.Small deletion in intron 1 of PREX1 gene. Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol-3,4,5-triphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.

Very large inversion, spanning almost the entire p arm of chrX and about 1/3 of the q arm. The left end breakpoint is in the ARSH gene, arylsulfatase H.2 mb inversion with the left side in intron 1 of the ARHGAP6 gene (Rho GTPase-activating protein 6,Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology.) and the right side in the first intron of the GPM6B gene (poorly characterised protein, may be involved in neuronal transport).Duplication of about 1,5 mb. CNV from 6 to 7. It involves many genes. The right breakpoint is in HDAC8 (Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. May play a role in smooth muscle cell contractility.)

Small deletion inside intron 17 of SDK1 gene (Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.)Small deletion inside intron 11 of ANO1 (Acts as a calcium-activated chloride channel. Required for normal tracheal development. Gene is known to be amplified certain gastrointestinal cancers.

One of three copies affected. In this copy, the NPHP4 gene loses it's exon 6 and most of intron 5. NPHP4 is Nephrocystin-4, Involved in the organization of apical junctions in kidney cells together with NPHP1 and RPGRIP1L/NPHP8 By similarity. Does not seem to be strictly required for ciliogenesis.


This deletion affects exon 3 of the tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.



Deletion of 1.3 kb part in intron 1 of DAD1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1, Component of the N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.

PCSK6 is Proprotein convertase subtilisin/kexin type 6, Likely to represent an endoprotease activity within the constitutive secretory pathway, with unique restricted distribution in both neuroendocrine and non-neuroendocrine tissues and capable of cleavage at the RX(K/R)R consensus motif.

MAZ, Myc associated Zinc Finger: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

TAOK2: Serine/threonine-protein kinase involved in different processes such as membrane blebbing and apoptotic bodies formation DNA damage response and MAPK14/p38 MAPK stress-activated MAPK cascade. Phosphorylates itself, MBP, activated MAPK8, MAP2K3, MAP2K6 and tubulins. Activates the MAPK14/p38 MAPK signaling pathway through the specific activation and phosphorylation of the upstream MAP2K3 and MAP2K6 kinases. In response to DNA damage, involved in the G2/M transition DNA damage checkpoint by activating the p38/MAPK14 stress-activated MAPK cascade, probably by mediating phosphorylation of upstream MAP2K3 and MAP2K6 kinases. Isoform 1, but not isoform 2, plays a role in apoptotic morphological changes, including cell contraction, membrane blebbing and apoptotic bodies formation. This function, which requires the activation of MAPK8/JNK and nuclear localization of C-terminally truncated isoform 1, may be linked to the mitochondrial CASP9-associated death pathway. Isoform 1 binds to microtubules and affects their organization and stability independently of its kinase activity. Prevents MAP3K7-mediated activation of CHUK, and thus NF-kappa-B activation, but not that of MAPK8/JNK. May play a role in the osmotic stress-MAPK8 pathway. Isoform 2, but not isoform 1, is required for PCDH8 endocytosis. Following homophilic interactions between PCDH8 extracellular domains, isoform 2 phosphorylates and activates MAPK14/p38 MAPK which in turn phosphorylates isoform 2. This process leads to PCDH8 endocytosis and CDH2 cointernalization. Both isoforms are involved in MAPK14 phosphorylation.

PPP4C: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase By similarity. In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin. MAPK3: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK-1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1. Phosphorylates heat shock factor protein 4 (HSF4). Participates in a signaling cascade initiated by activated KIT and KITLG/SCF. GIYD2: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.

Right end of inversion in first intron of PRKACA, left end not in annotated element. PRKACA is cAMP-dependent protein kinase catalytic subunit alpha. Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis.

Tandem duplication with right breakpoint in GTBP3 (GTPase involved in the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs) and left breakpoint in ANO8 (Calcium activated Chloride channel)Deletion of 1 of 4 copies. Inside this is c19orf2 (Unconventional prefoldin RPB5 interactor), ZNF536 (unknown function), DKZp566F0947 (ncRNA with unknown function) and on right breakpoint TSHZ3 (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start sites)

Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.Deletion of 2 of 3 copies of exon 2 and large pieces of the surrounding introns 1 and 2 of the SLC23A2 gene. It contains only 5' UTR elements. Sodium/ascorbate cotransporter. Mediates electrogenic uptake of vitamin C, with a stoichiometry of 2 Na+ for each ascorbate.Small deletion in intron 1 of PREX1 gene. Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol-3,4,5-triphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.

2 mb inversion with the left side in intron 1 of the ARHGAP6 gene (Rho GTPase-activating protein 6,Could regulate the interactions of signaling molecules with the actin cytoskeleton. Promotes continuous elongation of cytoplasmic processes during cell motility and simultaneous retraction of the cell body changing the cell morphology.) and the right side in the first intron of the GPM6B gene (poorly characterised protein, may be involved in neuronal transport).Duplication of about 1,5 mb. CNV from 6 to 7. It involves many genes. The right breakpoint is in HDAC8 (Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. May play a role in smooth muscle cell contractility.)

Small deletion inside intron 17 of SDK1 gene (Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.)

Deletion of 1.3 kb part in intron 1 of DAD1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1, Component of the N-oligosaccharyl transferase enzyme which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains.

MAZ, Myc associated Zinc Finger: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.




Deletion of 1 of 4 copies. Inside this is c19orf2 (Unconventional prefoldin RPB5 interactor), ZNF536 (unknown function), DKZp566F0947 (ncRNA with unknown function) and on right breakpoint TSHZ3 (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start sites)

Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.

Small deletion in intron 1 of PREX1 gene. Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol-3,4,5-triphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.



Deletion of probably 1 of 5 copies of SHPRH: large part of intron 28, exon 29 and small part of intron 29. No noticeable CNV breakpoints in any line... SHPRH is an E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. This gene is important for genomic stability through it's interaction with PCNA, and aputative tumor suppressor gene.





Left side overlaps with ZNF841, a ZFN with unknown function. Inversion that overlaps with inversion with Id 4252, it's assumed to have happened in independent copies, else this would probably result in a different type of rearrangement (complex) in which a piece is located in a completely different part of the chromosome. It would not be possible to reconstruct what happened, since there is no way to know which of the inversions took place first.


Deletion of probably 1 of 5 copies of SHPRH: large part of intron 28, exon 29 and small part of intron 29. No noticeable CNV breakpoints in any line... SHPRH is an E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. This gene is important for genomic stability through it's interaction with PCNA, and aputative tumor suppressor gene.


PPP4C: Protein phosphatase that is involved in many processes such as microtubule organization at centrosomes, maturation of spliceosomal snRNPs, apoptosis, DNA repair, tumor necrosis factor (TNF)-alpha signaling, activation of c-Jun N-terminal kinase MAPK8, regulation of histone acetylation, DNA damage checkpoint signaling, NF-kappa-B activation and cell migration. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on Ser-140 (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Dephosphorylates NDEL1 at CDK1 phosphorylation sites and negatively regulates CDK1 activity in interphase By similarity. In response to DNA damage, catalyzes RPA2 dephosphorylation, an essential step for DNA repair since it allows the efficient RPA2-mediated recruitment of RAD51 to chromatin.


>Id LeftChr LeftPosition LeftStrand LeftLength RightChr RightPosition3806 chr1 170689001 + 477 chr5 763610901838 chr1 170689014 - 400 chr5 763610753884 chr1 206201312 + 533 chr2 658377764461 chr2 132747163 + 405 chr16 338635324607 chr2 141488007 + 441 chr2 1414922033698 chr2 141907997 + 516 chr2 1420063351604 chr2 141989086 - 635 chr5 1303514543667 chr2 211938534 + 416 chr2 2119741544603 chr2 212066574 + 542 chr2 2121028511028 chr2 212084374 - 500 chr2 2121623313639 chr3 21108697 + 454 chr3 214828643202 chr3 21491018 + 469 chr19 489811151650 chr3 23515499 - 664 chr3 25356513

1643 chr3 60819237 - 491 chr3 62727301

3585 chr3 117943518 + 485 chr3 1182224323584 chr3 118202899 + 577 chr3 1183574503575 chr3 132067158 + 362 chr3 1320684424354 chr3 137822765 + 412 chr16 594697

1636 chr3 174289849 - 528 chr3 174645894

3553 chr3 174377004 + 370 chr3 1743785851629 chr4 11174549 - 336 chr4 111751483515 chr4 62427955 + 473 chr4 624786591021 chr4 142156670 - 250 chr4 1421573683384 chr4 190847757 + 375 chr7 920576201605 chr5 66448938 - 177 chr5 67597981

3159 chr5 145747094 + 453 chr5 145763459

887 chr6 78954861 - 537 chr6 83827142

3089 chr6 79954429 + 443 chr6 83600480888 chr6 82671676 - 505 chr6 83349703

4252 chr6 88498298 + 414 chr13 331907253048 chr6 142530339 + 288 chr6 1425340054264 chr7 899343 + 778 chr8 499279221541 chr7 42090944 - 350 chr7 44892832

2293 chr7 68757558 + 550 chr19 879591

2974 chr7 110628806 + 410 chr7 1106889762915 chr8 8764151 + 436 chr8 87660922222 chr8 112332555 + 503 chrX 1234537601117 chr8 112332567 - 485 chrX 1234537352835 chr9 8060272 + 313 chr9 8061089

771 chr9 33614218 - 437 chr16 19502018

823 chr9 66195511 - 350 chr9 679039161491 chr9 86730225 - 597 chr9 89227007

1487 chr9 125033976 - 508 chr9 125197388

1280 chr9 130414253 - 440 chr15 738844132730 chr10 52970367 + 200 chr10 530796691413 chr10 53652666 - 186 chr10 536634052639 chr11 67086662 + 341 chr11 67089051

680 chr11 77981521 - 453 chr11 78127010679 chr11 84098087 - 485 chr11 84108078

2611 chr12 1185080 + 210 chr12 12026042608 chr12 6718000 + 235 chr12 6718785

673 chr12 16374001 - 397 chr12 163938352530 chr13 30094960 + 528 chr13 30095771

564 chr13 32129447 - 362 chr19 9804855

4032 chr13 32230863 + 372 chr20 18542725

562 chr13 32394179 - 73 chr13 32541871

576 chr13 32394492 - 363 chr13 32549436575 chr13 32399549 - 326 chr13 32641774

561 chr13 32640844 - 501 chr20 19930868

560 chr13 32667041 - 500 chr21 45620358

555 chr13 84960512 - 479 chr13 85019936546 chr14 22663155 - 455 chr14 27442360

2455 chr14 33685685 + 483 chr14 33687010

4162 chr14 63243922 + 210 chr14 63629872

501 chr15 70139794 - 487 chr15 70294611

489 chr16 1186088 - 221 chr16 1274956

454 chr16 77154461 - 550 chr16 773200994021 chr17 26581329 + 165 chr17 265819402144 chr17 35256195 + 437 chr17 35256963

378 chr18 44379122 - 535 chr18 46768138

1950 chr19 902245 + 502 chr20 18542658

3996 chr19 8943608 + 361 chr19 18656438

325 chr19 44115845 - 336 chr19 44375931259 chr19 48532599 - 473 chr19 48536935258 chr19 49347897 - 638 chr19 49370888

3994 chr19 49467081 + 570 chr19 494710801930 chr20 9973449 + 335 chr20 9975700

252 chr20 18153490 - 542 chr20 181571051890 chr20 61862278 + 188 chr20 61862811

225 chr20 61981411 + 348 chr20 61982251145 chr22 48809296 + 475 chr22 48809992245 chrX 16446293 - 458 chrX 32139586

1222 chrX 34255556 + 236 chrX 64403828238 chrX 64475599 - 257 chrX 89728706

19 chrX 64476577 - 461 chrX 897291201216 chrX 64476582 + 484 chrX 89430477

124 chrX 74070808 + 435 chrX 74076765237 chrX 81958351 - 445 chrX 81978585109 chrX 117905654 + 466 chrX 117907917

RightStrand RightLength StrandConsiste Interchromoso Distance DiscordantMateJunctionSeque+ 426 Y Y 59 Y- 502 Y Y 48 Y+ 155 Y Y 16 Y- 772 N Y 201 Y- 478 N N 4196 28 Y+ 392 Y N 98338 15 Y- 363 Y Y 35 Y+ 400 Y N 35620 44 Y- 416 N N 36277 19 Y+ 359 N N 77957 40 Y+ 480 Y N 374167 77 Y+ 489 Y Y 95 Y- 410 Y N 1841014 96 Y

- 395 Y N 1908064 99 Y

+ 498 Y N 278914 100 Y+ 435 Y N 154551 51 Y+ 364 Y N 1284 21 Y- 414 N Y 13 Y

- 117 Y N 356045 19 Y

+ 442 Y N 1581 34 Y- 411 Y N 599 23 Y+ 420 Y N 50704 30 Y+ 456 N N 698 65 Y+ 426 Y Y 22 Y- 452 Y N 1149043 28 Y

+ 567 Y N 16365 11 Y

+ 417 N N 4872281 29 Y

+ 368 Y N 3646051 88 Y+ 449 N N 678027 75 Y- 389 N Y 31 Y+ 497 Y N 3666 33 Y- 472 N Y 72 Y- 439 Y N 2801888 10 Y

+ 485 Y Y 142 Y

+ 372 Y N 60170 35 Y+ 458 Y N 1941 54 Y+ 651 Y Y 48 Y- 435 Y Y 46 Y+ 409 Y N 817 21 Y+ 323 N Y 14 Y

+ 338 N N 1708405 12 Y- 455 Y N 2496782 134 Y

- 633 Y N 163412 112 Y

- 493 Y Y 18 Y+ 411 Y N 109302 16 Y- 462 Y N 10739 25 Y+ 245 Y N 2389 19 Y- 545 Y N 145489 63 Y- 440 Y N 9991 45 Y+ 445 Y N 17524 39 Y+ 384 Y N 785 14 Y- 429 Y N 19834 39 Y+ 564 Y N 811 146 Y+ 395 N Y 25 Y

- 478 N Y 69 Y

+ 577 N N 147692 12 Y

- 473 Y N 154944 16 Y- 435 Y N 242225 19 Y

+ 667 N Y 88 Y

- 438 Y Y 66 Y

- 211 Y N 59424 11 Y- 148 Y N 4779205 13 Y+ 452 Y N 1325 66 Y

- 568 N N 385950 54 Y

- 408 Y N 154817 11 Y

- 273 Y N 88868 14 Y

- 422 Y N 165638 84 Y- 468 N N 611 22 Y+ 454 Y N 768 51 Y- 417 Y N 2389016 121 Y

+ 596 Y Y 20 Y

- 621 N N 9712830 134 Y

- 384 Y N 260086 21 Y+ 362 N N 4336 20 Y+ 496 N N 22991 210 Y- 437 N N 3999 398 Y+ 450 Y N 2251 13 Y+ 75 N N 3615 16 Y+ 451 Y N 533 21 Y+ 129 Y N 840 25 Y+ 355 Y N 696 13 Y- 371 Y N 15693293 23 Y- 442 N N 30148272 27 Y- 98 Y N 25253107 15 Y+ 381 N N 25252543 21 Y- 262 N N 24953895 20 Y+ 404 Y N 5957 24 Y- 413 Y N 20234 50 Y+ 390 Y N 2263 40 Y

TransitionSequ TransitionLeng LeftRepeatClassRightRepeatClasLeftGenes RightGenes XRef0 LOR1a:LTR:ERV NM_139240:+0 LOR1a:LTR:ERV NM_139240:+0 MLT1D:LTR:MaMLT1E-int:LTR:MaLR

CGTTTATGTTG 11 SegDup;Self ch SegDup;Self chain0 NM_018557:- NM_018557:-0 L1M4b:LINE:L1;Self chain;Tan NM_018557:- NM_018557:-0 AluSp:SINE:Alu AluSx:SINE:Alu;NM_018557:-

CTTCAGA 7 LTR49:LTR:ERV1 NM_001042599:-;NM_005235:-AGCTCTGTCGA 12 L1MA3:LINE:L1 NM_001042599NM_001042599:-;NM_005235:-

0 NM_001042599NM_001042599:-;NM_005235:-0 NM_024697:-0 MSR1:Satellite: NM_024697:-0 NM_152653:+

TATC 4 NM_001166243NM_003716:-;NM_183393:-;NM_183394:-

00 MIR3:SINE:MIR0 Self chain;THE Tigger1:DNA:MER2_type0 L1ME2:LINE:L1;NM_005862:- NM_021168:+

0 Tandem period NM_031955:- NM_014932:+

0 MLT1F2:LTR:M Kanga1:DNA:Tc20 L1MA7:LINE:L10 NM_015236:+ NM_015236:+

A 1 NM_020724:- NM_020724:-T 1 Self chain Self chain NM_001040057:-;NM_152789:-

0 Self chain NM_001164664NM_181523:+

0 L2:LINE:L2 AluJo:SINE:Alu

0 MSTA:LTR:MaL L1MC4:LINE:L1 NM_198920:-

0 MER20B:DNA:MER1_type0 AluJo:SINE:Alu0 MLT1E2:LTR:MaLR0 Self chain AluSq:SINE:Alu NM_016485:+ NM_016485:+

TTGGGTGTTTG 25 (TG)n:Simple_repeat:Simple_r NM_015949:+0 AluSx:SINE:Alu NM_000168:-

0 MIR:SINE:MIR;SMIRb:SINE:MIR;NM_001127231NM_005224:+

0 AluJb:SINE:Alu NM_032549:- NM_032549:-0 Self chain MIRb:SINE:MIR;NM_004225:- NM_004225:-0 NM_001163278:-;NM_001163279:-;NM_014253:-0 NM_001163278:-;NM_001163279:-;NM_014253:-

G 1 L1PA16:LINE:L1L1PA16:LINE:L1GCC 3 SegDup;Self ch L1MB8:LINE:L1;Self chain NM_020314:+

0 SegDup;Self ch SegDup;Self chain0 Self chain NM_001018064:+;NM_006180:+

0 L2:LINE:L2 NM_018387:- NM_020946:-

0 Self chain L1MA5:LINE:L1;NM_001130438:+;NM_003127:+0 Self chain MER51A:LTR:ERVNM_001098512NM_001098512:+;NM_006258:+0 Self chain L1PA2:LINE:L1;SNM_001098512NM_001098512:+;NM_006258:+0 AluSq:SINE:Alu;AluSg/x:SINE:Alu;Self chain0 AluSx:SINE:Alu;MIRb:SINE:MIR;Self chain NM_001098816:-

AG 2 Self chain Self chain NM_001142699NM_001142699:-;NM_001364:-CAAA 4 NM_178039:+; NM_178039:+;NM_178040:+;NR_027946:+;NR_027948:+;NR_

0 AluSg:SINE:Alu AluY:SINE:Alu0 MIRb:SINE:MIR NM_020300:+;NM_145791:+;NM_145792:+0 MER21B:LTR:E NM_005800:+ NM_005800:+

CTT 3 L1PA14:LINE:L1AluJo:SINE:Alu; NM_015032:+

0 Self chain AluJb:SINE:Alu NM_015032:+ NM_080820:+

0

CTGCTTTACTCA 21 LTR16D:LTR:ERVL0 L1ME1:LINE:L1 NM_052851:-;NM_178006:-;NM_178007:-

0 NM_052851:-; NM_018993:+

CTACTTCATGG 64 Self chain;Tan NM_052851:-;NM_178006:-

0 MSTC-int:LTR:MaLR0 Self chain Self chain0

T 1 NM_030791:- NM_015180:+;NM_182914:+

0 (TAAAAA)n:SimpSelf chain NM_006901:- NM_002654:-;NM_182470:-;NM_182471:-

GGCCCTGGAAT 12 Self chain Self chain;Tan NM_001005407:+;NM_021098:+

AAAT 4 MIR3:SINE:MIR NM_016373:+ NM_016373:+0 SegDup;Self ch SegDup;Self ch NM_000267:+; NM_000267:+;NM_001042492:+0 Self chain Self chain NM_012481:-;NNM_012481:-;NM_183228:-;NM_183229:-;NM_183230:-;NM_0 MER20B:DNA:MNM_001142397NM_018696:+

TATGCCCGGCC 55 FLAM_C:SINE:AlAluJb:SINE:Alu NM_005224:+ NM_080820:+

0 Self chain Self chain NM_024690:- NM_001098482:+;NM_015321:+

0 AluSx:SINE:Alu;AluSx:SINE:Alu;Self chain0 L2:LINE:L2;SegDSegDup;Self chain0 MLT1D:LTR:MaLRSelf chain NM_001144824NM_001032372:+;NM_001032373:+;NM_001032374:+;NM_00 Self chain L2:LINE:L2;Self NM_181756:+ NM_181756:+

ATA 3 NM_022096:+; NM_022096:+;NM_198798:+0 Self chain AluY:SINE:Alu0 AluY:SINE:Alu;SAluSx:SINE:Alu;NM_025224:- NM_025224:-0 Self chain;Tan Self chain;Tan NM_003288:+; NM_003288:+;NM_199359:+;NM_199360:+;NM_199361:+;N0 Self chain;Tan Self chain;Tan NM_001080447NM_001080447rs71198204 (chr22:48809248-48809685)0 L1M1:LINE:L1;SeSelf chain NM_000109:-;NM_004006:-;NM_004007:-;NM_004009:-;NM_0 Self chain;Tig L1M4:LINE:L1;Self chain0 L1P4:LINE:L1;SeL1PA16:LINE:L1;SegDup;Self chain

AGAAAAATA 9 L1PA13:LINE:L1;L1PA16:LINE:L1;SegDup;Self chainCATATATACCT 54 L1PA13:LINE:L1;SegDup;Self chain

0 MIR:SINE:MIR;SL1PA15:LINE:L1;Self chain0 MLT1G1:LTR:MaLLTR29:LTR:ERV1;Self chain

CT 2 HERVP71A:LTR AluY:SINE:Alu

DeletedTransp KnownUnderrepFrequencyInBa AssembledSeq EventId Type RelatedJunctio0 ctgaggtagagta 62 complex 18380 atggtctttgtg 62 complex 38060 cacaatggctct 122 interchromosomal0 tgaaagaggcatg 138 interchromosomal0 gggcatgctattt 140 probable-inversion0 accttctgctatt 120 deletion0 ctcccaggttca 54 interchromosomal

NM_001042599:-;NM_005235:- 0 accagcttgtttt 118 deletionNM_001042599:-;NM_005235:- 0 aaaaacaaaaac 139 probable-inversionNM_001042599:-;NM_005235:- 0 ttcttagaatatca 41 probable-inversion

0 caatatgtttcttt 116 deletion0 gaggttctgggag 105 interchromosomal0 gcttctttctaccc 61 tandem-duplication

NM_003716:-;NM_183393:-;NM_183394:- 0 tagaagaaagaag 60 tandem-duplication

0 tccagcaatcatt 115 deletion0 ttgaattcctgaa 114 deletion0 tgggatggaccca 113 deletion0 acaaggattcag 136 interchromosomal

0 accaccatgtct 59 tandem-duplication

0 tgaataaactatg 112 deletion0 aaaaacttccatca 58 tandem-duplication0 gcttagggatgctt 110 deletion0 gtcattagaaggt 40 probable-inversion

NM_001040057:-;NM_152789:- 0 gtaactgacatg 106 interchromosomal0 tagataaaaatg 55 tandem-duplication

0 catcttgtgagtc 104 deletion

0 ttcccctcttcct 38 probable-inversion

0 cagtgacaaggga 103 deletion0 aagcaacatgtcca 39 probable-inversion0 actgcacctggc 133 interchromosomal0 ttgtattatttt 102 deletion0 tgtgggggtgt 134 interchromosomal0 gagctataactg 52 tandem-duplication

0 agtgatgcaatcaa 78 interchromosomal

0 tattaagaggtg 100 deletion0 aatgaaaaatcaa 98 deletion

NM_001163278:-;NM_001163279:-;NM_014253:- 0 gtctggatcaggtc 43 complex 1117NM_001163278:-;NM_001163279:-;NM_014253:- 0 acacaataaacct 43 complex 2222

0 attggtcagttc 97 deletion0 cccatatgcact 36 interchromosomal

0 cactgctcctgc 37 probable-inversion0 atcagggaaagac 49 tandem-duplication

0 taaggagattgg 48 tandem-duplication

0 tgcttgttggcttc 45 interchromosomalNM_001098512:+;NM_006258:+ 0 cagatctattca 93 deletionNM_001098512:+;NM_006258:+ 0 tgttccaaaaga 46 tandem-duplication

0 aaatgcctaca 89 deletion0 cactgaagactta 32 tandem-duplication

NM_001142699:-;NM_001364:- 0 tgtctcacatgta 31 tandem-duplicationNM_178039:+;NM_178040:+;NR_027946:+;NR_027948:+;NR_ 0 agtgtttgtaat 88 deletion

0 tccgcctccac 87 deletionNM_020300:+;NM_145791:+;NM_145792:+ 0 tgaggaggaggca 30 tandem-duplication

0 agactaaatcacat 85 deletion0 caacaatgacaaa 26 interchromosomal

0 gaaataaaatgt 70 complex 1950

0 caagatacgca 25 complex 576

0 gcaatcccagga 25 complex 562NM_052851:-;NM_178006:-;NM_178007:- 0 actatgaaatat 27 tandem-duplication

0 aggcccagggtga 24 interchromosomal

0 cactgcaagatt 23 interchromosomal

0 ttacatttttgag 22 tandem-duplication0 ccttcttggagt 21 tandem-duplication0 cataactggatgcc 80 deletion

0 gagctacaggca 129 probable-inversion

NM_002654:-;NM_182470:-;NM_182471:- 0 ttgccatggtag 20 tandem-duplication

0 cttcatttccca 19 tandem-duplication

0 tcacaagacaact 17 tandem-duplicationNM_000267:+;NM_001042492:+ 0 atcttattgttt 127 probable-inversionNM_012481:-;NM_183228:-;NM_183229:-;NM_183230:-;NM_ 0 catgcttactaaga 77 deletion

0 ccatgctgaatac 16 tandem-duplication

0 aagaagagacgg 70 complex 4032

NM_001098482:+;NM_015321:+ 0 gagtggatgttgg 125 probable-inversion

0 aaaatacagtag 14 tandem-duplication0 tataactagaccc 12 probable-inversion

NM_001032372:+;NM_001032373:+;NM_001032374:+;NM_0 0 agaatatgtcaggt 11 probable-inversion0 acaattatcaatgc 124 probable-inversion0 aatattattcatag 69 deletion0 attgtcagctcg 10 probable-inversion0 gagttatatcag 67 deletion

NM_003288:+;NM_199359:+;NM_199360:+;NM_199361:+;N 0.1 gttgttttctctc 6 deletionrs71198204 (chr22:48809248-48809685) 0.06 ccagcccctgaa 4 deletion

NM_000109:-;NM_004006:-;NM_004007:-;NM_004009:-;NM_ 0 agtccacgacaag 9 tandem-duplication0 gctgttgttgaa 44 probable-inversion0 atgatttgacttc 1 complex 19;12160 gcaatggtggta 1 complex 238;12160 ttcctctctaca 1 complex 19;2380 cagtgtagtgtaag 3 deletion0 tagagttgagct 8 tandem-duplication0 caggaactaacc 2 deletion

Notes"left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 1838, is same event. CNV not affected."left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 3806, is same event. CNV not affected."left end" and "right end" of this rearrangement are not in an annotated element. CNV not affected."left end" and "right end" of this rearrangement are not in an annotated element. CNV not affected."left end" of this rearrangement is in the intron between exon 13 and 14 of LRP1B. "right end" is in the intron between exon 12 and 13 of the same gene. Exon 13 is probably inverted. Same gene has a deletion of exon 3 (Id 3698 ), confirmed by SNP array and CNV (no call), probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604. Both SNP array and CNV data show exons 3 to 13 of LRP1B are deleted (CN = 0), and exons 1-2 and exons 14-31 a CN of 2, whereas exons 32-91 + 944 kb upstream the gene have a CN of 1. LRP1B = low density lipoprotein receptor-related protein 1B , LRP1B belongs to the low density lipoprotein (LDL) receptor gene family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands (Liu et al., 2001 (PubMed 11384978). The gene is preferentially inactivated in one histological type of lung cancer (non-small cell lung cancer (NSCLC)). May thus play an important role in tumorigenesis of NSCLCs. This gene is also affected in the T, S and SG (SGendoT?), but not in A.Deletion exon 3 LRP1B gene, probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604 and see Id 4461 for more information."left end" is in intron between exon 2 and 3 of the LRP1B gene, "right end" is not in an annotated element (CN is not changed), both ends are Alu repeats. Translocation probably occurred together with a deletion (see Id 3698 and Id 4461). Deletion of exon 26-28 of ERBB4 isoform 1 (exons 26-27 of isovorm 2). CN drops from 2 (1.75) to 1 (0.93). Same gene affected by Id 4603 and Id 1028, both probable inversion of exon 20, here the CN also drops from 2 to 1 (CNV of ERBB4 not detected by SNP array). ERBB4 = v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian). This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Mutations in this gene have been associated with melanoma and schizophrenia. Same gene is also affected in the T line. probable inversion of exon 20 of ERBB4, the CN drops from 2 to 1, see Id 1028 and Id 3667 probable inversion of exon 20 of ERBB4, the CN drops from 2 to 1, see Id 4603 and Id 3667"left end" is not in an annotated element, the "right end" is in the intron between exon 4 and 5 of the ZNF385D gene = zinc finger protein 385D, deletion of exon 5-8 (last exon), function unknown. It also removes the one exon of VENTXP7 = VENT homeobox pseudogene 7, non-coding RNA. CN drops from 3 (2.4) to 1.6 (2), also detected by SNP array. Probably happened during translocation of same intron of ZNF385D to chr 19 (Id 3202)."left end" is in in the intron between exon 4 and 5 of the ZNF385D gene, goes together with deletion (Id 3639). CN stays 1.6 after drop of 2.4 to 1.6 due to Id 3639, but SNP array drops form 3 to 2 due to Id 3639 and extra from 2 to 1 due to Id 3202. "right end" is not in an annotated element (CN is not changed)."left end is in intron between exon 3 and 4 of UBE2E2, the "right end" is not in an annotated element. But in between are 4 extra genes of which the CN increases from 1.9 to 3 (SNP array 1 to 3).UBE2E2, involving exons 4-6 (last exon) = ubiquitin-conjugating enzyme E2E2. Involved in selective protein degradation. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination.UBE2E1, complete gene = ubiquitin-conjugating enzyme E2E1. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination.NR1D2, complete gene = nuclear receptor subfamily 1, group D, member 2. This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism. LOC152024, hypothetical proteinTHRB, complete gene = thyroid hormone receptor, beta. The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH). "left end" is in intron between exon 3 and 4 of the FHIT gene, "right end" is intron between exon 2 and 3 of the gene CADPS (all 3 isoforms). CN increases from 2 to 3 (both CNV as SNP array) involving 6 genes. This region is also affected in the T line.FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.PTPRG = protein tyrosine phosphatase, receptor type, G. The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene.ID2B = inhibitor of DNA binding 2B, dominant negative helix-loop-helix protein (pseudogene)C3orf14, hypothetical proteinFEZF2 = FEZ family zinc finger 2. Transcription repressor. Required for the specification of corticospinal motor neurons and other subcerebral projection neurons. May play a role in layer and neuronal subtype-specific patterning of subcortical projections and axonal fasciculation. Controls the development of dendritic arborization and spines of large layer V pyramidal neurons. May be involved in innate immunity (By similarity)CADPS = Ca++-dependent secretion activator. Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. "left end" and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well. Connected to Id 3584.connected to Id 3585, "left end and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well."left end" and "right end" of this rearrangement are not in an annotated element. No CNV detected."left end" of this rearrangement is between exon 3 and 4 of the STAG1 gene, no CNV. "right end" of this rearrangement is in intron between exon 2 and 3 of RAB40C (for all 5 isoforms but breakpoint is between exon 1-2 for isoform 2). No CNV detected. Fusion first 42 aa of STAG1 to aa 54 -end of RAB40C.STAG1 = stromal antigen 1. Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosisRAB40C = member RAS oncogene family. Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins."left end" of this rearrangement is between exon 2 and 3 of SPATA16 (encodes first 204 amino acids). The "right end" of this rearrangement is between exon 2 and 3 of NLGN1 ( is 5'UTR). CNV increases from 1.8 to 2.6. No difference on SNP array.SPATA16 = spermatogenesis associated 16. Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and sperm-egg fusion.NLGN1 = neuroligin 1. Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions."left end" and "right end" of this rearrangement are not in an annotated element. Falls withing Id 1636, tandem duplication."left end" and "right end" of this rearrangement are not in an annotated element. "left end" and "right end" of this rearrangement are in LPHN3. "left end" between exon 6-7, "right end" between exon 10-11, deleting amino acids 426 - 636. LPHN3 = latrophilin 3. This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors (GPCR). Latrophilins may function in both cell adhesion and signal transduction."left end" and "right end" of this rearrangement are in RNF150. Falls within the intron between exon 1 and 2. RNF150 = ring finger protein 150, function unknown. No CNV detected."left end" is not in an annotated element. "Right end" is in exob 1 of FAM133B (5' UTR). No CNV detected. FAM133B = family with sequence similarity 133, member B , function unknown."left end" of this rearrangement is in intron between exon 11 and 12 (isoform 1, exon 12-13 of isoform 3, isoform 2 not affected) of MAST4, rearranged region also includes CD180 and the "right end" is in intron between exon 2 - 3 of PIK3R1 (only isoform 1, other 3 isoforms are not affected). CN goes from 2.6/3.0 to 3.5. (no CNV detected on SNP array)FAM133B = family with sequence similarity 133, member B. Function unknown.CD180. May cooperate with MD-1 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) in B-cells. Leads to NF-kappa-B activation. Also involved in the life/death decision of B-cells.

"left end" and "right end" of this rearrangement are not in an annotated element.

IRAKBP1 = interleukin-1 receptor-associated kinase 1 binding protein 1. Component of the IRAK1-dependent TNFRSF1A signaling pathway that leads to NF-kappa-B activation and is required for cell survival. Acts by enhancing RELA transcriptional activity (By similarity). CNV goes from 3 to 5PHIP = pleckstrin homology domain interacting protein. Probable regulator of the insulin and insulin-like growth factor signaling pathways. Stimulates cell proliferation through regulation of cyclin transcription and has an anti-apoptotic activity through AKT1 phosphorylation and activation.CN is 5HMGN3 = high mobility group nucleosomal binding domain 3, Binds to nucleosomes, regulating chromatin structure and consequently, chromatin-dependent processes such as transcription, DNA replication and DNA repair. Affects both insulin and glucagon levels and modulates the expression of pancreatic genes involved in insulin secretion. CN is 4

PIK3R1 = phosphoinositide-3-kinase, regulatory subunit 1 (alpha). Binds to activated (phosphorylated) protein-Tyr kinases, through its SH2 domain, and acts as an adapter,mediating the association of the p110 catalytic unit to the plasma membrane. Necessary for the insulin-stimulated increase in glucose uptake and glycogen synthesis in insulin-sensitive tissues.

"left end" of this rearrangmen is not in an annotated element, "right end" is in intron between exon 1 and 2 of UBE2CBP, 12 genes in between, see below. This rearrangment overlaps with Id 887 and Id 3089. SNP array shows similar CN variation.

LCA5 = Leber congenital amaurosis 5. This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Might be involved in minus end-directed microtubule transport. Mutations in this gene cause Leber congenital amaurosis type V. CN is 3SH3BGRL2 = SH3 domain binding glutamic acid-rich protein like 2, function unknown. CN is 3C6orf7, function unknown. CN is 3ELOVL4 = ELOVL fatty acid elongase 4. Condensing enzyme that elongates saturated and monounsaturated very long chain fatty acids. CN is 3TTK = TTK protein kinase. This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. CN is 3BCKDHB = branched chain keto acid dehydrogenase E1, beta polypeptide. Branched-chain keto acid dehydrogenase is a multienzyme complex associated with the inner membrane of mitochondria, and functions in the catabolism of branched-chain amino acids. The complex consists of multiple copies of 3 components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). This gene encodes the E1 beta subunit. CN is 3FAM46A = family with sequence similarity 46, member A, function unknown, CN not known.IBTK = inhibitor of Bruton agammaglobulinemia tyrosine kinase, Acts as an inhibitor of BTK tyrosine kinase activity, thereby playing a role in B-cell development. Down-regulates BTK kinase activity, leading to interference with BTK-mediated calcium mobilization and NF-kappa-B-driven transcription. CN is 5.

UBE2CBP = ubiquitin-conjugating enzyme E2C binding protein. E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. CN is 3.See Id 887See Id 887"left end" and "right end" of this rearrangement are not in an annotated element. "left end" of this rearrangement is in an intron between exon 2 and 3 of VTA1, the "right end " is in an intron between exon 4 and 5 of the same gene, deleting exons 3 and 4 (amino acids 70 - 137). VTA1 = Vps20-associated 1 homolog (S. cerevisiae). Involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. CN from 2.3 to 2.9, no effect detected on SNP array."left end" of this rearrangement contains exons 7 and 8 of GET4. No effect on CN. "The right end" is not in an annotated element, No effect on CN. GET4 = golgi to ER traffic protein 4 homolog (S. cerevisiae). Component of the BAT3 complex, a multiprotein complex involved in the post-translational delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum membrane."left end" of this rearrangement is in an intron between exon 3 and 4 of GLI3. The "right end" is in not in an annotated element. Many genes in between see below. All region SNP array CN from 2 to 3.GLI3 = GLI family zinc finger 3. Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. CN 1.8C7orf25, function unknown. CN 2.6PSMA2 = proteasome (prosome, macropain) subunit, alpha type, 2. The proteasome is a multicatalytic proteinase complex and has an ATP-dependent proteolytic activity. PSMA2 may have a potential regulatory effect on another component(s) of the proteasome complex through tyrosine phosphorylation. CN 2.6NR_038276, non coding RNA CN 2.6

STK17A = serine/threonine kinase 17a. This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. CN 2.6C7orf44, function unknown. CN 2.6BLVRA = biliverdin reductase A. Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor. CN 2.73NM_001204871: This locus represents naturally occurring read-through transcription between the neighboring URGCP and MRPS24. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. CN 2.63MRPS24 = mitochondrial ribosomal protein S24. Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. This gene encodes a 28S subunit protein. CN 2.63URGCP = upregulator of cell proliferation. URG4 is upregulated in the presence of hepatitis B virus (HBV)-encoded X antigen (HBxAg) and may contribute to the development of hepatocellular carcinoma by promoting hepatocellular growth and survival (Tufan et al., 2002 (PubMed 12082552)). CN 2.63UBE2D4 = ubiquitin-conjugating enzyme E2D 4 (putative). Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. CN 2.63POLR2J4 = polymerase (RNA) II (DNA directed) polypeptide J4, pseudogene. CN not knownSPDYE1 = speedy homolog E1 (Xenopus laevis), function unknown. CN not knownRASA4P = RAS p21 protein activator 4 pseudogene. CN not knownFLJ35390, hypothetical protein. CN not knownDBNL = drebrin-like. Actin-binding adapter protein. May act as a common effector of antigen receptor-signaling pathways in leukocytes. CN 2.63PGAM2 = phosphoglycerate mutase 2 (muscle). Phosphoglycerate mutase (PGAM) catalyzes the reversible reaction of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in the glycolytic pathway. CN 2.63POLM = polymerase (DNA directed), mu. Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. CN 2.63AEBP1 = AE binding protein 1. CN 2.63POLD2 = polymerase (DNA directed), delta 2, regulatory subunit 50kDa. The DNA polymerase delta complex is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA), the multisubunit replication factor C, and the 4 subunit polymerase complex POLD1. The function of the small subunit is not yet clear. CN 2.63MYL7 = myosin, light chain 7, regulatory. Myosins are a large family of motor proteins that share the common features of ATP hydrolysis, actin binding and potential for kinetic energy transduction. CN 2.63GCK = glucokinase (hexokinase 4). Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. Mutations in this gene have been associated with non-insulin dependent diabetes mellitus (NIDDM), maturity onset diabetes of the young, type 2 (MODY2) and persistent hyperinsulinemic hypoglycemia of infancy (PHHI). CN 2.63YKT6 = YKT6 v-SNARE homolog (S. cerevisiae). This gene product is one of the SNARE recognition molecules implicated in vesicular transport between secretory compartments. CN 2.63CAMK2B = calcium/calmodulin-dependent protein kinase II beta. CaM-kinase II (CAMK2) is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. CN 2.63NUDCD3 = NudC domain containing 3. The product of this gene functions to maintain the stability of dynein intermediate chain. Depletion of this gene product results in aggregation and degradation of dynein intermediate chain, mislocalization of the dynein complex from kinetochores, spindle microtubules, and spindle poles, and loss of gamma-tubulin from spindle poles. The protein localizes to the Golgi apparatus during interphase, and levels of the protein increase after the G1/S transition.CN not knownNPC1L1 = NPC1 (Niemann-Pick disease, type C1, gene)-like 1. Play a major role in cholesterol homeostasis. Is critical for the uptake of cholesterol across the plasma membrane of the intestinal enterocyte. CN 2.03DDX56 = DEAD (Asp-Glu-Ala-Asp) box polypeptide 56, May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity. CN 2.03TMED4 = transmembrane emp24 protein transport domain containing 4. Involved in endoplasmic reticulum stress response. May play a role in the regulation of heat-shock response and apoptosis (By similarity).CN 2.03OGDH = oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide). This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle.CN 2.03ZMIZ2 = zinc finger, MIZ-type containing 2. Increases ligand-dependent transcriptional activity of AR and other nuclear hormone receptors. CN 2.03PPIA = peptidylprolyl isomerase A (cyclophilin A). PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.CN 2.03

TPBG = trophoblast glycoprotein. This gene encodes a leucine-rich transmembrane glycoprotein that may be involved in cell adhesion. The encoded protein is an oncofetal antigen that is specific to trophoblast cells. In adults this protein is highly expressed in many tumor cells and is associated with poor clinical outcome in numerous cancers. CN is 5

HECW1 = HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1. E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent degradation of DVL1. Also targets themutant SOD1 protein involved in familial amyotrophic lateral sclerosis (FALS). Forms cytotoxic aggregates with DVL1, SSR3 and mutant SOD1 that lead to motor neuron death in FALS .CN 2.6

H2AFV = H2A histone family, member V. Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. CN 2.03PURB = purine-rich element binding protein B. This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia.CN 2.03"Left end" of rearrangment is in intron between exon 1 and 2 of AUTS2 (all 3 isoforms). "Right end" is in intron between exon 1-2 of ARID3A (5'UTR), same gene involved in another breakpoint (Id 1950). AUTS2 = autism susceptibility candidate 2 , function unknown. No CNV.

"left end" and "right end" of this deletion is in intron between exon 1-2 of MFHAS1, is malignant fibrous histiocytoma amplified sequence 1. Identified in a human 8p amplicon, this gene is a potential oncogene whose expression is enhanced in some malignant fibrous histiocytomas (MFH). "left end" and "right end" of this rearrangement are not in an annotated element. "left end" and "right end" of this rearrangement are not in an annotated element. "left end" and "right end" of this rearrangement are not in an annotated element. "left end" of this rearrangment is just upstream of the ANXA2P2 gene. No CNV. "Right end" is in intron between exon 7-8 of C16orf62. No CNV.ANXA2P2 = annexin A2 pseudogene 2 C16orf62, function unknown"left end" and "right end" of this rearrangement are not in an annotated element. Genes in between: ANKRD20A1, FAM27B, AQP7P1, NR_024443, MGC21881, LOC442421. No CNV detected."left end of this rearrangment is in intron of NTRK2. Only affects isoforms a (exon 16-17) and c (exon 15-16). "Right end" is not in an annotated region. Genes in between AGTPB1, LOC389765, NAA35, GOLM1, C9orf153, ISCA1, ZCCHC6, GAS1, LOC440173, LOC494127, C9orf170. CN goes from 1.96 to 3.1/3.4. SNP array goes from 1 to 4 in this region.NTRK2 = neurotrophic tyrosine kinase, receptor, type 2. This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders."left end" of this rearrangment is in intron between exon 1-2/2-3 of STRBP (all 3 isoforms). "right end" is intron between exon 20-21 of DENND1A. Gene in between is CRB2 and microRNA 601. CN from 2 to 4, not detected in SNP array or HMM.

DENND1A = DENN/MADD domain containing 1A, Guanine nucleotide exchange factor (GEF) for RAB35. May be involved in the clathrin-mediated endocytosis of synaptic vesicles.

"left end" of this rearrangement contains exons 37 and 38 of SPTAN1 (depending on isoform exon 38+39 or 36+37). CN goes from 2.06 to 2.95 (No change on SNP array). "Right end" is not in an annotated element. SPTAN1 = spectrin, alpha, non-erythrocytic 1 (alpha-fodrin). Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5."left end" and "right end" of this rearrangement are in an intron between exon 3 and 4 of PRKG1, is protein kinase, cGMP-dependent, type I. Phosphorylates PPP1R12A, who regulates myosin phosphatase activity. No CNV. Same gene involved in Id 2730. "left end" and "right end" of this rearrangement are in an intron between exon 9 and 10 of PRKG1. No CNV. Same gene involved in Id 1413. "left end" and "right end" of this rearrangement are not in an annotated element."left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 20-21 of ODZ4, is odz, odd Oz/ten-m homolog 4 (Drosophila). May function as a cellular signal transducer . No CNV."left end" and "right end" of this rearrangement are in an intron between exon 6-7 from isoform 1, exon 1-2 isoform 2 (other isoforms not affected) of DLG2, discs, large homolog 2 (Drosophila). Required for perception of chronic pain through NMDA receptor signaling. No CNV.

"left end" and "right end" of this rearrangement are not in an annotated element."left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 1 and 2 of all 3 isoforms of MGST1. MGST1 = microsomal glutathione S-transferase 1. This gene encodes a protein that catalyzes the conjugation of glutathione to electrophiles and the reduction of lipid hydroperoxides. This protein is localized to the endoplasmic reticulum and outer mitochondrial membrane where it is thought to protect these membranes from oxidative stress. No CNV detected."left end" and "right end" of this rearrangement are in intron between exon 3 and 4 of USPL1. USPL1 = ubiquitin specific peptidase like 1. Function is unknown. No CNV detected."left end" of this rearrangment is in intron between exon 3 and 4 of PDS5B. Same gene has another breakpoint downstream (Id = 4032 ). "Right end" of this rearrangment is not in an annotated element. But overlaps with probable inversion Id 3996. No CNV.

"left end" of this rearrangment is in intron between exon 28 and 29 of PDS5B. Same gene has another breakpoint upstream (Id = 564). "Right end" of this rearrangement is in intron between exon 3 and 4 of DTD1. Overlaps with Id 1950.PDS5B = PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae). CNV (2 kB) drops again from 3 to 2 (see Id 564). No CNV on HMM or SNP array.

"left end" and "right end" of this rearrangement are not in an annotated element. Encompasses the KL gene. Overlaps with rearrangments with Id 575 (tandem duplication) and 576 (complex). No CNV.KL = klotho. This gene encodes a type-I membrane protein that is related to beta-glucosidases. Reduced production of this protein has been observed in patients with chronic renal failure (CRF), and this may be one of the factors underlying the degenerative processes (e.g., arteriosclerosis, osteoporosis, and skin atrophy) seen in CRF. Also, mutations within this protein have been associated with ageing and bone loss.Idem Id 562."left end" of this rearrangement is not in an annotated element. Overlaps with Id 562 and Id 576. "Right end" is in intron between exon 1-2 (all 6 isoforms except isoform 4, is between exon 5-6 ) of STARD13. CN goes from 2 to 4 downstream of this rearrangment, but is probably due to translocation Id 560.

"Left end" is in intron between exon 1-2 (all 6 isoforms except isoform 4, is between exon 5-6 ) of STARD13. CN goes from 2 to 4 downstream of this rearrangment, but is probably due to translocation Id 560. Overlaps with "right end" of Id 575. "Right end" of this rearrangment is exon 11/12 of RIN2. CNV 2KB goes from 1.7 to 2.5 , SNP array also goes from 2 to 3, CNV HMM goes from 1.9 to 2.6 a bit more upstream.STARD13 = StAR-related lipid transfer (START) domain containing 13. GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells.

"left end" of this rearrangement is in intron of STARD13 between exon 1 and 2 for isoforms 1, 3, 6; between exon 5 and 6 of isoform 4; no effect on isoforms 2 and 5. CN goes from 2 to 3.7, SNP array also goes from 2 to 4. More downstream is another translocation (Id 561) and a tandem duplication (Id 575) involving the same gene. " Right end" of this rearrangment is in not in an annotated element. No CNV detected.STARD13 = StAR-related lipid transfer (START) domain containing 13. GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells. "left end" and "right end" of this rearrangement are not in an annotated element. CNV not detected."left end" and "right end" of this rearrangement are not in an annotated element. Many genes in between, but no CNV detected."left end" and "right end" of this rearrangement are not in an annotated element. No genes in between, no CNV detected.

ARID3A = AT rich interactive domain 3A (BRIGHT-like). Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. No CNV."left end" and "right end" of this deletion are in intron between exon 3-4/4-5 (depending on isoform) of IMMP2L, is IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae). Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

STRBP = spermatid perinuclear RNA binding protein. Involved in spermatogenesis and sperm function. Plays a role in regulation of cell growth. Binds to double-stranded DNA and RNA. Binds most efficiently to poly(I:C) RNA than to poly(dI:dC) DNA. Binds also to single-stranded poly(G) RNA. Binds non-specifically to the mRNA PRM1 3'-UTR and adenovirus VA RNA (By similarity).

CRB2 = crumbs homolog 2 (Drosophila). May play a role in polarized cells morphogenesis.

"left end" and "right end" of this rearrangement are in intron of ERC1 (of all 5 isoforms). ERC1 = ELKS/RAB6-interacting/CAST family member 1, Regulatory subunit of the IKK complex. Probably recruits IkappaBalpha/NFKBIA to the complex. May be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. May be involved in vesicle trafficking at the CAZ. May be involved in Rab-6 regulated endosomes to Golgi transport.

PDS5B = PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae). CNV (2 kB) from 2 to 3 for exons 4-28, HMM not called, no CNV on SNP array. This gene encodes a protein that interacts with the conserved protein complex termed cohesion. The cohesion complex holds together sister chromatids and facilitates accurate chromosome segregation during mitosis and meiosis. This protein is also a negative regulator of cell proliferation and may be a tumor-suppressor gene. Plays a role in androgen-induced proliferative arrest in prostate cells.

DTD1 = D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae). Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (Potential).

STARD13 = StAR-related lipid transfer (START) domain containing 13. GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells.

RIN2 = Ras and Rab interactor 2 . Ras effector protein. May function as an upstream activator and/or downstream effector for RAB5B in endocytic pathway. May function as a guanine nucleotide exchange (GEF) of RAB5B, required for activating the RAB5 proteins by exchanging bound GDP for free GTP.

"left end" of this rearrangement is in intron between exon 1-2 of SGPP1. "Right end" is in exon 61 of SYNE2. CN goes from 2.7 to 3.5 for exons 7- 60 of SYNE2, thereafter drops to 1.8. No effect seen on SNP array.

"left end" of this rearrangment is in intron between exon 1-2 of MYO9A. "Right end" is in intron between exon 3-4 (all 7 isoforms, except isoform 4: exon 4-5) of PKM2. Two genes in between: SENP8 and GRAMD2. CN goes from 3.7 to 4.4, not detected on SNP array.

GRAMD2 = GRAM domain containing 2 , function unknown.PKM2 = pyruvate kinase, muscle, This gene encodes a protein involved in glycolysis. The encoded protein is a pyruvate kinase that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP, generating ATP and pyruvate. This protein has been shown to interact with thyroid hormone and may mediate cellular metabolic effects induced by thyroid hormones."left end" of this rearrangement is in intron between exon 4-5 of CACNA1H. "Right end" is not in an annotated element. Genes in between are TPSG1, TPSB2, TPSAB1, TPSD1. CN 2KB goes from 2.8 to 3.4 No CNV detected for HMM or on SNP array.

TPS genes encode tryptases, a family of trypsin-like serine proteases, the peptidase family S1. Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity). Tryptases have been implicated as mediators in the pathogenesis of asthma and other allergic and inflammatory disorders.

"left end" of this rearrangement is in an intron between exon 1-2 or 2-3 of CTIF. "Right end" is in exon 4 of ELAC1 (3'UTR). Genes in between are: SMAD7, DYM, C18orf32, LIPG, ACAA2, MYO5B, CCDC11, SKA1, MAPK4, MRO, ME2. CNV goes from 2 to 4 (SNP array), 1.7/1.9 to 3.1 (HMM).

"Left end" is in intron between exon 3 and 4 of ARID3A. Same gene has another breakpoint downstream (Id = 2293). "Right end" is in intron between exon 3-4 of DTD1, overlaps with Id 4031. No CNV.

"Left end" of this rearrangement is in exon 1 of MUC16. "Right end" of this rearrangement is in exon 1 of CRTC1. Many genes in between. SNP array: CN drops from 4 to 2 for some genes at the left side of this rearrangement, then goes back to 4 and drops again to 2 upstream of this rearrangement. HMM and 2kb CNV follow the same trend but go from 2.7 to 1.7, CNV drops for the following genes:

and other zinc finger proteins like ZNF699, ZNF559, ZNF177, ZNF266, ZNF560 and ZNF426 that all may be involved in transcriptional regulation. CRTC1 = CREB regulated transcription coactivator 1. Acts as a coactivator, in the SIK/TORC signaling pathway."left end" and "right end" of this rearrangment are not in an annotated element. Genes in between are: PAK4, PAPL, FBX027, FBXO17. No CNV detected."left end" and "right end" of this rearrangment are not in an annotated element. No genes in between.

"left end" and "right end" of this rearrangment are in an intron of ANKRD5, encompassing exon 5 (isoform 2) or 6 (isoform 1). And falls within the non-coding RNA NR_040710. ANKRD5 = ankyrin repeat domain 5, function unknown. No CNV detected. "left end" and "right end" of this rearrangment are not in an annotated element. No genes in between. But overlaps with a CN increase of 1.7 to 2.6 (not detected on SNP array). 430 kb upstream two rearrangments, Id 4032 and 1950."left end" and "right end" of this rearrangment are in intron between exon 3-4 of ZBTB46 = zinc finger and BTB domain containing 46, may be involved in transcriptional regulation."left end" and "right end" of this rearrangment are in intron between exon 3-4/4-5 of TPD52L2. And falls within non-coding RNA NR_045370. TPD52L2 = tumor protein D52-like 2. Family member TPD52 may be involved in calcium-mediated signal transduction and cell proliferation."left end" and "right end" of this rearrangment are not in an annotated element.

"left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 19 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 19."left end" and "right end" of this rearrangment are not in an annotated element. Falls within rearrangments Id's 238, 19 and 1216. No CNV detected."left end" and "right end" of this rearrangment are not in an annotated element. Falls within rearrangments Id's 238, 19 and 1216. No CNV detected."left end" and "right end" of this rearrangment are not in an annotated element. CN goes from 2.6 to 1 (2 KB) No CNV detected on HMM or SNP array.

SGPP1 = sphingosine-1-phosphate phosphatase 1. Has enzymatic activity against both sphingosine 1-phosphate (S1P) and dihydro-S1P. Regulates intracellular and extracellular S1P levels.SYNE2 = spectrin repeat containing, nuclear envelope 2. The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus.

MYO9A = myosin IXA. Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Regulates Rho activity in neurons, has a role in the regulation of neuronal morphology and function (By similarity).SENP8 = SUMO/sentrin specific peptidase family member 8 , Protease that catalyzes two essential functions in the NEDD8 pathway: processing of full-length NEDD8 to its mature form and deconjugation of NEDD8 from targeted proteins such as cullins or p53.

complex. T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle. They may also be involved in the modulation of firing patterns of neurons which is important for information processing as well as in cell growth processes.

"left end" and "right end" of this rearrangement are in an intron between exon 8-9 of WWOX. CN of this part of the intron goes from 2.6 to 3.3 (not seen on SNP array). WWOX = WW domain containing oxidoreductase. Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development (By similarity). May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm."left end" and "right end" of this rearrangement are in an intron of NF1, left between exon 22-23, right between exon 23-24. No CNV detected. NF1 = neurofibromin 1. This gene product appears to function as a negative regulator of the ras signal transduction pathway.Stimulates the GTPase activity of Ras. NF1 shows greater affinity for Ras GAP, but lower specific activity."left end" and "right end" of this rearrangement are in an intron between exon 1-2 of IKZF3 (for all 6 isoforms). No CNV detected. IKZF3 = IKAROS family zinc finger 3 (Aiolos).Transcription factor that plays an important role in the regulation of lymphocyte differentiation. Plays an essential role in regulation of B-cell differentiation, proliferation and maturation to an effector state. Involved in regulating BCL2 expression and controlling apoptosis in T-cells in an IL2-dependent manner.

CTIF = CBP80/20-dependent translation initiation factor . Specifically required for the pioneer round of mRNA translation mediated by the cap-binding complex (CBC), that takes place during or right after mRNA export via the nuclear pore complex (NPC). Also required for nonsense-mediated mRNA decay (NMD), the pioneer round of mRNA translation mediated by the cap-binding complex playing a central role in nonsense-mediated mRNA decay (NMD).ELAC1 = elaC homolog 1 (E. coli). Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.

ARID3A = AT rich interactive domain 3A (BRIGHT-like). Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. No CNV.DTD1 = D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae). Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (Potential).

MUC16 = mucin 16, cell surface associated. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces (By similarity).OR1M1, OR7G2, OR7G1, ORF7G3, ORF7D2, OR7D4, OR7E24 are olfactory receptors. These receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers theperception of a smell.ZNF317 = zinc finger protein 317. May function as a transcription factor. May play an important role in erythroid maturation and lymphoid proliferation.

"left end" of this rearrangment is in an intron between exon 5-6 of ZNF234 (both isoforms). "Right end" of this rearrangment is in 3'UTR or in intron before last exon of ZNF226, depending on the isoform. CN goes from 6.5 to 10.3, and goes down again after rearrangement Id 3994. Gene in between rearrangements is ZNF227. No change on SNP array detected. ZNF proteins may be involved in transcriptional regulation."left end" of this rearrangment is in an intron before the last exon (nr. 5) , and " right end" is in this exon 5 of ZNF233. CNV drops from 10 to 3 (2KB data, no call HMM), no change on SNP array. A bit more upstream is rearrangement Id 258. ZNF233 may involved in transcriptional regulation.

"left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exons 43-44/44-45 or 16-17 of DMD (depending on the isoform). Many genes in between, but no CNV detected. Only for (part of ) DMD gene CN goes from 2 to 4 (HMM, 2 KB and SNP array data). DMD = dystrophin. Anchors the extracellular matrix to the cytoskeleton via F-actin. Ligand for dystroglycan. Component of the dystrophin-associated glycoprotein complex which accumulates at the neuromuscular junction (NMJ) and at a variety of synapses in the peripheral and central nervous systems and has a structural function in stabilizing the sarcolemma. Also implicated in signaling events and synaptic transmission.

"left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 1838, is same event. CNV not affected."left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 3806, is same event. CNV not affected.

"left end" of this rearrangement is in the intron between exon 13 and 14 of LRP1B. "right end" is in the intron between exon 12 and 13 of the same gene. Exon 13 is probably inverted. Same gene has a deletion of exon 3 (Id 3698 ), confirmed by SNP array and CNV (no call), probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604. Both SNP array and CNV data show exons 3 to 13 of LRP1B are deleted (CN = 0), and exons 1-2 and exons 14-31 a CN of 2, whereas exons 32-91 + 944 kb upstream the gene have a CN of 1. LRP1B = low density lipoprotein receptor-related protein 1B , LRP1B belongs to the low density lipoprotein (LDL) receptor gene family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands (Liu et al., 2001 (PubMed 11384978). The gene is preferentially inactivated in one histological type of lung cancer (non-small cell lung cancer (NSCLC)). May thus play an important role in tumorigenesis of NSCLCs. This gene is also affected in the T, S and SG (SGendoT?), but not in A.Deletion exon 3 LRP1B gene, probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604 and see Id 4461 for more information."left end" is in intron between exon 2 and 3 of the LRP1B gene, "right end" is not in an annotated element (CN is not changed), both ends are Alu repeats. Translocation probably occurred together with a deletion (see Id 3698 and Id 4461). Deletion of exon 26-28 of ERBB4 isoform 1 (exons 26-27 of isovorm 2). CN drops from 2 (1.75) to 1 (0.93). Same gene affected by Id 4603 and Id 1028, both probable inversion of exon 20, here the CN also drops from 2 to 1 (CNV of ERBB4 not detected by SNP array). ERBB4 = v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian). This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Mutations in this gene have been associated with melanoma and schizophrenia. Same gene is also affected in the T line.

"left end" is not in an annotated element, the "right end" is in the intron between exon 4 and 5 of the ZNF385D gene = zinc finger protein 385D, deletion of exon 5-8 (last exon), function unknown. It also removes the one exon of VENTXP7 = VENT homeobox pseudogene 7, non-coding RNA. CN drops from 3 (2.4) to 1.6 (2), also detected by SNP array. Probably happened during translocation of same intron of ZNF385D to chr 19 (Id 3202)."left end" is in in the intron between exon 4 and 5 of the ZNF385D gene, goes together with deletion (Id 3639). CN stays 1.6 after drop of 2.4 to 1.6 due to Id 3639, but SNP array drops form 3 to 2 due to Id 3639 and extra from 2 to 1 due to Id 3202. "right end" is not in an annotated element (CN is not changed)."left end is in intron between exon 3 and 4 of UBE2E2, the "right end" is not in an annotated element. But in between are 4 extra genes of which the CN increases from 1.9 to 3 (SNP array 1 to 3).UBE2E2, involving exons 4-6 (last exon) = ubiquitin-conjugating enzyme E2E2. Involved in selective protein degradation. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination.UBE2E1, complete gene = ubiquitin-conjugating enzyme E2E1. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination.NR1D2, complete gene = nuclear receptor subfamily 1, group D, member 2. This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism.

THRB, complete gene = thyroid hormone receptor, beta. The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH). "left end" is in intron between exon 3 and 4 of the FHIT gene, "right end" is intron between exon 2 and 3 of the gene CADPS (all 3 isoforms). CN increases from 2 to 3 (both CNV as SNP array) involving 6 genes. This region is also affected in the T line.FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.PTPRG = protein tyrosine phosphatase, receptor type, G. The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene.

FEZF2 = FEZ family zinc finger 2. Transcription repressor. Required for the specification of corticospinal motor neurons and other subcerebral projection neurons. May play a role in layer and neuronal subtype-specific patterning of subcortical projections and axonal fasciculation. Controls the development of dendritic arborization and spines of large layer V pyramidal neurons. May be involved in innate immunity (By similarity)CADPS = Ca++-dependent secretion activator. Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. "left end" and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well. Connected to Id 3584.connected to Id 3585, "left end and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well.

"left end" of this rearrangement is between exon 3 and 4 of the STAG1 gene, no CNV. "right end" of this rearrangement is in intron between exon 2 and 3 of RAB40C (for all 5 isoforms but breakpoint is between exon 1-2 for isoform 2). No CNV detected. Fusion first 42 aa of STAG1 to aa 54 -end of RAB40C.STAG1 = stromal antigen 1. Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosisRAB40C = member RAS oncogene family. Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins."left end" of this rearrangement is between exon 2 and 3 of SPATA16 (encodes first 204 amino acids). The "right end" of this rearrangement is between exon 2 and 3 of NLGN1 ( is 5'UTR). CNV increases from 1.8 to 2.6. No difference on SNP array.SPATA16 = spermatogenesis associated 16. Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and sperm-egg fusion.NLGN1 = neuroligin 1. Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions."left end" and "right end" of this rearrangement are not in an annotated element. Falls withing Id 1636, tandem duplication.

"left end" and "right end" of this rearrangement are in LPHN3. "left end" between exon 6-7, "right end" between exon 10-11, deleting amino acids 426 - 636. LPHN3 = latrophilin 3. This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors (GPCR). Latrophilins may function in both cell adhesion and signal transduction."left end" and "right end" of this rearrangement are in RNF150. Falls within the intron between exon 1 and 2. RNF150 = ring finger protein 150, function unknown. No CNV detected."left end" is not in an annotated element. "Right end" is in exob 1 of FAM133B (5' UTR). No CNV detected. FAM133B = family with sequence similarity 133, member B , function unknown."left end" of this rearrangement is in intron between exon 11 and 12 (isoform 1, exon 12-13 of isoform 3, isoform 2 not affected) of MAST4, rearranged region also includes CD180 and the "right end" is in intron between exon 2 - 3 of PIK3R1 (only isoform 1, other 3 isoforms are not affected). CN goes from 2.6/3.0 to 3.5. (no CNV detected on SNP array)

CD180. May cooperate with MD-1 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) in B-cells. Leads to NF-kappa-B activation. Also involved in the life/death decision of B-cells.



LCA5 = Leber congenital amaurosis 5. This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Might be involved in minus end-directed microtubule transport. Mutations in this gene cause Leber congenital amaurosis type V. CN is 3

ELOVL4 = ELOVL fatty acid elongase 4. Condensing enzyme that elongates saturated and monounsaturated very long chain fatty acids. CN is 3TTK = TTK protein kinase. This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. CN is 3BCKDHB = branched chain keto acid dehydrogenase E1, beta polypeptide. Branched-chain keto acid dehydrogenase is a multienzyme complex associated with the inner membrane of mitochondria, and functions in the catabolism of branched-chain amino acids. The complex consists of multiple copies of 3 components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). This gene encodes the E1 beta subunit. CN is 3

IBTK = inhibitor of Bruton agammaglobulinemia tyrosine kinase, Acts as an inhibitor of BTK tyrosine kinase activity, thereby playing a role in B-cell development. Down-regulates BTK kinase activity, leading to interference with BTK-mediated calcium mobilization and NF-kappa-B-driven transcription. CN is 5.

UBE2CBP = ubiquitin-conjugating enzyme E2C binding protein. E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. CN is 3.

"left end" of this rearrangement is in an intron between exon 2 and 3 of VTA1, the "right end " is in an intron between exon 4 and 5 of the same gene, deleting exons 3 and 4 (amino acids 70 - 137). VTA1 = Vps20-associated 1 homolog (S. cerevisiae). Involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. CN from 2.3 to 2.9, no effect detected on SNP array."left end" of this rearrangement contains exons 7 and 8 of GET4. No effect on CN. "The right end" is not in an annotated element, No effect on CN. GET4 = golgi to ER traffic protein 4 homolog (S. cerevisiae). Component of the BAT3 complex, a multiprotein complex involved in the post-translational delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum membrane."left end" of this rearrangement is in an intron between exon 3 and 4 of GLI3. The "right end" is in not in an annotated element. Many genes in between see below. All region SNP array CN from 2 to 3.GLI3 = GLI family zinc finger 3. Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. CN 1.8

PSMA2 = proteasome (prosome, macropain) subunit, alpha type, 2. The proteasome is a multicatalytic proteinase complex and has an ATP-dependent proteolytic activity. PSMA2 may have a potential regulatory effect on another component(s) of the proteasome complex through tyrosine phosphorylation. CN 2.6

STK17A = serine/threonine kinase 17a. This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. CN 2.6

BLVRA = biliverdin reductase A. Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor. CN 2.73NM_001204871: This locus represents naturally occurring read-through transcription between the neighboring URGCP and MRPS24. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. CN 2.63MRPS24 = mitochondrial ribosomal protein S24. Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. This gene encodes a 28S subunit protein. CN 2.63URGCP = upregulator of cell proliferation. URG4 is upregulated in the presence of hepatitis B virus (HBV)-encoded X antigen (HBxAg) and may contribute to the development of hepatocellular carcinoma by promoting hepatocellular growth and survival (Tufan et al., 2002 (PubMed 12082552)). CN 2.63UBE2D4 = ubiquitin-conjugating enzyme E2D 4 (putative). Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. CN 2.63

DBNL = drebrin-like. Actin-binding adapter protein. May act as a common effector of antigen receptor-signaling pathways in leukocytes. CN 2.63PGAM2 = phosphoglycerate mutase 2 (muscle). Phosphoglycerate mutase (PGAM) catalyzes the reversible reaction of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in the glycolytic pathway. CN 2.63POLM = polymerase (DNA directed), mu. Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. CN 2.63

POLD2 = polymerase (DNA directed), delta 2, regulatory subunit 50kDa. The DNA polymerase delta complex is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA), the multisubunit replication factor C, and the 4 subunit polymerase complex POLD1. The function of the small subunit is not yet clear. CN 2.63MYL7 = myosin, light chain 7, regulatory. Myosins are a large family of motor proteins that share the common features of ATP hydrolysis, actin binding and potential for kinetic energy transduction. CN 2.63GCK = glucokinase (hexokinase 4). Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. Mutations in this gene have been associated with non-insulin dependent diabetes mellitus (NIDDM), maturity onset diabetes of the young, type 2 (MODY2) and persistent hyperinsulinemic hypoglycemia of infancy (PHHI). CN 2.63YKT6 = YKT6 v-SNARE homolog (S. cerevisiae). This gene product is one of the SNARE recognition molecules implicated in vesicular transport between secretory compartments. CN 2.63CAMK2B = calcium/calmodulin-dependent protein kinase II beta. CaM-kinase II (CAMK2) is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. CN 2.63NUDCD3 = NudC domain containing 3. The product of this gene functions to maintain the stability of dynein intermediate chain. Depletion of this gene product results in aggregation and degradation of dynein intermediate chain, mislocalization of the dynein complex from kinetochores, spindle microtubules, and spindle poles, and loss of gamma-tubulin from spindle poles. The protein localizes to the Golgi apparatus during interphase, and levels of the protein increase after the G1/S transition.CN not knownNPC1L1 = NPC1 (Niemann-Pick disease, type C1, gene)-like 1. Play a major role in cholesterol homeostasis. Is critical for the uptake of cholesterol across the plasma membrane of the intestinal enterocyte. CN 2.03DDX56 = DEAD (Asp-Glu-Ala-Asp) box polypeptide 56, May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity. CN 2.03TMED4 = transmembrane emp24 protein transport domain containing 4. Involved in endoplasmic reticulum stress response. May play a role in the regulation of heat-shock response and apoptosis (By similarity).CN 2.03OGDH = oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide). This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle.CN 2.03ZMIZ2 = zinc finger, MIZ-type containing 2. Increases ligand-dependent transcriptional activity of AR and other nuclear hormone receptors. CN 2.03PPIA = peptidylprolyl isomerase A (cyclophilin A). PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.CN 2.03

HECW1 = HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1. E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent degradation of DVL1. Also targets themutant SOD1 protein involved in familial amyotrophic lateral sclerosis (FALS). Forms cytotoxic aggregates with DVL1, SSR3 and mutant SOD1 that lead to motor neuron death in FALS .CN 2.6

H2AFV = H2A histone family, member V. Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. CN 2.03PURB = purine-rich element binding protein B. This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia.CN 2.03"Left end" of rearrangment is in intron between exon 1 and 2 of AUTS2 (all 3 isoforms). "Right end" is in intron between exon 1-2 of ARID3A (5'UTR), same gene involved in another breakpoint (Id 1950).

"left end" and "right end" of this deletion is in intron between exon 1-2 of MFHAS1, is malignant fibrous histiocytoma amplified sequence 1. Identified in a human 8p amplicon, this gene is a potential oncogene whose expression is enhanced in some malignant fibrous histiocytomas (MFH).

"left end" of this rearrangment is just upstream of the ANXA2P2 gene. No CNV. "Right end" is in intron between exon 7-8 of C16orf62. No CNV.

"left end" and "right end" of this rearrangement are not in an annotated element. Genes in between: ANKRD20A1, FAM27B, AQP7P1, NR_024443, MGC21881, LOC442421. No CNV detected."left end of this rearrangment is in intron of NTRK2. Only affects isoforms a (exon 16-17) and c (exon 15-16). "Right end" is not in an annotated region. Genes in between AGTPB1, LOC389765, NAA35, GOLM1, C9orf153, ISCA1, ZCCHC6, GAS1, LOC440173, LOC494127, C9orf170. CN goes from 1.96 to 3.1/3.4. SNP array goes from 1 to 4 in this region.NTRK2 = neurotrophic tyrosine kinase, receptor, type 2. This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders."left end" of this rearrangment is in intron between exon 1-2/2-3 of STRBP (all 3 isoforms). "right end" is intron between exon 20-21 of DENND1A. Gene in between is CRB2 and microRNA 601. CN from 2 to 4, not detected in SNP array or HMM.

DENND1A = DENN/MADD domain containing 1A, Guanine nucleotide exchange factor (GEF) for RAB35. May be involved in the clathrin-mediated endocytosis of synaptic vesicles.

"left end" of this rearrangement contains exons 37 and 38 of SPTAN1 (depending on isoform exon 38+39 or 36+37). CN goes from 2.06 to 2.95 (No change on SNP array). "Right end" is not in an annotated element. SPTAN1 = spectrin, alpha, non-erythrocytic 1 (alpha-fodrin). Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5."left end" and "right end" of this rearrangement are in an intron between exon 3 and 4 of PRKG1, is protein kinase, cGMP-dependent, type I. Phosphorylates PPP1R12A, who regulates myosin phosphatase activity. No CNV. Same gene involved in Id 2730. "left end" and "right end" of this rearrangement are in an intron between exon 9 and 10 of PRKG1. No CNV. Same gene involved in Id 1413.

"left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 20-21 of ODZ4, is odz, odd Oz/ten-m homolog 4 (Drosophila). May function as a cellular signal transducer . No CNV."left end" and "right end" of this rearrangement are in an intron between exon 6-7 from isoform 1, exon 1-2 isoform 2 (other isoforms not affected) of DLG2, discs, large homolog 2 (Drosophila). Required for perception of chronic pain through NMDA receptor signaling. No CNV.

"left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 1 and 2 of all 3 isoforms of MGST1. MGST1 = microsomal glutathione S-transferase 1. This gene encodes a protein that catalyzes the conjugation of glutathione to electrophiles and the reduction of lipid hydroperoxides. This protein is localized to the endoplasmic reticulum and outer mitochondrial membrane where it is thought to protect these membranes from oxidative stress. No CNV detected."left end" and "right end" of this rearrangement are in intron between exon 3 and 4 of USPL1. USPL1 = ubiquitin specific peptidase like 1. Function is unknown. No CNV detected."left end" of this rearrangment is in intron between exon 3 and 4 of PDS5B. Same gene has another breakpoint downstream (Id = 4032 ). "Right end" of this rearrangment is not in an annotated element. But overlaps with probable inversion Id 3996. No CNV.

"left end" of this rearrangment is in intron between exon 28 and 29 of PDS5B. Same gene has another breakpoint upstream (Id = 564). "Right end" of this rearrangement is in intron between exon 3 and 4 of DTD1. Overlaps with Id 1950.PDS5B = PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae). CNV (2 kB) drops again from 3 to 2 (see Id 564). No CNV on HMM or SNP array.

"left end" and "right end" of this rearrangement are not in an annotated element. Encompasses the KL gene. Overlaps with rearrangments with Id 575 (tandem duplication) and 576 (complex). No CNV.KL = klotho. This gene encodes a type-I membrane protein that is related to beta-glucosidases. Reduced production of this protein has been observed in patients with chronic renal failure (CRF), and this may be one of the factors underlying the degenerative processes (e.g., arteriosclerosis, osteoporosis, and skin atrophy) seen in CRF. Also, mutations within this protein have been associated with ageing and bone loss.

"left end" of this rearrangement is not in an annotated element. Overlaps with Id 562 and Id 576. "Right end" is in intron between exon 1-2 (all 6 isoforms except isoform 4, is between exon 5-6 ) of STARD13. CN goes from 2 to 4 downstream of this rearrangment, but is probably due to translocation Id 560.


"left end" of this rearrangement is in intron of STARD13 between exon 1 and 2 for isoforms 1, 3, 6; between exon 5 and 6 of isoform 4; no effect on isoforms 2 and 5. CN goes from 2 to 3.7, SNP array also goes from 2 to 4. More downstream is another translocation (Id 561) and a tandem duplication (Id 575) involving the same gene. " Right end" of this rearrangment is in not in an annotated element. No CNV detected.STARD13 = StAR-related lipid transfer (START) domain containing 13. GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells.

"left end" and "right end" of this rearrangement are not in an annotated element. Many genes in between, but no CNV detected."left end" and "right end" of this rearrangement are not in an annotated element. No genes in between, no CNV detected.

ARID3A = AT rich interactive domain 3A (BRIGHT-like). Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. No CNV."left end" and "right end" of this deletion are in intron between exon 3-4/4-5 (depending on isoform) of IMMP2L, is IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae). Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.




DTD1 = D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae). Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (Potential).


"left end" of this rearrangement is in intron between exon 1-2 of SGPP1. "Right end" is in exon 61 of SYNE2. CN goes from 2.7 to 3.5 for exons 7- 60 of SYNE2, thereafter drops to 1.8. No effect seen on SNP array.


PKM2 = pyruvate kinase, muscle, This gene encodes a protein involved in glycolysis. The encoded protein is a pyruvate kinase that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP, generating ATP and pyruvate. This protein has been shown to interact with thyroid hormone and may mediate cellular metabolic effects induced by thyroid hormones."left end" of this rearrangement is in intron between exon 4-5 of CACNA1H. "Right end" is not in an annotated element. Genes in between are TPSG1, TPSB2, TPSAB1, TPSD1. CN 2KB goes from 2.8 to 3.4 No CNV detected for HMM or on SNP array.



"Left end" is in intron between exon 3 and 4 of ARID3A. Same gene has another breakpoint downstream (Id = 2293). "Right end" is in intron between exon 3-4 of DTD1, overlaps with Id 4031. No CNV.


and other zinc finger proteins like ZNF699, ZNF559, ZNF177, ZNF266, ZNF560 and ZNF426 that all may be involved in transcriptional regulation.

"left end" and "right end" of this rearrangment are not in an annotated element. Genes in between are: PAK4, PAPL, FBX027, FBXO17. No CNV detected.

"left end" and "right end" of this rearrangment are in an intron of ANKRD5, encompassing exon 5 (isoform 2) or 6 (isoform 1). And falls within the non-coding RNA NR_040710. ANKRD5 = ankyrin repeat domain 5, function unknown. No CNV detected. "left end" and "right end" of this rearrangment are not in an annotated element. No genes in between. But overlaps with a CN increase of 1.7 to 2.6 (not detected on SNP array). 430 kb upstream two rearrangments, Id 4032 and 1950."left end" and "right end" of this rearrangment are in intron between exon 3-4 of ZBTB46 = zinc finger and BTB domain containing 46, may be involved in transcriptional regulation."left end" and "right end" of this rearrangment are in intron between exon 3-4/4-5 of TPD52L2. And falls within non-coding RNA NR_045370. TPD52L2 = tumor protein D52-like 2. Family member TPD52 may be involved in calcium-mediated signal transduction and cell proliferation.

"left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 19 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 19."left end" and "right end" of this rearrangment are not in an annotated element. Falls within rearrangments Id's 238, 19 and 1216. No CNV detected."left end" and "right end" of this rearrangment are not in an annotated element. Falls within rearrangments Id's 238, 19 and 1216. No CNV detected."left end" and "right end" of this rearrangment are not in an annotated element. CN goes from 2.6 to 1 (2 KB) No CNV detected on HMM or SNP array.

SGPP1 = sphingosine-1-phosphate phosphatase 1. Has enzymatic activity against both sphingosine 1-phosphate (S1P) and dihydro-S1P. Regulates intracellular and extracellular S1P levels.SYNE2 = spectrin repeat containing, nuclear envelope 2. The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus.




CTIF = CBP80/20-dependent translation initiation factor . Specifically required for the pioneer round of mRNA translation mediated by the cap-binding complex (CBC), that takes place during or right after mRNA export via the nuclear pore complex (NPC). Also required for nonsense-mediated mRNA decay (NMD), the pioneer round of mRNA translation mediated by the cap-binding complex playing a central role in nonsense-mediated mRNA decay (NMD).ELAC1 = elaC homolog 1 (E. coli). Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.

ARID3A = AT rich interactive domain 3A (BRIGHT-like). Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. No CNV.DTD1 = D-tyrosyl-tRNA deacylase 1 homolog (S. cerevisiae). Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (Potential).

MUC16 = mucin 16, cell surface associated. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces (By similarity).OR1M1, OR7G2, OR7G1, ORF7G3, ORF7D2, OR7D4, OR7E24 are olfactory receptors. These receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers theZNF317 = zinc finger protein 317. May function as a transcription factor. May play an important role in erythroid maturation and lymphoid proliferation.



"left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 1838, is same event. CNV not affected."left end" of this rearrangement is in the intron between exon 3 and 4 of C1orf105, uncharacterized protein, unknown function . "right end" is not in an annotated element. This SV is connected to SV 3806, is same event. CNV not affected.

"left end" of this rearrangement is in the intron between exon 13 and 14 of LRP1B. "right end" is in the intron between exon 12 and 13 of the same gene. Exon 13 is probably inverted. Same gene has a deletion of exon 3 (Id 3698 ), confirmed by SNP array and CNV (no call), probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604. Both SNP array and CNV data show exons 3 to 13 of LRP1B are deleted (CN = 0), and exons 1-2 and exons 14-31 a CN of 2, whereas exons 32-91 + 944 kb upstream the gene have a CN of 1. LRP1B = low density lipoprotein receptor-related protein 1B , LRP1B belongs to the low density lipoprotein (LDL) receptor gene family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands (Liu et al., 2001 (PubMed 11384978). The gene is preferentially inactivated in one histological type of lung cancer (non-small cell lung cancer (NSCLC)). May thus play an important role in tumorigenesis of NSCLCs. This gene is also affected in the T, S and SG (SGendoT?), but not in A.Deletion exon 3 LRP1B gene, probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604 and see Id 4461 for more information."left end" is in intron between exon 2 and 3 of the LRP1B gene, "right end" is not in an annotated element (CN is not changed), both ends are Alu repeats. Translocation probably occurred together with a deletion (see Id 3698 and Id 4461). Deletion of exon 26-28 of ERBB4 isoform 1 (exons 26-27 of isovorm 2). CN drops from 2 (1.75) to 1 (0.93). Same gene affected by Id 4603 and Id 1028, both probable inversion of exon 20, here the CN also drops from 2 to 1 (CNV of ERBB4 not detected by SNP array). ERBB4 = v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian). This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Mutations in this gene have been associated with melanoma and schizophrenia. Same gene is also affected in the T line.

"left end" is not in an annotated element, the "right end" is in the intron between exon 4 and 5 of the ZNF385D gene = zinc finger protein 385D, deletion of exon 5-8 (last exon), function unknown. It also removes the one exon of VENTXP7 = VENT homeobox pseudogene 7, non-coding RNA. CN drops from 3 (2.4) to 1.6 (2), also detected by SNP array. Probably happened during translocation of same intron of ZNF385D to chr 19 (Id 3202)."left end" is in in the intron between exon 4 and 5 of the ZNF385D gene, goes together with deletion (Id 3639). CN stays 1.6 after drop of 2.4 to 1.6 due to Id 3639, but SNP array drops form 3 to 2 due to Id 3639 and extra from 2 to 1 due to Id 3202. "right end" is not in an annotated element (CN is not changed).

UBE2E2, involving exons 4-6 (last exon) = ubiquitin-conjugating enzyme E2E2. Involved in selective protein degradation. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination.UBE2E1, complete gene = ubiquitin-conjugating enzyme E2E1. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination.NR1D2, complete gene = nuclear receptor subfamily 1, group D, member 2. This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism.

THRB, complete gene = thyroid hormone receptor, beta. The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH). "left end" is in intron between exon 3 and 4 of the FHIT gene, "right end" is intron between exon 2 and 3 of the gene CADPS (all 3 isoforms). CN increases from 2 to 3 (both CNV as SNP array) involving 6 genes. This region is also affected in the T line.FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.PTPRG = protein tyrosine phosphatase, receptor type, G. The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene.

FEZF2 = FEZ family zinc finger 2. Transcription repressor. Required for the specification of corticospinal motor neurons and other subcerebral projection neurons. May play a role in layer and neuronal subtype-specific patterning of subcortical projections and axonal fasciculation. Controls the development of dendritic arborization and spines of large layer V pyramidal neurons. May be involved in innate immunity (By similarity)

"left end" and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well. Connected to Id 3584.connected to Id 3585, "left end and "right end" of this rearrangement are not in an annotated element. CNV drops from 2 to 1, small region no CN. Total region gone in T line, and in S, SG en SGendoT CN drops as well.

"left end" of this rearrangement is between exon 3 and 4 of the STAG1 gene, no CNV. "right end" of this rearrangement is in intron between exon 2 and 3 of RAB40C (for all 5 isoforms but breakpoint is between exon 1-2 for isoform 2). No CNV detected. Fusion first 42 aa of STAG1 to aa 54 -end of RAB40C.STAG1 = stromal antigen 1. Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosisRAB40C = member RAS oncogene family. Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins."left end" of this rearrangement is between exon 2 and 3 of SPATA16 (encodes first 204 amino acids). The "right end" of this rearrangement is between exon 2 and 3 of NLGN1 ( is 5'UTR). CNV increases from 1.8 to 2.6. No difference on SNP array.

NLGN1 = neuroligin 1. Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions.

"left end" and "right end" of this rearrangement are in LPHN3. "left end" between exon 6-7, "right end" between exon 10-11, deleting amino acids 426 - 636. LPHN3 = latrophilin 3. This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors (GPCR). Latrophilins may function in both cell adhesion and signal transduction.

"left end" of this rearrangement is in intron between exon 11 and 12 (isoform 1, exon 12-13 of isoform 3, isoform 2 not affected) of MAST4, rearranged region also includes CD180 and the "right end" is in intron between exon 2 - 3 of PIK3R1 (only isoform 1, other 3 isoforms are not affected). CN goes from 2.6/3.0 to 3.5. (no CNV detected on SNP array)



LCA5 = Leber congenital amaurosis 5. This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Might be involved in minus end-directed microtubule transport. Mutations in this gene cause Leber congenital amaurosis type V. CN is 3

TTK = TTK protein kinase. This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. CN is 3BCKDHB = branched chain keto acid dehydrogenase E1, beta polypeptide. Branched-chain keto acid dehydrogenase is a multienzyme complex associated with the inner membrane of mitochondria, and functions in the catabolism of branched-chain amino acids. The complex consists of multiple copies of 3 components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). This gene encodes the E1 beta subunit. CN is 3

IBTK = inhibitor of Bruton agammaglobulinemia tyrosine kinase, Acts as an inhibitor of BTK tyrosine kinase activity, thereby playing a role in B-cell development. Down-regulates BTK kinase activity, leading to interference with BTK-mediated calcium mobilization and NF-kappa-B-driven transcription. CN is 5.

UBE2CBP = ubiquitin-conjugating enzyme E2C binding protein. E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. CN is 3.

"left end" of this rearrangement is in an intron between exon 2 and 3 of VTA1, the "right end " is in an intron between exon 4 and 5 of the same gene, deleting exons 3 and 4 (amino acids 70 - 137). VTA1 = Vps20-associated 1 homolog (S. cerevisiae). Involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. CN from 2.3 to 2.9, no effect detected on SNP array."left end" of this rearrangement contains exons 7 and 8 of GET4. No effect on CN. "The right end" is not in an annotated element, No effect on CN. GET4 = golgi to ER traffic protein 4 homolog (S. cerevisiae). Component of the BAT3 complex, a multiprotein complex involved in the post-translational delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum membrane.

PSMA2 = proteasome (prosome, macropain) subunit, alpha type, 2. The proteasome is a multicatalytic proteinase complex and has an ATP-dependent proteolytic activity. PSMA2 may have a potential regulatory effect on another component(s) of the proteasome complex through tyrosine phosphorylation. CN 2.6

STK17A = serine/threonine kinase 17a. This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. CN 2.6

NM_001204871: This locus represents naturally occurring read-through transcription between the neighboring URGCP and MRPS24. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. CN 2.63MRPS24 = mitochondrial ribosomal protein S24. Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. This gene encodes a 28S subunit protein. CN 2.63URGCP = upregulator of cell proliferation. URG4 is upregulated in the presence of hepatitis B virus (HBV)-encoded X antigen (HBxAg) and may contribute to the development of hepatocellular carcinoma by promoting hepatocellular growth and survival (Tufan et al., 2002 (PubMed 12082552)). CN 2.63UBE2D4 = ubiquitin-conjugating enzyme E2D 4 (putative). Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. CN 2.63

POLM = polymerase (DNA directed), mu. Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. CN 2.63

POLD2 = polymerase (DNA directed), delta 2, regulatory subunit 50kDa. The DNA polymerase delta complex is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA), the multisubunit replication factor C, and the 4 subunit polymerase complex POLD1. The function of the small subunit is not yet clear. CN 2.63

GCK = glucokinase (hexokinase 4). Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. Mutations in this gene have been associated with non-insulin dependent diabetes mellitus (NIDDM), maturity onset diabetes of the young, type 2 (MODY2) and persistent hyperinsulinemic hypoglycemia of infancy (PHHI). CN 2.63

CAMK2B = calcium/calmodulin-dependent protein kinase II beta. CaM-kinase II (CAMK2) is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. CN 2.63NUDCD3 = NudC domain containing 3. The product of this gene functions to maintain the stability of dynein intermediate chain. Depletion of this gene product results in aggregation and degradation of dynein intermediate chain, mislocalization of the dynein complex from kinetochores, spindle microtubules, and spindle poles, and loss of gamma-tubulin from spindle poles. The protein localizes to the Golgi apparatus during interphase, and levels of the protein increase after the G1/S transition.CN not known

TMED4 = transmembrane emp24 protein transport domain containing 4. Involved in endoplasmic reticulum stress response. May play a role in the regulation of heat-shock response and apoptosis (By similarity).CN 2.03OGDH = oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide). This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle.CN 2.03

H2AFV = H2A histone family, member V. Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. CN 2.03PURB = purine-rich element binding protein B. This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia.CN 2.03

"left end" and "right end" of this deletion is in intron between exon 1-2 of MFHAS1, is malignant fibrous histiocytoma amplified sequence 1. Identified in a human 8p amplicon, this gene is a potential oncogene whose expression is enhanced in some malignant fibrous histiocytomas (MFH).

"left end of this rearrangment is in intron of NTRK2. Only affects isoforms a (exon 16-17) and c (exon 15-16). "Right end" is not in an annotated region. Genes in between AGTPB1, LOC389765, NAA35, GOLM1, C9orf153, ISCA1, ZCCHC6, GAS1, LOC440173, LOC494127, C9orf170. CN goes from 1.96 to 3.1/3.4. SNP array goes from 1 to 4 in this region.NTRK2 = neurotrophic tyrosine kinase, receptor, type 2. This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders."left end" of this rearrangment is in intron between exon 1-2/2-3 of STRBP (all 3 isoforms). "right end" is intron between exon 20-21 of DENND1A. Gene in between is CRB2 and microRNA 601. CN from 2 to 4, not detected in SNP array or HMM.

"left end" of this rearrangement contains exons 37 and 38 of SPTAN1 (depending on isoform exon 38+39 or 36+37). CN goes from 2.06 to 2.95 (No change on SNP array). "Right end" is not in an annotated element. SPTAN1 = spectrin, alpha, non-erythrocytic 1 (alpha-fodrin). Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5."left end" and "right end" of this rearrangement are in an intron between exon 3 and 4 of PRKG1, is protein kinase, cGMP-dependent, type I. Phosphorylates PPP1R12A, who regulates myosin phosphatase activity. No CNV. Same gene involved in Id 2730.

"left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 20-21 of ODZ4, is odz, odd Oz/ten-m homolog 4 (Drosophila). May function as a cellular signal transducer . No CNV."left end" and "right end" of this rearrangement are in an intron between exon 6-7 from isoform 1, exon 1-2 isoform 2 (other isoforms not affected) of DLG2, discs, large homolog 2 (Drosophila). Required for perception of chronic pain through NMDA receptor signaling. No CNV.

"left end" of this rearrangment is not in an annotated element. "Right end" is in intron between exon 1 and 2 of all 3 isoforms of MGST1. MGST1 = microsomal glutathione S-transferase 1. This gene encodes a protein that catalyzes the conjugation of glutathione to electrophiles and the reduction of lipid hydroperoxides. This protein is localized to the endoplasmic reticulum and outer mitochondrial membrane where it is thought to protect these membranes from oxidative stress. No CNV detected.

"left end" of this rearrangment is in intron between exon 3 and 4 of PDS5B. Same gene has another breakpoint downstream (Id = 4032 ). "Right end" of this rearrangment is not in an annotated element. But overlaps with probable inversion Id 3996. No CNV.

"left end" of this rearrangment is in intron between exon 28 and 29 of PDS5B. Same gene has another breakpoint upstream (Id = 564). "Right end" of this rearrangement is in intron between exon 3 and 4 of DTD1. Overlaps with Id 1950.

KL = klotho. This gene encodes a type-I membrane protein that is related to beta-glucosidases. Reduced production of this protein has been observed in patients with chronic renal failure (CRF), and this may be one of the factors underlying the degenerative processes (e.g., arteriosclerosis, osteoporosis, and skin atrophy) seen in CRF. Also, mutations within this protein have been associated with ageing and bone loss.

"left end" of this rearrangement is not in an annotated element. Overlaps with Id 562 and Id 576. "Right end" is in intron between exon 1-2 (all 6 isoforms except isoform 4, is between exon 5-6 ) of STARD13. CN goes from 2 to 4 downstream of this rearrangment, but is probably due to translocation Id 560.


"left end" of this rearrangement is in intron of STARD13 between exon 1 and 2 for isoforms 1, 3, 6; between exon 5 and 6 of isoform 4; no effect on isoforms 2 and 5. CN goes from 2 to 3.7, SNP array also goes from 2 to 4. More downstream is another translocation (Id 561) and a tandem duplication (Id 575) involving the same gene. " Right end" of this rearrangment is in not in an annotated element. No CNV detected.STARD13 = StAR-related lipid transfer (START) domain containing 13. GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells.

"left end" and "right end" of this deletion are in intron between exon 3-4/4-5 (depending on isoform) of IMMP2L, is IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae). Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.






PKM2 = pyruvate kinase, muscle, This gene encodes a protein involved in glycolysis. The encoded protein is a pyruvate kinase that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP, generating ATP and pyruvate. This protein has been shown to interact with thyroid hormone and may mediate cellular metabolic effects induced by thyroid hormones."left end" of this rearrangement is in intron between exon 4-5 of CACNA1H. "Right end" is not in an annotated element. Genes in between are TPSG1, TPSB2, TPSAB1, TPSD1. CN 2KB goes from 2.8 to 3.4 No CNV detected for HMM or on SNP array.




"left end" and "right end" of this rearrangment are in an intron of ANKRD5, encompassing exon 5 (isoform 2) or 6 (isoform 1). And falls within the non-coding RNA NR_040710. ANKRD5 = ankyrin repeat domain 5, function unknown. No CNV detected. "left end" and "right end" of this rearrangment are not in an annotated element. No genes in between. But overlaps with a CN increase of 1.7 to 2.6 (not detected on SNP array). 430 kb upstream two rearrangments, Id 4032 and 1950.

"left end" and "right end" of this rearrangment are in intron between exon 3-4/4-5 of TPD52L2. And falls within non-coding RNA NR_045370. TPD52L2 = tumor protein D52-like 2. Family member TPD52 may be involved in calcium-mediated signal transduction and cell proliferation.

"left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 19 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 1216."left end" and "right end" of this rearrangment are not in an annotated element. Many genes are in between. No CNV detected that would affect a certain gene. Downstream of Id 1222, and similar to Id 238 and Id 19.

SYNE2 = spectrin repeat containing, nuclear envelope 2. The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus.




CTIF = CBP80/20-dependent translation initiation factor . Specifically required for the pioneer round of mRNA translation mediated by the cap-binding complex (CBC), that takes place during or right after mRNA export via the nuclear pore complex (NPC). Also required for nonsense-mediated mRNA decay (NMD), the pioneer round of mRNA translation mediated by the cap-binding complex playing a central role in nonsense-mediated mRNA decay (NMD).



"left end" of this rearrangement is in the intron between exon 13 and 14 of LRP1B. "right end" is in the intron between exon 12 and 13 of the same gene. Exon 13 is probably inverted. Same gene has a deletion of exon 3 (Id 3698 ), confirmed by SNP array and CNV (no call), probably occurred simultaneously with translocation to chromosome 5 ("left end" in intron between exon 2 and 3, both ends are Alu repeats), Id 1604. Both SNP array and CNV data show exons 3 to 13 of LRP1B are deleted (CN = 0), and exons 1-2 and exons 14-31 a CN of 2, whereas exons 32-91 + 944 kb upstream the gene have a CN of 1. LRP1B = low density lipoprotein receptor-related protein 1B , LRP1B belongs to the low density lipoprotein (LDL) receptor gene family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands (Liu et al., 2001 (PubMed 11384978). The gene is preferentially inactivated in one histological type of lung cancer (non-small cell lung cancer (NSCLC)). May thus play an important role in tumorigenesis of NSCLCs. This gene is also affected in the T, S and SG (SGendoT?), but not in A.

Deletion of exon 26-28 of ERBB4 isoform 1 (exons 26-27 of isovorm 2). CN drops from 2 (1.75) to 1 (0.93). Same gene affected by Id 4603 and Id 1028, both probable inversion of exon 20, here the CN also drops from 2 to 1 (CNV of ERBB4 not detected by SNP array). ERBB4 = v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian). This gene is a member of the Tyr protein kinase family and the epidermal growth factor receptor subfamily. The protein binds to and is activated by neuregulins and other factors and induces a variety of cellular responses including mitogenesis and differentiation. Mutations in this gene have been associated with melanoma and schizophrenia. Same gene is also affected in the T line.

"left end" is not in an annotated element, the "right end" is in the intron between exon 4 and 5 of the ZNF385D gene = zinc finger protein 385D, deletion of exon 5-8 (last exon), function unknown. It also removes the one exon of VENTXP7 = VENT homeobox pseudogene 7, non-coding RNA. CN drops from 3 (2.4) to 1.6 (2), also detected by SNP array. Probably happened during translocation of same intron of ZNF385D to chr 19 (Id 3202).

UBE2E1, complete gene = ubiquitin-conjugating enzyme E2E1. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination.NR1D2, complete gene = nuclear receptor subfamily 1, group D, member 2. This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism.

THRB, complete gene = thyroid hormone receptor, beta. The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH).

FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.PTPRG = protein tyrosine phosphatase, receptor type, G. The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene.

FEZF2 = FEZ family zinc finger 2. Transcription repressor. Required for the specification of corticospinal motor neurons and other subcerebral projection neurons. May play a role in layer and neuronal subtype-specific patterning of subcortical projections and axonal fasciculation. Controls the development of dendritic arborization and spines of large layer V pyramidal neurons. May be involved in innate immunity (By similarity)

STAG1 = stromal antigen 1. Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis

"left end" and "right end" of this rearrangement are in LPHN3. "left end" between exon 6-7, "right end" between exon 10-11, deleting amino acids 426 - 636. LPHN3 = latrophilin 3. This gene encodes a member of the latrophilin subfamily of G-protein coupled receptors (GPCR). Latrophilins may function in both cell adhesion and signal transduction.

"left end" of this rearrangement is in intron between exon 11 and 12 (isoform 1, exon 12-13 of isoform 3, isoform 2 not affected) of MAST4, rearranged region also includes CD180 and the "right end" is in intron between exon 2 - 3 of PIK3R1 (only isoform 1, other 3 isoforms are not affected). CN goes from 2.6/3.0 to 3.5. (no CNV detected on SNP array)

HMGN3 = high mobility group nucleosomal binding domain 3, Binds to nucleosomes, regulating chromatin structure and consequently, chromatin-dependent processes such as transcription, DNA replication and DNA repair. Affects both insulin and glucagon levels and modulates the expression of pancreatic genes involved in insulin secretion. CN is 4



"left end" of this rearrangement is in an intron between exon 2 and 3 of VTA1, the "right end " is in an intron between exon 4 and 5 of the same gene, deleting exons 3 and 4 (amino acids 70 - 137). VTA1 = Vps20-associated 1 homolog (S. cerevisiae). Involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. CN from 2.3 to 2.9, no effect detected on SNP array."left end" of this rearrangement contains exons 7 and 8 of GET4. No effect on CN. "The right end" is not in an annotated element, No effect on CN. GET4 = golgi to ER traffic protein 4 homolog (S. cerevisiae). Component of the BAT3 complex, a multiprotein complex involved in the post-translational delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum membrane.

NM_001204871: This locus represents naturally occurring read-through transcription between the neighboring URGCP and MRPS24. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. CN 2.63MRPS24 = mitochondrial ribosomal protein S24. Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. This gene encodes a 28S subunit protein. CN 2.63

POLD2 = polymerase (DNA directed), delta 2, regulatory subunit 50kDa. The DNA polymerase delta complex is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA), the multisubunit replication factor C, and the 4 subunit polymerase complex POLD1. The function of the small subunit is not yet clear. CN 2.63

GCK = glucokinase (hexokinase 4). Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. Mutations in this gene have been associated with non-insulin dependent diabetes mellitus (NIDDM), maturity onset diabetes of the young, type 2 (MODY2) and persistent hyperinsulinemic hypoglycemia of infancy (PHHI). CN 2.63

NUDCD3 = NudC domain containing 3. The product of this gene functions to maintain the stability of dynein intermediate chain. Depletion of this gene product results in aggregation and degradation of dynein intermediate chain, mislocalization of the dynein complex from kinetochores, spindle microtubules, and spindle poles, and loss of gamma-tubulin from spindle poles. The protein localizes to the Golgi apparatus during interphase, and levels of the protein increase after the G1/S transition.CN not known

H2AFV = H2A histone family, member V. Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. CN 2.03PURB = purine-rich element binding protein B. This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia.CN 2.03

"left end of this rearrangment is in intron of NTRK2. Only affects isoforms a (exon 16-17) and c (exon 15-16). "Right end" is not in an annotated region. Genes in between AGTPB1, LOC389765, NAA35, GOLM1, C9orf153, ISCA1, ZCCHC6, GAS1, LOC440173, LOC494127, C9orf170. CN goes from 1.96 to 3.1/3.4. SNP array goes from 1 to 4 in this region.NTRK2 = neurotrophic tyrosine kinase, receptor, type 2. This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders.

"left end" of this rearrangement contains exons 37 and 38 of SPTAN1 (depending on isoform exon 38+39 or 36+37). CN goes from 2.06 to 2.95 (No change on SNP array). "Right end" is not in an annotated element. SPTAN1 = spectrin, alpha, non-erythrocytic 1 (alpha-fodrin). Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5.


KL = klotho. This gene encodes a type-I membrane protein that is related to beta-glucosidases. Reduced production of this protein has been observed in patients with chronic renal failure (CRF), and this may be one of the factors underlying the degenerative processes (e.g., arteriosclerosis, osteoporosis, and skin atrophy) seen in CRF. Also, mutations within this protein have been associated with ageing and bone loss.

"Left end" is in intron between exon 1-2 (all 6 isoforms except isoform 4, is between exon 5-6 ) of STARD13. CN goes from 2 to 4 downstream of this rearrangment, but is probably due to translocation Id 560. Overlaps with "right end" of Id 575. "Right end" of this rearrangment is exon 11/12 of RIN2. CNV 2KB goes from 1.7 to 2.5 , SNP array also goes from 2 to 3, CNV HMM goes from 1.9 to 2.6 a bit more upstream.

"left end" of this rearrangement is in intron of STARD13 between exon 1 and 2 for isoforms 1, 3, 6; between exon 5 and 6 of isoform 4; no effect on isoforms 2 and 5. CN goes from 2 to 3.7, SNP array also goes from 2 to 4. More downstream is another translocation (Id 561) and a tandem duplication (Id 575) involving the same gene. " Right end" of this rearrangment is in not in an annotated element. No CNV detected.

"left end" and "right end" of this deletion are in intron between exon 3-4/4-5 (depending on isoform) of IMMP2L, is IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae). Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.




PKM2 = pyruvate kinase, muscle, This gene encodes a protein involved in glycolysis. The encoded protein is a pyruvate kinase that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP, generating ATP and pyruvate. This protein has been shown to interact with thyroid hormone and may mediate cellular metabolic effects induced by thyroid hormones.






"left end" of this rearrangment is in an intron between exon 5-6 of ZNF234 (both isoforms). "Right end" of this rearrangment is in 3'UTR or in intron before last exon of ZNF226, depending on the isoform. CN goes from 6.5 to 10.3, and goes down again after rearrangement Id 3994. Gene in between rearrangements is ZNF227. No change on SNP array detected. ZNF proteins may be involved in transcriptional regulation.




"left end" is not in an annotated element, the "right end" is in the intron between exon 4 and 5 of the ZNF385D gene = zinc finger protein 385D, deletion of exon 5-8 (last exon), function unknown. It also removes the one exon of VENTXP7 = VENT homeobox pseudogene 7, non-coding RNA. CN drops from 3 (2.4) to 1.6 (2), also detected by SNP array. Probably happened during translocation of same intron of ZNF385D to chr 19 (Id 3202).


FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.PTPRG = protein tyrosine phosphatase, receptor type, G. The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene.

STAG1 = stromal antigen 1. Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis


"left end" of this rearrangement is in an intron between exon 2 and 3 of VTA1, the "right end " is in an intron between exon 4 and 5 of the same gene, deleting exons 3 and 4 (amino acids 70 - 137). VTA1 = Vps20-associated 1 homolog (S. cerevisiae). Involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. CN from 2.3 to 2.9, no effect detected on SNP array.

NUDCD3 = NudC domain containing 3. The product of this gene functions to maintain the stability of dynein intermediate chain. Depletion of this gene product results in aggregation and degradation of dynein intermediate chain, mislocalization of the dynein complex from kinetochores, spindle microtubules, and spindle poles, and loss of gamma-tubulin from spindle poles. The protein localizes to the Golgi apparatus during interphase, and levels of the protein increase after the G1/S transition.CN not known

PURB = purine-rich element binding protein B. This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia.CN 2.03





"left end" and "right end" of this rearrangement are in an intron between exon 8-9 of WWOX. CN of this part of the intron goes from 2.6 to 3.3 (not seen on SNP array). WWOX = WW domain containing oxidoreductase. Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development (By similarity). May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm.

"left end" and "right end" of this rearrangement are in an intron between exon 1-2 of IKZF3 (for all 6 isoforms). No CNV detected. IKZF3 = IKAROS family zinc finger 3 (Aiolos).Transcription factor that plays an important role in the regulation of lymphocyte differentiation. Plays an essential role in regulation of B-cell differentiation, proliferation and maturation to an effector state. Involved in regulating BCL2 expression and controlling apoptosis in T-cells in an IL2-dependent manner.






FHIT = fragile histidine triad gene. Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues. This gene, a member of the histidine triad gene family, encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. The gene encompasses the common fragile site FRA3B on chromosome 3, where carcinogen-induced damage can lead to translocations and aberrant transcripts of this gene. In fact, aberrant transcripts from this gene have been found in about half of all esophageal, stomach, and colon carcinomas.

TTK = TTK protein kinase. This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. CN is 3


>Id LeftChr LeftPosition LeRightChRightPosition Ri Str AssembledSeq EventId5869 chr1 1604411 + chr2 1145894 + Y ccgacatcgaga 3015913 chr1 10482368 + chr1 10484222 + Y cctctttcctgc 3031825 chr1 27876317 - chr1 54312586 + N ttttggttttta 761826 chr1 27879627 - chr1 35284504 + N ccactccagctg 776213 chr1 33927935 + chr1 33930399 - N tgaacacatcctt 3115884 chr1 55124018 + chr1 55126193 + Y actcgctaggctg 3026188 chr1 78811603 + chr4 20149767 - N acgttggaatatt 3102177 chr1 86888933 - chr1 86939104 - Y gagaagataatgca 1015097 chr1 141906695 + chr2 11847365 + Y tgaatttaaatc 2742151 chr1 184031437 - chr1 185060212 - Y aatttaaaaggga 992150 chr1 187912877 - chr1 187921208 - Y gacaacatttgtg 982148 chr1 210557564 - chr1 210934739 - Y tggtgggcagtaag 972145 chr1 243470595 - chr1 243489819 - Y atggctatatctc 96

919 chr2 62468320 - chr2 62471146 + N ttttgaggctga 302044 chr2 116690611 - chr2 116694898 - Y ctataaaactac 955636 chr2 132747163 + chr16 33863532 - N tgctttcatctt 2942034 chr2 133856722 - chr2 134185500 - Y atgcttattcatga 944905 chr2 141292311 + chr2 141306668 + Y ggattaacttcca 2684903 chr2 141516602 + chr2 141791303 + Y ctaatgttttagtt 2674900 chr2 141516966 + chr2 141842341 + Y tttgtactcttgg 2674897 chr2 142095481 + chr2 142358008 + Y agacagaaaatac 2664896 chr2 144043944 + chr2 144044480 + Y ataatagtggtgg 932032 chr2 144043948 - chr2 144058641 - Y ggctttctaactc 932025 chr2 153754485 - chr2 153755443 - Y caaaagtaacaga 924864 chr2 184030015 + chr2 184030887 + Y aatatttcttaaa 2644851 chr2 212489917 + chr2 212535912 + Y aaaatgtagactgc 2624849 chr2 212793182 + chr2 212932647 + Y atgagaattgcag 2612022 chr2 240289311 - chr2 240311596 - Y cacttaagtgct 904816 chr3 2908507 + chr3 3274238 + Y ttctctgagtaaa 258

865 chr3 8849562 - chr3 37106868 + N tcagctcactgc 296101 chr3 8874930 + chr3 37199905 - N ataaagttgggtg 3086096 chr3 30472559 + chr3 30474195 - N atttcttagtga 3072011 chr3 41159818 - chr3 41203932 - Y tctgatgagcaagg 854748 chr3 59791166 + chr3 60398110 + Y aaaagccaggaat 2542010 chr3 59938455 - chr3 60127589 - Y atgagagaatctct 844744 chr3 60883299 + chr3 60939556 + Y cagtgtcagatg 2534731 chr3 76724461 + chr3 76753800 + Y acatgattttag 2524727 chr3 77322425 + chr3 77325575 + Y gagaaaacagtgaa 2512004 chr3 84620803 - chr3 84628664 - Y tgtcatttgtaga 834722 chr3 85257840 + chr3 85260586 + Y tgttcattgtatc 2504718 chr3 98113460 + chr3 98213330 + Y gctctctgtata 249

568 chr3 114281021 - chr16 87318514 + N ttggaggaggta 236088 chr3 114281099 + chr3 114473354 - N ttgaattgtgac 23

851 chr3 114281108 - chr3 114473371 + N ccaccacaaaaa 234346 chr3 114473362 + chr16 87318511 + Y ttcagtgagttc 23

850 chr3 115579032 - chr3 115584975 + N agccaccatctt 286087 chr3 115579124 + chr3 115582247 - N cagttcatatgc 284703 chr3 115582255 + chr3 115584973 + Y cctgtcccagaa 28

4699 chr3 117837589 + chr3 117931363 + Y ctccctccatccc 2474698 chr3 117955761 + chr3 117996544 + Y atgtcccagatc 2464696 chr3 118128716 + chr3 118277792 + Y ttcattaagtga 2452000 chr3 143847257 - chr3 145059367 - Y ccttgttcctatt 821998 chr3 175386386 - chr3 175474457 - Y aggtcacagtcta 811759 chr3 186999263 - chr12 73463942 - Y agcctgggagcc 75843 chr4 90294 - chr4 95430 + N attcagaatgcaa 27

4614 chr4 33957965 + chr4 33973536 + Y tttattttttattt 2411980 chr4 41303589 - chr4 181820093 - Y tggaggggccg 78

838 chr4 43152461 - chr4 127740545 + N ggtatggaaactt 261992 chr4 43408033 - chr4 43970988 - Y aggtgggagggt 804545 chr4 43559026 + chr5 163279472 + Y tttccaaaacag 2351983 chr4 87936887 - chr4 87992097 - Y acatatgacattca 794586 chr4 91978522 + chr4 92025038 + Y taaaacatttcag 239

530 chr4 108102137 - chr22 27395610 + N gacttttaccaga 224564 chr4 123348281 + chr4 123350932 + Y gtatgtatagttga 236

831 chr4 137283452 - chr6 32978878 + N gattacctcaata 251692 chr4 172646047 - chr4 172649137 - Y accatcaggtct 741690 chr4 180318145 - chr4 180348908 - Y tttgtctttttat 72

522 chr4 191129916 - chr9 67915726 + N ccttaaaataca 211357 chr4 191179707 - chr18 102542 - Y tccaggcgcctc 481279 chr5 23050109 - chr22 27396108 - Y gaaaaccttatgt 221678 chr5 86718801 - chr5 86834076 - Y gaactgtgtcatc 714210 chr5 98294024 + chr5 98309135 + Y acagtttggttcaa 2284208 chr5 101108334 + chr5 101371803 + Y aaaggttccatgc 2274194 chr5 120253252 + chr5 120495940 + Y agcatccttgtct 2264192 chr5 121952170 + chr5 121955333 + Y tgaccagtggtgta 2251617 chr5 161521039 - chr14 30217970 - Y aaagacatttata 664162 chr5 164931865 + chr5 165078441 + Y ttcacatcttgaa 2214141 chr5 178041672 + chr5 178046022 + Y cggcctcccaga 2181660 chr6 44864888 - chr6 45047295 - Y agattcaaccca 694083 chr6 57107765 + chr6 57153705 + Y tattacctctta 19

514 chr6 57153821 - chr6 57161628 + N cactctccacag 195550 chr6 130183997 + chr6 132245890 - N ttatttaacaaat 292

513 chr6 130331483 - chr6 132886312 + N aataagcacttg 185548 chr6 132250067 + chr6 132890097 - N taatttcaaagtg 291

511 chr6 148756898 - chr6 148772214 + N ctggaatttcat 171645 chr6 152564421 - chr6 152580615 - Y gcagttgatgaaa 684014 chr6 162410104 + chr6 162685824 + Y aatttcaaataa 2144011 chr6 162859718 + chr6 162932556 + Y gctgagactgcag 213

509 chr6 167730551 - chr6 167736636 + N ggcgggcatgacc 163925 chr6 167738310 + chr13 86917347 + Y gtggtgactggag 2095546 chr6 168101456 + chr6 168262571 - N tgacaaagctatt 2903998 chr7 948622 + chr7 950039 + Y caacaccaaag 2123991 chr7 3101894 + chr7 3104755 + Y gtcacattctt 2105302 chr7 110113967 + chr22 27395889 - N cagggtatcccc 221599 chr7 133132748 - chr7 133143312 - Y acaataaagctc 65

306 chr7 133520247 - chr18 25580290 + N taccaaaagagg 53885 chr7 140066224 + chr7 140255041 + Y agaggaatgtgtg 206

3878 chr7 144703513 + chr7 144708635 + Y gaagatataaaaa 2043872 chr7 151795880 + chr7 151796549 + Y aacgtctaattt 2033859 chr7 156789004 + chr7 156789828 + Y ggcacgagccgc 2013833 chr8 8764151 + chr8 8766092 + Y tgaaaaatcaaag 196

465 chr8 36078973 - chr8 36081402 + N tgtggtgatgtga 153818 chr8 36080521 + chr8 36081402 + Y actgatttcatg 152895 chr8 36141670 + chrX 69663172 + Y tgtgcactgca 1503766 chr8 124426774 + chr8 124524002 + Y atctagaagattt 195

451 chr9 18065011 - chr9 18068296 + N gtgagggagggca 133725 chr9 28432994 + chr9 28570679 + Y aatattaaaaatat 192

441 chr9 80972830 - chr9 80973151 + N atcttagcagcta 111426 chr9 81951826 - chr13 61645677 - Y taaatgaaatattg 553662 chr9 128256355 + chr9 128457801 + Y aaggagaagtttgg 1903633 chr9 140032250 + chr9 140033878 + Y aggggtccctga 1873632 chr9 140138980 + chr9 140153504 + Y ggggtcagaaga 1863575 chr10 52595633 + chr10 52992070 + Y gtataaaatttt 1823572 chr10 56356483 + chr10 56381113 + Y agagccattagtg 1803571 chr10 56423945 + chr10 56603586 + Y atgtagctttttaa 1793481 chr11 19708432 + chr11 19714181 + Y tctgtcaacaatc 1771471 chr11 37679545 - chr11 37695111 - Y gttcattgtagca 583413 chr11 84193894 + chr11 84260053 + Y acatgcacagta 1753369 chr12 6718238 + chr12 6718881 + Y gattggccaaa 1743359 chr12 17507658 + chr12 17508880 + Y ctaacacatctga 1731436 chr12 66618500 - chr12 66620972 - Y cagcgtttgtcaa 571435 chr12 76479343 - chr12 76508897 - Y aaaggaataagaa 565156 chr12 99859423 + chr22 27395889 - N ggtatcatgtggt 221416 chr12 123675891 - chr12 123904486 - Y ccaataggcctg 533264 chr13 23620946 + chr13 23644955 + Y acacctaaacagg 1703262 chr13 25170862 + chr13 25172085 + Y tgggaaaaatgat 1693252 chr13 30094958 + chr13 30095770 + Y gtttggaaaatact 166

372 chr13 61214041 - chr13 61220487 + N gacatgtttgattt 7161 chr13 62847983 - chr19 18924852 + N ctttcctatgt 4

5243 chr13 67887094 + chr18 36916953 - N caagctgaccatat 2793218 chr13 73503518 + chr13 73505572 + Y ttctgaattacca 1613209 chr13 91740904 + chr13 92563358 + Y gaatgagtctcca 1603208 chr13 92724372 + chr13 92781542 + Y ttgaactcctga 6

369 chr13 92780393 - chr13 92781545 + N gtagaaacccaa 63207 chr13 93255345 + chr13 93631737 + Y tttctttaacaaa 1595416 chr13 94244887 + chr13 94286246 - N acgctactgaact 2813156 chr14 60669760 + chr14 60675276 + Y tcagggaagttgt 1563154 chr14 66909183 + chr14 66950119 + Y aacctaaaaaat 1551392 chr14 86617680 - chr14 86629211 - Y attctgagggcag 493109 chr15 22884280 + chr15 22885422 + Y atatcaaggcgt 1543032 chr16 1972851 + chr16 2013149 + Y tgttgagacctc 1511174 chr16 68282304 - chr16 68282978 - Y catatacacacac 475139 chr17 15162438 + chr22 27395912 - N actttttcaaatg 225224 chr17 18070771 + chr17 18090238 - N caccaaggtggag 2782724 chr17 25525595 + chr17 25538316 + Y tttcattttactat 1461013 chr17 36849689 - chr22 39682618 - Y tggaggataaggc 382685 chr17 50234983 + chr17 50235514 + Y aatgtatggctt 144

1161 chr17 52380988 - chr17 52600388 - Y gtcagagggatca 442682 chr17 52384579 + chr17 52387530 + Y gatcatagagct 1421156 chr17 77835344 - chr17 77835703 - Y ctcccccactgc 431092 chr18 60936679 - chr18 60991253 - Y taaaggtgttgg 422545 chr19 8404114 + chr19 8431839 + Y gaacttcagcct 1355179 chr19 16434073 + chr19 16560179 - N acagggacaatg 2761055 chr19 34869318 - chr19 35397720 - Y aaaaaagctaag 392459 chr20 9115210 + chr20 9236871 + Y gtgttttaattttt 1342455 chr20 14651687 + chr20 14908280 + Y ccactcccttgtc 1332453 chr20 14696547 + chr20 14848129 + Y ttgttcaactccc 1312454 chr20 14714542 + chr20 14721636 + Y cagatgacttgct 1322451 chr20 15007016 + chr20 15070396 + Y ctccatttcagtt 1302448 chr20 15247611 + chr20 15301668 + Y tttgctttcaata 1292446 chr20 15735950 + chr20 15883357 + Y atgaagttggctt 1282352 chr21 24821509 + chr21 24857083 + Y taaatctatgga 1222280 chr22 48809296 + chr22 48809992 + Y tgggaatcaggg 1172273 chrX 1411270 + chrX 1413443 + Y taaagggctgt 1142264 chrX 7019265 + chrX 7108602 + Y aataaaaaagaaa 1092262 chrX 7226561 + chrX 7274436 + Y tggagatgataca 1085131 chrX 26074161 + chrX 40220013 - N gactacctagatg 1

36 chrX 26074169 - chrX 40220026 + N gggctgaggaatt 1975 chrX 73416421 - chrX 73516231 - Y atgtatggaatctc 37

2211 chrX 96576197 + chrX 96699308 + Y acatttgggtta 1062205 chrX 117905654 + chrX 117907917 + Y ctccttggtcaa 1052201 chrX 122896658 + chrX 122897659 + Y attacagacat 103

Type RelatedJunctio Also present in other lines? Notesinterchromosomal Interchromosomal translocation with breakpoint on chr11 inside intron 6/7 of CDK11B and breakpoint on chr2 in intron 6 of SNTG2. The break is strand consistent, but genes are on opposite strands, so no functional fusion gene is formed. Genes are in a region of 3 copies on each chromosome. CDK11B is cyclin dependent kinase 11b, and appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. SNTG2 is gamma-2-syntrophin, a putative adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex deletion Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.probable-inversion Very large probable inversion with left breakpoint in intergenic region and right breakpoint in intron 3 of C1orf83, an uncharacterized protein.probable-inversion No annotated elements involved. Large inversion with both breakpoints in intergenic regionprobable-inversion Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.deletion A deletion partially overlapping with the first exon and intron of DHCR24. It's occuring in a pentaploid region and not clear how many affected copies. No drop in CNV is observed. DHCR24: Catalyzes the reduction of the delta-24 double bond of sterol intermediates. Protects cells from oxidative stress by reducing caspase 3 activity during apoptosis induced by oxidative stress. Also protects against amyloid-beta peptide-induced apoptosisinterchromosomal Interchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.tandem-duplication Tandem duplication with left breakpoint in CLCA3P and right breakpoint in intergenic region. No fusion genes ar formed, a truncated version of CLCA3P is not formed either, since it's onlythe C-terminal part that's duplicated (exons 14 and 15). CLCA3P is a calcium activated chloride channel regulator, very few details on protein are known.interchromosomal Interchromosomal translocation with breakpoint on chr1 in intergenic region close to centromere. Breakpoint on chr2 is in intron 11 of LPIN1 and occurs in an area with copy number 3, so presumably 2 intact LPIN1 copies are still present. LPIN1 plays important roles in controlling the metabolism of fatty acids at differents levels. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis in the reticulum endoplasmic membrane. tandem-duplication Tandem duplication with left breakpoint in the first intron of HMCN1 and right breakpoint not in a gene. Copy number from 4 to 5.tandem-duplication No annotated elements involved.tandem-duplication Tandem duplication with left breakpoint in PPP2R5A and right breakpoint in BATF3. Genes are on opposite strands, so no fucntyional fusion gene is created. Copy number from 4 to 5 inside duplication.tandem-duplication Small tandem duplication inside intron 1 of KIF26B. Not clear whether splicing is affected. Copy number probably from 2 to 3, so it's happening in 1 of two copies. KIF26B, essential for embryonic kidney development. Plays an important role in the compact adhesion between mesenchymal cells adjacent to the ureteric buds, possibly by interacting with MYH10. probable-inversion No annotated elements involved.tandem-duplication No annotated elements involved.interchromosomal See Flp, 4461tandem-duplication Tandem duplication overlapping with exons and introns 1 and 2 and part of promotor region of NCKAP5. It's possible that a truncated NCKAP5 is produced. Protein is poorly characterized, only known that it interacts with SH3 containing domain of adapter protein Nck.deletion LRP1B One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.complex 4900 LRP1B One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.complex 4903 LRP1B One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.deletion LRP1B One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.distal-duplication 2032 Together with 2032 a distal duplication, happening inside intron 11 of ARHGAP15, GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction.distal-duplication 4896 Together with 4896 a distal duplication, happening inside intron 11 of ARHGAP15, GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction.tandem-duplication No annotated elements involved.deletion No annotated elements involved.deletion Partial deletion (2 of 3 copies) of exon 3 and parts of flanking introns of ERBB4, which specifically binds and is activated by neuregulins, including NRG2 and NRG3, HBEGF, BTC and NTAK. Interaction with these factors induces cell differentiation. Plays a role in the regulation of cell growth and cell proliferation. Not activated by EGF, TGF-A, and AREGAREGB. The C-terminal fragment (CTF) of isoform JMA-A CYT-2 (containing E4ICD2) can stimulate transcription in the presence of YAP1. Conflicting reports are likely due at least in part to the opposing effects of the isoform-specific and nuclear-translocated ERBB4 intracellular domains (E4ICD1 and E4ICD2). Overexpression studies in epithelium show growth inhibition using E4ICD1 and increased proliferation using E4ICD2. E4ICD2 has greater in vitro kinase activity than E4ICD1. The kinase activity is required for the nuclear translocation of E4ICD2.deletion Partial deletion (1 of 3 copies) inintron1 of ERBB4, which specifically binds and is activated by neuregulins, including NRG2 and NRG3, HBEGF, BTC and NTAK. Interaction with these factors induces cell differentiation. Plays a role in the regulation of cell growth and cell proliferation. Not activated by EGF, TGF-A, and AREGAREGB. The C-terminal fragment (CTF) of isoform JMA-A CYT-2 (containing E4ICD2) can stimulate transcription in the presence of YAP1. Conflicting reports are likely due at least in part to the opposing effects of the isoform-specific and nuclear-translocated ERBB4 intracellular domains (E4ICD1 and E4ICD2). Overexpression studies in epithelium show growth inhibition using E4ICD1 and increased proliferation using E4ICD2. E4ICD2 has greater in vitro kinase activity than E4ICD1. The kinase activity is required for the nuclear translocation of E4ICD2.tandem-duplication No annotated elements involved.deletion Deletion with left breakpoint in CNTN4 and right breakpoint in intergenic region. No fusion genes are formed, the copy number probably goes from 4 to 3, so CNTN4 has 3 intact copies left. CNTN4 or contactin 4 mediates cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity.probable-inversion Inversion with left breakpoint in intergenic region and right breakpoint in LRRFIP2 gene. It largely overlaps with inversion 6101 so that the overlapping part is actually not inversed. LRRFIP2 may function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.probable-inversion No annotated elements involved. Inversion with left and right breakpoint in intergenic region.probable-inversion No annotated elements involved.tandem-duplication No annotated elements involved.deletion One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2. tandem-duplication One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2. deletion One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2. deletion No annotated elements involved.deletion small deletion in intron 2 of ROBO2, receptor for SLIT2, and probably SLIT1, which are thought to act as molecular guidance cue in cellular migration, including axonal navigation at the ventral midline of the neural tube and projection of axons to different regions during neuronal development. 4 copies in this region and it seems only 1 affected, since only a small drop in CNV is observed.tandem-duplication No annotated elements involved.deletion Small deletion in intron 1 of CADM2, Cell adhesion molecule 2. Not many details known about protein. 4 copies in this region and it seems only 1 affected, since only a small drop in CNV is observed. deletion Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.complex 851;4346;6088 Interchromosomal translocation to chr16 coupled to complex events just upstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.complex 568;851;4346 Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.complex 568;4346;6088 Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.complex 568;851;6088 Interchromosomal translocation to chr16 coupled to complex events just downstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.complex 4703;6087 One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.complex 850;4703 One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.complex 850;6087 One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.

deletion Deletion of 1 of 3 copies of the LOC285194 gene, unknown in uniprot.deletion No annotated elements involved.deletion No annotated elements involved.tandem-duplication Tandem duplication with left breakpoint in intron 2 of PLS1 and right breakpoint in intergenic region. No fusion gene formed, and no truncated PLS1 either, because the break occurs before the first coding exon.tandem-duplication Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels. interchromosomal Interchromosomal translocation with breakpoint on chr3 in intron 2 of IGF2BP2 and breakpoint on chr12 in intergenic region. No fusion genes formed. 3 copies of IGF2BP2 present, so probably 2 intact. IGF2BP2 is Insulin-like growth factor 2 mRNA-binding protein 2. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs. probable-inversion Small inversion in intron 4 of ZNF718. Not clear what impact would be on splicing. ZNF718, Zinc finger transcription factor with unknown function.deletion No annotated elements involved.tandem-duplication Large tandem duplication with left breakpoint in LIMCH1 gene and right breakpoint in intergenic region. In this way, no fusion genes or truncated genes are formed (only C-terminal part of LIMCH1). LIMCH1, function unknown.probable-inversion No annotated elements involved. Both breakpoints in intergenic region.tandem-duplication Left breakpoint in intergenic region, right breakpoint in only intron of KCTD8. No fusion genes or functional truncated genes are created (only C-terminal part of KCTD8). KCTD8: Auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. Increases agonist potency and markedly alter the G-protein signaling of the receptors by accelerating onset and promoting desensitizationinterchromosomal No annotated elements involved. Breakoints on both chr4 and 5 in intergenic region.tandem-duplication Tandem duplication with right breakoint in PTPN13 and left breakpoint in intergenic region. No fusion genes or functional truncated genes are created. (C-terminal part of PTPN13. Copy number from 3 to 5, so probably 2 tandem repeats? PTPN13 is a tyrosine phosphatase which regulates negatively FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling.deletion Small deletion inside intron 8 of FAM190A. Not clear whether splicing is affected. FAM190A is an uncharacterized protein.complex 1279;5139;5156;5302 Interchromosomal translocation with breakpoint on chr4 in intron 1 of DKK2. No change in copy number observed here. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. DKK2 antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease. TTC28: function unknown. deletion Deletion of 1 or 2 copies of exons 16 and 17 and most of flanking introns of the KIAA1109 gene. Altered proteins missing exons 16 and 17 and probably undergoing splicing difficulties could be created. At least one intact copy left. KIAA1109 is an uncharacterized protein.interchromosomal Interchromosomal translocation with breakpoint on chr4 in intergenic region and breakpoint on chr6 in 2nd exon of NR_037178, an uncharacterized non coding RNA gene.tandem-duplication No annotated elements involved.tandem-duplication No annotated elements involved.interchromosomal No annotated elements involved.interchromosomal Interchromosomal translocation with breakpoint on chr 4 in intergenic region and on chr18 in intron 1 of ROCK1P1. No fusion genes created. ROCK1P1 is a pseudogene.complex 530;5139;5156;5302 Interchromosomal translocation with breakpoint on chr5 in intergenic region and breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown.tandem-duplication Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.deletion Deletion partially overlapping with NR_036530, it's a hypothetical gene.deletion No annotated elements involved.deletion No annotated elements involved.deletion No annotated elements involved.interchromosomal Interchromosomal translocation with deletion No annotated elements involved.deletion No annotated elements involved.tandem-duplication Tandem duplication partially overlapping with the C-terminal end of SUPT3H. It's a poorly characerized protein, probable transcriptional activator. complex 514 Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part is probably a deletion, eliminating 1 of 3 copies and spanning ZNF415 and BAG2, thus creating a fusion gene. If splicing occurs correctly, the open reading frame would switch and terminate after 1 extra amino acid, in effect creating a truncated ZNF415. ZNF415: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.complex 4083 Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part spans BAG2 and RAB23. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.RAB23, not well characterized, known to be involved in Carpenter syndrome.probable-inversion Probable inversion with left breakpoint in intergenic region and right breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.probable-inversion No annotated elements involved.probable-inversion Probable inversion with right breakpoint in intergenic region and left breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.probable-inversion Probable inversion inside intron 2 of SASH1 affecting 1 of 2 copies, not clear whether splicing is affected. SASH2: May have a role in a signaling pathway. Could act as a tumor suppressor, is often downregulated in breast cancer.tandem-duplication Small tandem duplication, one extra repeat probably. This duplication comprises exons 121-126 of SYNE1, a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Component of SUN-protein-containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer nuclear membrane attachment sites for cytoskeletal filaments. Involved in the maintenance of nuclear organization and structural integrity. Connects nuclei to the cytoskeleton by interacting with the nuclear envelope and with F-actin in the cytoplasm. Required for centrosome migration to the apical cell surface during early ciliogenesis. deletion Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.deletion Small deletion of 1/5 copies in intron 1 of PARK2. Not clear whether splicing is affected. PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.probable-inversion No annotated elements involved.interchromosomal Interchromosomal translocation with chr6 breakpoint in intergenic region and chr13 breakpoint in MIR4500HG, causing a change in copy number from 6 to 7. No details are known about this MIR.probable-inversion Inversion with right breakpoint in intergenic region and right breakpoint in intron 28/29 of MLLT4. No fusion genes are created. MLLT4: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. A chromosomal aberration involving MLLT4 is associated with acute leukemias. Translocation t(6;11)(q27;q23) with MLL/HRX. The result is a rogue activator protein. No such aberration in HEK cells.deletion Small deletion in intron 1 of ADAP1, GTPase-activating protein for the ADP ribosylation factor family Probable. Binds phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Not clear how many copies hit, since it's not observed in the CNV track (too short compared to 2kb binning size).deletion No annotated elements involved.complex 530;1279;5139;5156 Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.tandem-duplication Small tandem duplication insinde intron 10 of EXOC4. Copy number change cannot be observed from CNV track, it's in a triploid region. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membraneinterchromosomal Interchromosomal translocation with chr7 breakpoint in LRGUK and chr18 breakpoint in intergenic region. LRGUK is an poorly characterized protein.deletion Deletion comprising almost complete BRAF gene, copy number goes from 4 or 5 to 3. BRAF is a proto-oncogene, involved in the transduction of mitogenic signals from the cell membrane to the nucleus.

deletion No annotated elements involved.deletion No annotated elements involved.deletion No annotated elements involved.deletion See Flp, 2915 Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised. complex 3818 No annotated elements involved.complex 465 No annotated elements involved.interchromosomal Interchromosomal translocation with chr8 breakpoint in intergenic region and chrX breakpoint in intergenic region as well.deletion Deletion comprising WDYHV1 and most part of ATAD2. WDYHV1: Mediates the side-chain deamidation of N-terminal glutamine residues to glutamate, an important step in N-end rule pathway of protein degradation. Conversion of the resulting N-terminal glutamine to glutamate renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. Does not act on substrates with internal or C-terminal glutamine and does not act on non-glutamine residues in any position. Does not deaminate acetylated N-terminal glutamine. With the exception of proline, all tested second-position residues on substrate peptides do not greatly influence the activity. In contrast, a proline at position 2, virtually abolishes deamidation of N-terminal glutamine. ATAD2: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. Up-regulated in breast, uterus, colon, ovary, and stomach tumors. Induced in breast cancer cells overexpressing NCOA3 or treated with estrogen. Down-regulated in 5-fluorouracil-resistant derivatives of the colon cancer cell line HCT116. probable-inversion No annotated elements involved.deletion Small deletion in intron 1 of LINGO2. From 3 to 2 copies. LINGO2 is poorly characterized.probable-inversion No annotated elements involved.interchromosomal No annotated elements involved.deletion Deletion spanning FAM125B and LMX1B creating a fusion gene with aa 1-252 of FAM125B and 19 extra aa's before a termination codon causes premature termination. In effect a sort of truncated FAM125B is created. It concerns 1 of 3 or 4 copies.deletion Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.deletion No annotated elements involved.deletion Deletion of 1 of 3 copies of a part of the PRKG1 gene, creating a shorter form of it lacking exons 3 and 4. PRKG1 is a cGMP-dependent protein kinase 1, Phosphorylates PPP1R17 leading to its activation, Phosphorylates PPP1R12A. Further downstream, the copy number rises to 5.deletion No annotated elements involved.deletion No annotated elements involved.deletion Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. tandem-duplication No annotated elements involved.deletion Small deletion inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses deletion No annotated elements involved.deletion Tandem duplication partially overlapping with MGST1, possibly creating a truncated MGST1, but it concerns only 5' UTR exons, so no problem. No fusion genes created. MGST1; microsomal Glutathion-S-transferase. Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Has a wide substrate specificity.tandem-duplication No annotated elements involved.tandem-duplication No annotated elements involved.complex 530;1279;5139;5302 Interchromosomal translocation with breakpoint on chr12 in intron 3 of ANO4. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. ANO4: putative calcium activated chloride channel.tandem-duplication Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl esterdeletion Deletion comprising promotor region and exon 1 and 2 of SPATA13. Only one functional copy left. SPAT13 acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression. deletion Deletion (1 of 2 copies?) of exon 25 and small parts of flanking introns of ATP8A2. Probable phospholipid-transporting ATPase IB. It seems to be a tumor suppressor gene. PMID:10551800deletion See Flp, 2530probable-inversion No annotated elements involved.interchromosomal No annotated elements involved. Interchromosomal translocation with both breakpoints in intergenic region.interchromosomal No annotated elements involved. Interchromosomal translocation with both breakpoints in intergenic region.deletion Small deletion inside intron 1 of KLF12. KLF12 confers strong transcriptional repression to the AP-2-alpha gene (transcription factor). Binds to a regulatory element (A32) in the AP-2-alpha gene promoter. deletion Deletion of 1 of 6 copies of the last exon and big part of last intron of GPC5: cell surface proteoglycan that bears heparan sulfate.complex 369 Deletion of 1 of 6 copies of a part of intron 1 of GPC6, cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases.complex 3208 Not clear what this rearrangement does, but completely overlapping with the 3' end of rearrangement 369. GPC6: Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteasesdeletion Deletion of 1 of 6 copies of the exon 3 and 4 and parts of flanking introns of GPC6: cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteasesprobable-inversion No annotated elements involved.deletion No annotated elements involved.deletion Deletion 3 to 2 copies. Deletion spans EIF2S1 and PLEK2 genes, but since they are on the opposite strand, no fusion gene is created. 2 intact copies of each still present. EIF2S1: Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B. PLEK2: May help orchestrate cytoskeletal arrangement. Contribute to lamellipodia formation.tandem-duplication No annotated elements involved.deletion Deletion comprising SNORD116-21. Homo sapiens small nucleolar RNA, C/D box 116-21 (SNORD116-21), small nucleolar RNA. Not clear how many copies deleted.deletion Deletion with breakpoints in intergenic region. Still 3 copies left. tandem-duplication Tandem duplication comprising exon 11/12/13 (depending on splice form) of NFAT5. Not clear how many copies affected. NFAT5 plays a role in the inducible expression of genes. Regulates hypertonicity-induced cellular accumulation of osmolytes.complex 530;1279;5156;5302 Interchromosomal translocation with chr17 breakpoint in intron 4 of TEKT3 gene. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. TEKT3 is a structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. Required for progressive sperm mobilityprobable-inversion Inversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.deletion Deletion of 1 of 2 copies of the last 4 exons of NSRP1: RNA-binding protein that mediates pre-mRNA alternative splicing regulation.interchromosomal Interchromosomal translocation with chr17 breakpoint in intron 2 of KRT38 and breakpoint on chr22 in intron 2 of RBX1 gene. Fusion gene is not created, it has both genes on the opposite strand. One extra copy on each chromosome due to translocation. At least 2 or 3 intact copies left on each. RBX1: E3 ubiquitin ligase component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription-coupled nucleotide excision repair. The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M. KRT38: Keratin, type I cuticular Ha8deletion No annotated elements involved.

tandem-duplication Duplication with right breakpoint in intergenic region and left breakpoint in COIL, possibly creating a truncated coil protein. It concerns one copy only probably that has a duplication. COIL: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.deletion Small deletion in intron 1 of COIL: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.tandem-duplication No annotated elements involved.tandem-duplication No annotated elements involved.deletion Deletion in one of 5 copies, fusing MARCH2 with HNRNPM. A fusion gene would be created with out of frame splicing causing a truncated MARCH2 with extra 3 amino acids. MARCH1: E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, downregulates their cell surface localization thus sequestering them in the intracellular endosomal system. HNRNPM: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.probable-inversion Breakpoints of inversion are in EPS15L1 and MED26. Inversion not creating functional fusion genes, because genes are fused in antisense fashion. This means that for both these genes, probably two intact copies are left. MED26: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. EPS15L1: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis.tandem-duplication Tandem duplication with both breakpoints in intergenic region. Copy number from 3 to 4. Some genes inside with thus 4 copies instead of 3.deletion Deletion of 1 copy of exon 1/2/3 (depending on splice form) and a large part of upstream intron of PLCB4. Thus affected proteins all miss the aa's encoded by the first coding exon (and thus also the ATG start codon). If the first start codon available is used, proteins consisting of only 6 amino acids would be produced. PLCB4: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-4, The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.deletion One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. deletion One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.deletion One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.deletion One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.deletion One of a series of deletions in MACROD2, this one affecting intron 6. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.deletion One of a series of deletions in MACROD2, this one affecting exons 9-12 or 2-4 (depending on splice form). No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.deletion No annotated elements involved.deletion No annotated elements involved.deletion No annotated elements involved.deletion Deletion of 2 of 3 copies overlapping with first 3 exons and promotor region of HDHD1. Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. Only one intact copy left.deletion Deletion of 1 of 2 copies of a part of the STS gene involving exons 6-8. STS: Conversion of sulfated steroid precursors to estrogens during pregnancy.complex 36 No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…complex 5131 No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…tandem-duplication Duplication with first breakpoint in FTX, comprising first 3 exons and right breakpoint in intergenic regions. 3 MIR genes with unknown functions and ZCCHC13 (uncharacterized protein) are inside. FTX: XIST regulatordeletion Deletion of 1 of 4 copies of a large part of the last intron or last intron and exon, (depending on the splice form) of DIAPH2. Could be involved in oogenesis. Involved in the regulation of endosome dynamics. Implicated in a novel signal transduction pathway, in which a specific isoform and CSK are sequentially activated by RHOD to regulate the motility of early endosomes through interactions with the actin cytoskeleton. deletion No annotated elements involved.deletion No annotated elements involved.

Interchromosomal translocation with breakpoint on chr11 inside intron 6/7 of CDK11B and breakpoint on chr2 in intron 6 of SNTG2. The break is strand consistent, but genes are on opposite strands, so no functional fusion gene is formed. Genes are in a region of 3 copies on each chromosome. CDK11B is cyclin dependent kinase 11b, and appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. SNTG2 is gamma-2-syntrophin, a putative adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.Very large probable inversion with left breakpoint in intergenic region and right breakpoint in intron 3 of C1orf83, an uncharacterized protein.No annotated elements involved. Large inversion with both breakpoints in intergenic regionSmall inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.A deletion partially overlapping with the first exon and intron of DHCR24. It's occuring in a pentaploid region and not clear how many affected copies. No drop in CNV is observed. DHCR24: Catalyzes the reduction of the delta-24 double bond of sterol intermediates. Protects cells from oxidative stress by reducing caspase 3 activity during apoptosis induced by oxidative stress. Also protects against amyloid-beta peptide-induced apoptosisInterchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.Tandem duplication with left breakpoint in CLCA3P and right breakpoint in intergenic region. No fusion genes ar formed, a truncated version of CLCA3P is not formed either, since it's onlythe C-terminal part that's duplicated (exons 14 and 15). CLCA3P is a calcium activated chloride channel regulator, very few details on protein are known.Interchromosomal translocation with breakpoint on chr1 in intergenic region close to centromere. Breakpoint on chr2 is in intron 11 of LPIN1 and occurs in an area with copy number 3, so presumably 2 intact LPIN1 copies are still present. LPIN1 plays important roles in controlling the metabolism of fatty acids at differents levels. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis in the reticulum endoplasmic membrane. Tandem duplication with left breakpoint in the first intron of HMCN1 and right breakpoint not in a gene. Copy number from 4 to 5.

Tandem duplication with left breakpoint in PPP2R5A and right breakpoint in BATF3. Genes are on opposite strands, so no fucntyional fusion gene is created. Copy number from 4 to 5 inside duplication.Small tandem duplication inside intron 1 of KIF26B. Not clear whether splicing is affected. Copy number probably from 2 to 3, so it's happening in 1 of two copies. KIF26B, essential for embryonic kidney development. Plays an important role in the compact adhesion between mesenchymal cells adjacent to the ureteric buds, possibly by interacting with MYH10.

Tandem duplication overlapping with exons and introns 1 and 2 and part of promotor region of NCKAP5. It's possible that a truncated NCKAP5 is produced. Protein is poorly characterized, only known that it interacts with SH3 containing domain of adapter protein Nck.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.Together with 2032 a distal duplication, happening inside intron 11 of ARHGAP15, GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction.Together with 4896 a distal duplication, happening inside intron 11 of ARHGAP15, GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction.

Partial deletion (2 of 3 copies) of exon 3 and parts of flanking introns of ERBB4, which specifically binds and is activated by neuregulins, including NRG2 and NRG3, HBEGF, BTC and NTAK. Interaction with these factors induces cell differentiation. Plays a role in the regulation of cell growth and cell proliferation. Not activated by EGF, TGF-A, and AREGAREGB. The C-terminal fragment (CTF) of isoform JMA-A CYT-2 (containing E4ICD2) can stimulate transcription in the presence of YAP1. Conflicting reports are likely due at least in part to the opposing effects of the isoform-specific and nuclear-translocated ERBB4 intracellular domains (E4ICD1 and E4ICD2). Overexpression studies in epithelium show growth inhibition using E4ICD1 and increased proliferation using E4ICD2. E4ICD2 has greater in vitro kinase activity than E4ICD1. The kinase activity is required for the nuclear translocation of E4ICD2.Partial deletion (1 of 3 copies) inintron1 of ERBB4, which specifically binds and is activated by neuregulins, including NRG2 and NRG3, HBEGF, BTC and NTAK. Interaction with these factors induces cell differentiation. Plays a role in the regulation of cell growth and cell proliferation. Not activated by EGF, TGF-A, and AREGAREGB. The C-terminal fragment (CTF) of isoform JMA-A CYT-2 (containing E4ICD2) can stimulate transcription in the presence of YAP1. Conflicting reports are likely due at least in part to the opposing effects of the isoform-specific and nuclear-translocated ERBB4 intracellular domains (E4ICD1 and E4ICD2). Overexpression studies in epithelium show growth inhibition using E4ICD1 and increased proliferation using E4ICD2. E4ICD2 has greater in vitro kinase activity than E4ICD1. The kinase activity is required for the nuclear translocation of E4ICD2.

Deletion with left breakpoint in CNTN4 and right breakpoint in intergenic region. No fusion genes are formed, the copy number probably goes from 4 to 3, so CNTN4 has 3 intact copies left. CNTN4 or contactin 4 mediates cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity.Inversion with left breakpoint in intergenic region and right breakpoint in LRRFIP2 gene. It largely overlaps with inversion 6101 so that the overlapping part is actually not inversed. LRRFIP2 may function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.No annotated elements involved. Inversion with left and right breakpoint in intergenic region.

One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2. One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2. One of several events happening in FHIT, it concerns a deletion, a tandem duplication in that deletion and an upstream deletion. It's possible that 2 intact copies remain, but no more than that. FHIT: Bis(5'-adenosyl)-triphosphatase, Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues, numerous tumor types are found to have aberrant forms of FHIT protein due to deletions in a coding region of chromosome 3p14.2.

small deletion in intron 2 of ROBO2, receptor for SLIT2, and probably SLIT1, which are thought to act as molecular guidance cue in cellular migration, including axonal navigation at the ventral midline of the neural tube and projection of axons to different regions during neuronal development. 4 copies in this region and it seems only 1 affected, since only a small drop in CNV is observed.

Small deletion in intron 1 of CADM2, Cell adhesion molecule 2. Not many details known about protein. 4 copies in this region and it seems only 1 affected, since only a small drop in CNV is observed. Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.Interchromosomal translocation to chr16 coupled to complex events just upstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Interchromosomal translocation to chr16 coupled to complex events just downstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.

Deletion of 1 of 3 copies of the LOC285194 gene, unknown in uniprot.

Tandem duplication with left breakpoint in intron 2 of PLS1 and right breakpoint in intergenic region. No fusion gene formed, and no truncated PLS1 either, because the break occurs before the first coding exon.Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels. Interchromosomal translocation with breakpoint on chr3 in intron 2 of IGF2BP2 and breakpoint on chr12 in intergenic region. No fusion genes formed. 3 copies of IGF2BP2 present, so probably 2 intact. IGF2BP2 is Insulin-like growth factor 2 mRNA-binding protein 2. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs. Small inversion in intron 4 of ZNF718. Not clear what impact would be on splicing. ZNF718, Zinc finger transcription factor with unknown function.

Large tandem duplication with left breakpoint in LIMCH1 gene and right breakpoint in intergenic region. In this way, no fusion genes or truncated genes are formed (only C-terminal part of LIMCH1). LIMCH1, function unknown.No annotated elements involved. Both breakpoints in intergenic region.Left breakpoint in intergenic region, right breakpoint in only intron of KCTD8. No fusion genes or functional truncated genes are created (only C-terminal part of KCTD8). KCTD8: Auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. Increases agonist potency and markedly alter the G-protein signaling of the receptors by accelerating onset and promoting desensitizationNo annotated elements involved. Breakoints on both chr4 and 5 in intergenic region.Tandem duplication with right breakoint in PTPN13 and left breakpoint in intergenic region. No fusion genes or functional truncated genes are created. (C-terminal part of PTPN13. Copy number from 3 to 5, so probably 2 tandem repeats? PTPN13 is a tyrosine phosphatase which regulates negatively FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling.Small deletion inside intron 8 of FAM190A. Not clear whether splicing is affected. FAM190A is an uncharacterized protein.Interchromosomal translocation with breakpoint on chr4 in intron 1 of DKK2. No change in copy number observed here. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. DKK2 antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease. TTC28: function unknown. Deletion of 1 or 2 copies of exons 16 and 17 and most of flanking introns of the KIAA1109 gene. Altered proteins missing exons 16 and 17 and probably undergoing splicing difficulties could be created. At least one intact copy left. KIAA1109 is an uncharacterized protein.Interchromosomal translocation with breakpoint on chr4 in intergenic region and breakpoint on chr6 in 2nd exon of NR_037178, an uncharacterized non coding RNA gene.

Interchromosomal translocation with breakpoint on chr 4 in intergenic region and on chr18 in intron 1 of ROCK1P1. No fusion genes created. ROCK1P1 is a pseudogene.Interchromosomal translocation with breakpoint on chr5 in intergenic region and breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown.Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.Deletion partially overlapping with NR_036530, it's a hypothetical gene.

tion

Tandem duplication partially overlapping with the C-terminal end of SUPT3H. It's a poorly characerized protein, probable transcriptional activator. Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part is probably a deletion, eliminating 1 of 3 copies and spanning ZNF415 and BAG2, thus creating a fusion gene. If splicing occurs correctly, the open reading frame would switch and terminate after 1 extra amino acid, in effect creating a truncated ZNF415. ZNF415: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part spans BAG2 and RAB23. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.RAB23, not well characterized, known to be involved in Carpenter syndrome.Probable inversion with left breakpoint in intergenic region and right breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.

Probable inversion with right breakpoint in intergenic region and left breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.Probable inversion inside intron 2 of SASH1 affecting 1 of 2 copies, not clear whether splicing is affected. SASH2: May have a role in a signaling pathway. Could act as a tumor suppressor, is often downregulated in breast cancer.Small tandem duplication, one extra repeat probably. This duplication comprises exons 121-126 of SYNE1, a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Component of SUN-protein-containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer nuclear membrane attachment sites for cytoskeletal filaments. Involved in the maintenance of nuclear organization and structural integrity. Connects nuclei to the cytoskeleton by interacting with the nuclear envelope and with F-actin in the cytoplasm. Required for centrosome migration to the apical cell surface during early ciliogenesis. Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.Small deletion of 1/5 copies in intron 1 of PARK2. Not clear whether splicing is affected. PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

Interchromosomal translocation with chr6 breakpoint in intergenic region and chr13 breakpoint in MIR4500HG, causing a change in copy number from 6 to 7. No details are known about this MIR.Inversion with right breakpoint in intergenic region and right breakpoint in intron 28/29 of MLLT4. No fusion genes are created. MLLT4: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. A chromosomal aberration involving MLLT4 is associated with acute leukemias. Translocation t(6;11)(q27;q23) with MLL/HRX. The result is a rogue activator protein. No such aberration in HEK cells.Small deletion in intron 1 of ADAP1, GTPase-activating protein for the ADP ribosylation factor family Probable. Binds phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Not clear how many copies hit, since it's not observed in the CNV track (too short compared to 2kb binning size).

Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.Small tandem duplication insinde intron 10 of EXOC4. Copy number change cannot be observed from CNV track, it's in a triploid region. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membraneInterchromosomal translocation with chr7 breakpoint in LRGUK and chr18 breakpoint in intergenic region. LRGUK is an poorly characterized protein.Deletion comprising almost complete BRAF gene, copy number goes from 4 or 5 to 3. BRAF is a proto-oncogene, involved in the transduction of mitogenic signals from the cell membrane to the nucleus.

Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised.

Interchromosomal translocation with chr8 breakpoint in intergenic region and chrX breakpoint in intergenic region as well.Deletion comprising WDYHV1 and most part of ATAD2. WDYHV1: Mediates the side-chain deamidation of N-terminal glutamine residues to glutamate, an important step in N-end rule pathway of protein degradation. Conversion of the resulting N-terminal glutamine to glutamate renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. Does not act on substrates with internal or C-terminal glutamine and does not act on non-glutamine residues in any position. Does not deaminate acetylated N-terminal glutamine. With the exception of proline, all tested second-position residues on substrate peptides do not greatly influence the activity. In contrast, a proline at position 2, virtually abolishes deamidation of N-terminal glutamine. ATAD2: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. Up-regulated in breast, uterus, colon, ovary, and stomach tumors. Induced in breast cancer cells overexpressing NCOA3 or treated with estrogen. Down-regulated in 5-fluorouracil-resistant derivatives of the colon cancer cell line HCT116.

Small deletion in intron 1 of LINGO2. From 3 to 2 copies. LINGO2 is poorly characterized.

Deletion spanning FAM125B and LMX1B creating a fusion gene with aa 1-252 of FAM125B and 19 extra aa's before a termination codon causes premature termination. In effect a sort of truncated FAM125B is created. It concerns 1 of 3 or 4 copies.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.

Deletion of 1 of 3 copies of a part of the PRKG1 gene, creating a shorter form of it lacking exons 3 and 4. PRKG1 is a cGMP-dependent protein kinase 1, Phosphorylates PPP1R17 leading to its activation, Phosphorylates PPP1R12A. Further downstream, the copy number rises to 5.

Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs.

Small deletion inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses

Tandem duplication partially overlapping with MGST1, possibly creating a truncated MGST1, but it concerns only 5' UTR exons, so no problem. No fusion genes created. MGST1; microsomal Glutathion-S-transferase. Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Has a wide substrate specificity.

Interchromosomal translocation with breakpoint on chr12 in intron 3 of ANO4. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. ANO4: putative calcium activated chloride channel.Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl esterDeletion comprising promotor region and exon 1 and 2 of SPATA13. Only one functional copy left. SPAT13 acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression. Deletion (1 of 2 copies?) of exon 25 and small parts of flanking introns of ATP8A2. Probable phospholipid-transporting ATPase IB. It seems to be a tumor suppressor gene. PMID:10551800

No annotated elements involved. Interchromosomal translocation with both breakpoints in intergenic region.No annotated elements involved. Interchromosomal translocation with both breakpoints in intergenic region.Small deletion inside intron 1 of KLF12. KLF12 confers strong transcriptional repression to the AP-2-alpha gene (transcription factor). Binds to a regulatory element (A32) in the AP-2-alpha gene promoter. Deletion of 1 of 6 copies of the last exon and big part of last intron of GPC5: cell surface proteoglycan that bears heparan sulfate.Deletion of 1 of 6 copies of a part of intron 1 of GPC6, cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases.Not clear what this rearrangement does, but completely overlapping with the 3' end of rearrangement 369. GPC6: Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteasesDeletion of 1 of 6 copies of the exon 3 and 4 and parts of flanking introns of GPC6: cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases

Deletion 3 to 2 copies. Deletion spans EIF2S1 and PLEK2 genes, but since they are on the opposite strand, no fusion gene is created. 2 intact copies of each still present. EIF2S1: Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B. PLEK2: May help orchestrate cytoskeletal arrangement. Contribute to lamellipodia formation.

Deletion comprising SNORD116-21. Homo sapiens small nucleolar RNA, C/D box 116-21 (SNORD116-21), small nucleolar RNA. Not clear how many copies deleted.Deletion with breakpoints in intergenic region. Still 3 copies left. Tandem duplication comprising exon 11/12/13 (depending on splice form) of NFAT5. Not clear how many copies affected. NFAT5 plays a role in the inducible expression of genes. Regulates hypertonicity-induced cellular accumulation of osmolytes.Interchromosomal translocation with chr17 breakpoint in intron 4 of TEKT3 gene. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. TEKT3 is a structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. Required for progressive sperm mobilityInversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.Deletion of 1 of 2 copies of the last 4 exons of NSRP1: RNA-binding protein that mediates pre-mRNA alternative splicing regulation.Interchromosomal translocation with chr17 breakpoint in intron 2 of KRT38 and breakpoint on chr22 in intron 2 of RBX1 gene. Fusion gene is not created, it has both genes on the opposite strand. One extra copy on each chromosome due to translocation. At least 2 or 3 intact copies left on each. RBX1: E3 ubiquitin ligase component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription-coupled nucleotide excision repair. The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M. KRT38: Keratin, type I cuticular Ha8

Duplication with right breakpoint in intergenic region and left breakpoint in COIL, possibly creating a truncated coil protein. It concerns one copy only probably that has a duplication. COIL: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.Small deletion in intron 1 of COIL: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.

Deletion in one of 5 copies, fusing MARCH2 with HNRNPM. A fusion gene would be created with out of frame splicing causing a truncated MARCH2 with extra 3 amino acids. MARCH1: E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, downregulates their cell surface localization thus sequestering them in the intracellular endosomal system. HNRNPM: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.Breakpoints of inversion are in EPS15L1 and MED26. Inversion not creating functional fusion genes, because genes are fused in antisense fashion. This means that for both these genes, probably two intact copies are left. MED26: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. EPS15L1: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis.Tandem duplication with both breakpoints in intergenic region. Copy number from 3 to 4. Some genes inside with thus 4 copies instead of 3.Deletion of 1 copy of exon 1/2/3 (depending on splice form) and a large part of upstream intron of PLCB4. Thus affected proteins all miss the aa's encoded by the first coding exon (and thus also the ATG start codon). If the first start codon available is used, proteins consisting of only 6 amino acids would be produced. PLCB4: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-4, The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting intron 6. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting exons 9-12 or 2-4 (depending on splice form). No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.

Deletion of 2 of 3 copies overlapping with first 3 exons and promotor region of HDHD1. Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. Only one intact copy left.Deletion of 1 of 2 copies of a part of the STS gene involving exons 6-8. STS: Conversion of sulfated steroid precursors to estrogens during pregnancy.No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…Duplication with first breakpoint in FTX, comprising first 3 exons and right breakpoint in intergenic regions. 3 MIR genes with unknown functions and ZCCHC13 (uncharacterized protein) are inside. FTX: XIST regulatorDeletion of 1 of 4 copies of a large part of the last intron or last intron and exon, (depending on the splice form) of DIAPH2. Could be involved in oogenesis. Involved in the regulation of endosome dynamics. Implicated in a novel signal transduction pathway, in which a specific isoform and CSK are sequentially activated by RHOD to regulate the motility of early endosomes through interactions with the actin cytoskeleton.

Interchromosomal translocation with breakpoint on chr11 inside intron 6/7 of CDK11B and breakpoint on chr2 in intron 6 of SNTG2. The break is strand consistent, but genes are on opposite strands, so no functional fusion gene is formed. Genes are in a region of 3 copies on each chromosome. CDK11B is cyclin dependent kinase 11b, and appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. SNTG2 is gamma-2-syntrophin, a putative adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.

Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.A deletion partially overlapping with the first exon and intron of DHCR24. It's occuring in a pentaploid region and not clear how many affected copies. No drop in CNV is observed. DHCR24: Catalyzes the reduction of the delta-24 double bond of sterol intermediates. Protects cells from oxidative stress by reducing caspase 3 activity during apoptosis induced by oxidative stress. Also protects against amyloid-beta peptide-induced apoptosisInterchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.Tandem duplication with left breakpoint in CLCA3P and right breakpoint in intergenic region. No fusion genes ar formed, a truncated version of CLCA3P is not formed either, since it's onlythe C-terminal part that's duplicated (exons 14 and 15). CLCA3P is a calcium activated chloride channel regulator, very few details on protein are known.Interchromosomal translocation with breakpoint on chr1 in intergenic region close to centromere. Breakpoint on chr2 is in intron 11 of LPIN1 and occurs in an area with copy number 3, so presumably 2 intact LPIN1 copies are still present. LPIN1 plays important roles in controlling the metabolism of fatty acids at differents levels. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis in the reticulum endoplasmic membrane.

Tandem duplication with left breakpoint in PPP2R5A and right breakpoint in BATF3. Genes are on opposite strands, so no fucntyional fusion gene is created. Copy number from 4 to 5 inside duplication.Small tandem duplication inside intron 1 of KIF26B. Not clear whether splicing is affected. Copy number probably from 2 to 3, so it's happening in 1 of two copies. KIF26B, essential for embryonic kidney development. Plays an important role in the compact adhesion between mesenchymal cells adjacent to the ureteric buds, possibly by interacting with MYH10.



Deletion with left breakpoint in CNTN4 and right breakpoint in intergenic region. No fusion genes are formed, the copy number probably goes from 4 to 3, so CNTN4 has 3 intact copies left. CNTN4 or contactin 4 mediates cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity.Inversion with left breakpoint in intergenic region and right breakpoint in LRRFIP2 gene. It largely overlaps with inversion 6101 so that the overlapping part is actually not inversed. LRRFIP2 may function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.



Small deletion in intron 1 of CADM2, Cell adhesion molecule 2. Not many details known about protein. 4 copies in this region and it seems only 1 affected, since only a small drop in CNV is observed. Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.Interchromosomal translocation to chr16 coupled to complex events just upstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Interchromosomal translocation to chr16 coupled to complex events just downstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.

Tandem duplication with left breakpoint in intron 2 of PLS1 and right breakpoint in intergenic region. No fusion gene formed, and no truncated PLS1 either, because the break occurs before the first coding exon.Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels. Interchromosomal translocation with breakpoint on chr3 in intron 2 of IGF2BP2 and breakpoint on chr12 in intergenic region. No fusion genes formed. 3 copies of IGF2BP2 present, so probably 2 intact. IGF2BP2 is Insulin-like growth factor 2 mRNA-binding protein 2. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs. Small inversion in intron 4 of ZNF718. Not clear what impact would be on splicing. ZNF718, Zinc finger transcription factor with unknown function.

Large tandem duplication with left breakpoint in LIMCH1 gene and right breakpoint in intergenic region. In this way, no fusion genes or truncated genes are formed (only C-terminal part of LIMCH1). LIMCH1, function unknown.

Left breakpoint in intergenic region, right breakpoint in only intron of KCTD8. No fusion genes or functional truncated genes are created (only C-terminal part of KCTD8). KCTD8: Auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. Increases agonist potency and markedly alter the G-protein signaling of the receptors by accelerating onset and promoting desensitization

Tandem duplication with right breakoint in PTPN13 and left breakpoint in intergenic region. No fusion genes or functional truncated genes are created. (C-terminal part of PTPN13. Copy number from 3 to 5, so probably 2 tandem repeats? PTPN13 is a tyrosine phosphatase which regulates negatively FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling.

Interchromosomal translocation with breakpoint on chr4 in intron 1 of DKK2. No change in copy number observed here. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. DKK2 antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease. TTC28: function unknown. Deletion of 1 or 2 copies of exons 16 and 17 and most of flanking introns of the KIAA1109 gene. Altered proteins missing exons 16 and 17 and probably undergoing splicing difficulties could be created. At least one intact copy left. KIAA1109 is an uncharacterized protein.Interchromosomal translocation with breakpoint on chr4 in intergenic region and breakpoint on chr6 in 2nd exon of NR_037178, an uncharacterized non coding RNA gene.

Interchromosomal translocation with breakpoint on chr 4 in intergenic region and on chr18 in intron 1 of ROCK1P1. No fusion genes created. ROCK1P1 is a pseudogene.Interchromosomal translocation with breakpoint on chr5 in intergenic region and breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown.Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.

Tandem duplication partially overlapping with the C-terminal end of SUPT3H. It's a poorly characerized protein, probable transcriptional activator. Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part is probably a deletion, eliminating 1 of 3 copies and spanning ZNF415 and BAG2, thus creating a fusion gene. If splicing occurs correctly, the open reading frame would switch and terminate after 1 extra amino acid, in effect creating a truncated ZNF415. ZNF415: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part spans BAG2 and RAB23. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.RAB23, not well characterized, known to be involved in Carpenter syndrome.Probable inversion with left breakpoint in intergenic region and right breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.

Probable inversion with right breakpoint in intergenic region and left breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.Probable inversion inside intron 2 of SASH1 affecting 1 of 2 copies, not clear whether splicing is affected. SASH2: May have a role in a signaling pathway. Could act as a tumor suppressor, is often downregulated in breast cancer.Small tandem duplication, one extra repeat probably. This duplication comprises exons 121-126 of SYNE1, a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Component of SUN-protein-containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer nuclear membrane attachment sites for cytoskeletal filaments. Involved in the maintenance of nuclear organization and structural integrity. Connects nuclei to the cytoskeleton by interacting with the nuclear envelope and with F-actin in the cytoplasm. Required for centrosome migration to the apical cell surface during early ciliogenesis. Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.Small deletion of 1/5 copies in intron 1 of PARK2. Not clear whether splicing is affected. PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

Interchromosomal translocation with chr6 breakpoint in intergenic region and chr13 breakpoint in MIR4500HG, causing a change in copy number from 6 to 7. No details are known about this MIR.Inversion with right breakpoint in intergenic region and right breakpoint in intron 28/29 of MLLT4. No fusion genes are created. MLLT4: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. A chromosomal aberration involving MLLT4 is associated with acute leukemias. Translocation t(6;11)(q27;q23) with MLL/HRX. The result is a rogue activator protein. No such aberration in HEK cells.Small deletion in intron 1 of ADAP1, GTPase-activating protein for the ADP ribosylation factor family Probable. Binds phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Not clear how many copies hit, since it's not observed in the CNV track (too short compared to 2kb binning size).

Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.Small tandem duplication insinde intron 10 of EXOC4. Copy number change cannot be observed from CNV track, it's in a triploid region. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membraneInterchromosomal translocation with chr7 breakpoint in LRGUK and chr18 breakpoint in intergenic region. LRGUK is an poorly characterized protein.Deletion comprising almost complete BRAF gene, copy number goes from 4 or 5 to 3. BRAF is a proto-oncogene, involved in the transduction of mitogenic signals from the cell membrane to the nucleus.

Deletion comprising WDYHV1 and most part of ATAD2. WDYHV1: Mediates the side-chain deamidation of N-terminal glutamine residues to glutamate, an important step in N-end rule pathway of protein degradation. Conversion of the resulting N-terminal glutamine to glutamate renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. Does not act on substrates with internal or C-terminal glutamine and does not act on non-glutamine residues in any position. Does not deaminate acetylated N-terminal glutamine. With the exception of proline, all tested second-position residues on substrate peptides do not greatly influence the activity. In contrast, a proline at position 2, virtually abolishes deamidation of N-terminal glutamine. ATAD2: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. Up-regulated in breast, uterus, colon, ovary, and stomach tumors. Induced in breast cancer cells overexpressing NCOA3 or treated with estrogen. Down-regulated in 5-fluorouracil-resistant derivatives of the colon cancer cell line HCT116.

Deletion spanning FAM125B and LMX1B creating a fusion gene with aa 1-252 of FAM125B and 19 extra aa's before a termination codon causes premature termination. In effect a sort of truncated FAM125B is created. It concerns 1 of 3 or 4 copies.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.


Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs.



Interchromosomal translocation with breakpoint on chr12 in intron 3 of ANO4. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. ANO4: putative calcium activated chloride channel.Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl esterDeletion comprising promotor region and exon 1 and 2 of SPATA13. Only one functional copy left. SPAT13 acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression. Deletion (1 of 2 copies?) of exon 25 and small parts of flanking introns of ATP8A2. Probable phospholipid-transporting ATPase IB. It seems to be a tumor suppressor gene. PMID:10551800

Small deletion inside intron 1 of KLF12. KLF12 confers strong transcriptional repression to the AP-2-alpha gene (transcription factor). Binds to a regulatory element (A32) in the AP-2-alpha gene promoter.

Deletion of 1 of 6 copies of a part of intron 1 of GPC6, cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases.Not clear what this rearrangement does, but completely overlapping with the 3' end of rearrangement 369. GPC6: Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteasesDeletion of 1 of 6 copies of the exon 3 and 4 and parts of flanking introns of GPC6: cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases


Deletion comprising SNORD116-21. Homo sapiens small nucleolar RNA, C/D box 116-21 (SNORD116-21), small nucleolar RNA. Not clear how many copies deleted.

Tandem duplication comprising exon 11/12/13 (depending on splice form) of NFAT5. Not clear how many copies affected. NFAT5 plays a role in the inducible expression of genes. Regulates hypertonicity-induced cellular accumulation of osmolytes.Interchromosomal translocation with chr17 breakpoint in intron 4 of TEKT3 gene. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. TEKT3 is a structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. Required for progressive sperm mobilityInversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.

Interchromosomal translocation with chr17 breakpoint in intron 2 of KRT38 and breakpoint on chr22 in intron 2 of RBX1 gene. Fusion gene is not created, it has both genes on the opposite strand. One extra copy on each chromosome due to translocation. At least 2 or 3 intact copies left on each. RBX1: E3 ubiquitin ligase component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription-coupled nucleotide excision repair. The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M. KRT38: Keratin, type I cuticular Ha8


Deletion in one of 5 copies, fusing MARCH2 with HNRNPM. A fusion gene would be created with out of frame splicing causing a truncated MARCH2 with extra 3 amino acids. MARCH1: E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, downregulates their cell surface localization thus sequestering them in the intracellular endosomal system. HNRNPM: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.Breakpoints of inversion are in EPS15L1 and MED26. Inversion not creating functional fusion genes, because genes are fused in antisense fashion. This means that for both these genes, probably two intact copies are left. MED26: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. EPS15L1: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis.

Deletion of 1 copy of exon 1/2/3 (depending on splice form) and a large part of upstream intron of PLCB4. Thus affected proteins all miss the aa's encoded by the first coding exon (and thus also the ATG start codon). If the first start codon available is used, proteins consisting of only 6 amino acids would be produced. PLCB4: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-4, The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting intron 6. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting exons 9-12 or 2-4 (depending on splice form). No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.

Deletion of 2 of 3 copies overlapping with first 3 exons and promotor region of HDHD1. Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. Only one intact copy left.Deletion of 1 of 2 copies of a part of the STS gene involving exons 6-8. STS: Conversion of sulfated steroid precursors to estrogens during pregnancy.No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…No annotated elements involved. Large complex rearrangement of 36 and 5131, they are largely overlapping and both breakpoints of both rearrangements are in intergenic region. No copy number changes are associated with these either…Duplication with first breakpoint in FTX, comprising first 3 exons and right breakpoint in intergenic regions. 3 MIR genes with unknown functions and ZCCHC13 (uncharacterized protein) are inside. FTX: XIST regulatorDeletion of 1 of 4 copies of a large part of the last intron or last intron and exon, (depending on the splice form) of DIAPH2. Could be involved in oogenesis. Involved in the regulation of endosome dynamics. Implicated in a novel signal transduction pathway, in which a specific isoform and CSK are sequentially activated by RHOD to regulate the motility of early endosomes through interactions with the actin cytoskeleton.

Interchromosomal translocation with breakpoint on chr11 inside intron 6/7 of CDK11B and breakpoint on chr2 in intron 6 of SNTG2. The break is strand consistent, but genes are on opposite strands, so no functional fusion gene is formed. Genes are in a region of 3 copies on each chromosome. CDK11B is cyclin dependent kinase 11b, and appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. SNTG2 is gamma-2-syntrophin, a putative adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex

Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.A deletion partially overlapping with the first exon and intron of DHCR24. It's occuring in a pentaploid region and not clear how many affected copies. No drop in CNV is observed. DHCR24: Catalyzes the reduction of the delta-24 double bond of sterol intermediates. Protects cells from oxidative stress by reducing caspase 3 activity during apoptosis induced by oxidative stress. Also protects against amyloid-beta peptide-induced apoptosisInterchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.Tandem duplication with left breakpoint in CLCA3P and right breakpoint in intergenic region. No fusion genes ar formed, a truncated version of CLCA3P is not formed either, since it's onlythe C-terminal part that's duplicated (exons 14 and 15). CLCA3P is a calcium activated chloride channel regulator, very few details on protein are known.Interchromosomal translocation with breakpoint on chr1 in intergenic region close to centromere. Breakpoint on chr2 is in intron 11 of LPIN1 and occurs in an area with copy number 3, so presumably 2 intact LPIN1 copies are still present. LPIN1 plays important roles in controlling the metabolism of fatty acids at differents levels. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis in the reticulum endoplasmic membrane.

Small tandem duplication inside intron 1 of KIF26B. Not clear whether splicing is affected. Copy number probably from 2 to 3, so it's happening in 1 of two copies. KIF26B, essential for embryonic kidney development. Plays an important role in the compact adhesion between mesenchymal cells adjacent to the ureteric buds, possibly by interacting with MYH10.



Deletion with left breakpoint in CNTN4 and right breakpoint in intergenic region. No fusion genes are formed, the copy number probably goes from 4 to 3, so CNTN4 has 3 intact copies left. CNTN4 or contactin 4 mediates cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity.Inversion with left breakpoint in intergenic region and right breakpoint in LRRFIP2 gene. It largely overlaps with inversion 6101 so that the overlapping part is actually not inversed. LRRFIP2 may function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.



Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.Interchromosomal translocation to chr16 coupled to complex events just upstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Events at BOC gene just upstream from 568. All happening in the BOC gene and upstream of it (in chr3), BOC is a Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. Not known whether intact copies of BOC are still present.Interchromosomal translocation to chr16 coupled to complex events just downstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.One of a series of rearrangements in the ZBTB20 gene. Depending on the splice form, it concerns different exons, but in any case it's the first two coding exonns that are affected. Probably 1 of 3 copies is deleted. ZBTB20 is a putative transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses.

Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels. Interchromosomal translocation with breakpoint on chr3 in intron 2 of IGF2BP2 and breakpoint on chr12 in intergenic region. No fusion genes formed. 3 copies of IGF2BP2 present, so probably 2 intact. IGF2BP2 is Insulin-like growth factor 2 mRNA-binding protein 2. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.



Interchromosomal translocation with breakpoint on chr4 in intron 1 of DKK2. No change in copy number observed here. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. DKK2 antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease. TTC28: function unknown. Deletion of 1 or 2 copies of exons 16 and 17 and most of flanking introns of the KIAA1109 gene. Altered proteins missing exons 16 and 17 and probably undergoing splicing difficulties could be created. At least one intact copy left. KIAA1109 is an uncharacterized protein.

Interchromosomal translocation with breakpoint on chr5 in intergenic region and breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown.Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.

Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part is probably a deletion, eliminating 1 of 3 copies and spanning ZNF415 and BAG2, thus creating a fusion gene. If splicing occurs correctly, the open reading frame would switch and terminate after 1 extra amino acid, in effect creating a truncated ZNF415. ZNF415: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part spans BAG2 and RAB23. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.RAB23, not well characterized, known to be involved in Carpenter syndrome.Probable inversion with left breakpoint in intergenic region and right breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.

Probable inversion with right breakpoint in intergenic region and left breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.

Small tandem duplication, one extra repeat probably. This duplication comprises exons 121-126 of SYNE1, a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Component of SUN-protein-containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer nuclear membrane attachment sites for cytoskeletal filaments. Involved in the maintenance of nuclear organization and structural integrity. Connects nuclei to the cytoskeleton by interacting with the nuclear envelope and with F-actin in the cytoplasm. Required for centrosome migration to the apical cell surface during early ciliogenesis. Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.Small deletion of 1/5 copies in intron 1 of PARK2. Not clear whether splicing is affected. PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

Inversion with right breakpoint in intergenic region and right breakpoint in intron 28/29 of MLLT4. No fusion genes are created. MLLT4: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. A chromosomal aberration involving MLLT4 is associated with acute leukemias. Translocation t(6;11)(q27;q23) with MLL/HRX. The result is a rogue activator protein. No such aberration in HEK cells.Small deletion in intron 1 of ADAP1, GTPase-activating protein for the ADP ribosylation factor family Probable. Binds phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Not clear how many copies hit, since it's not observed in the CNV track (too short compared to 2kb binning size).

Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.Small tandem duplication insinde intron 10 of EXOC4. Copy number change cannot be observed from CNV track, it's in a triploid region. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane


Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.




Interchromosomal translocation with breakpoint on chr12 in intron 3 of ANO4. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. ANO4: putative calcium activated chloride channel.Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl esterDeletion comprising promotor region and exon 1 and 2 of SPATA13. Only one functional copy left. SPAT13 acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression.

Not clear what this rearrangement does, but completely overlapping with the 3' end of rearrangement 369. GPC6: Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases


Interchromosomal translocation with chr17 breakpoint in intron 4 of TEKT3 gene. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. TEKT3 is a structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. Required for progressive sperm mobilityInversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.




Deletion of 1 copy of exon 1/2/3 (depending on splice form) and a large part of upstream intron of PLCB4. Thus affected proteins all miss the aa's encoded by the first coding exon (and thus also the ATG start codon). If the first start codon available is used, proteins consisting of only 6 amino acids would be produced. PLCB4: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-4, The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2 comprising mainly intron 5. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting intron 6. No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.One of a series of deletions in MACROD2, this one affecting exons 9-12 or 2-4 (depending on splice form). No exon has been completely deleted, but lots of rearrangement is going on. Not clear whether functional protein can be produced. Probably splicing in intron 5 affected. MACROD2: It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.

Deletion of 2 of 3 copies overlapping with first 3 exons and promotor region of HDHD1. Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. Only one intact copy left.

Deletion of 1 of 4 copies of a large part of the last intron or last intron and exon, (depending on the splice form) of DIAPH2. Could be involved in oogenesis. Involved in the regulation of endosome dynamics. Implicated in a novel signal transduction pathway, in which a specific isoform and CSK are sequentially activated by RHOD to regulate the motility of early endosomes through interactions with the actin cytoskeleton.


Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.A deletion partially overlapping with the first exon and intron of DHCR24. It's occuring in a pentaploid region and not clear how many affected copies. No drop in CNV is observed. DHCR24: Catalyzes the reduction of the delta-24 double bond of sterol intermediates. Protects cells from oxidative stress by reducing caspase 3 activity during apoptosis induced by oxidative stress. Also protects against amyloid-beta peptide-induced apoptosisInterchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.

Interchromosomal translocation with breakpoint on chr1 in intergenic region close to centromere. Breakpoint on chr2 is in intron 11 of LPIN1 and occurs in an area with copy number 3, so presumably 2 intact LPIN1 copies are still present. LPIN1 plays important roles in controlling the metabolism of fatty acids at differents levels. Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis in the reticulum endoplasmic membrane.

One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.One of several events happening in exons 2-11 of LRP1B. Basically it comes down to the complete deletion of exons 4-7 and partial deletion of exons 2 (2 of 3 copies left) and 8-11 (1 of 3 copies left). In this way, a LRP1B protein with internal deletion (longer or shorter) would be produced. Tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma. In the article with PMID:10766186, it's described that exons 4-7 are the deletion hotspot in many non small cell lung carcinoma (NSCLC). All of the involved exons are part of the extracellular domain of this receptor.


Inversion with left breakpoint in intergenic region and right breakpoint in LRRFIP2 gene. It largely overlaps with inversion 6101 so that the overlapping part is actually not inversed. LRRFIP2 may function as activator of the canonical Wnt signaling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. Positively regulates Toll-like receptor (TLR) signaling in response to agonist probably by competing with the negative FLII regulator for MYD88-binding.



Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.Interchromosomal translocation to chr16 coupled to complex events just upstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.

Interchromosomal translocation to chr16 coupled to complex events just downstream in chr3. All happening in the BOC gene (chr3), Component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells. Promotes differentiation of myogenic cells. The breakpoint on chr16 is inside FAM38A, component of mechanosensitive channel required for the mechanosensitive currents. Plays a key role in epithelial cell adhesion by maintaining integrin activation through R-Ras recruitment to the ER, most probably in its activated state, and subsequent stimulation of calpain signaling. Hard to predict how everything looks after rearrangements, not known whether intact copies of BOC and FAM38A are still present.

Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels. Interchromosomal translocation with breakpoint on chr3 in intron 2 of IGF2BP2 and breakpoint on chr12 in intergenic region. No fusion genes formed. 3 copies of IGF2BP2 present, so probably 2 intact. IGF2BP2 is Insulin-like growth factor 2 mRNA-binding protein 2. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.



Interchromosomal translocation with breakpoint on chr4 in intron 1 of DKK2. No change in copy number observed here. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. DKK2 antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero-posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease. TTC28: function unknown.

Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.

Complex rearrangement comprising about half of the ZNF451 gene, all of BAG2 and the 3' UTR of RAB23. This part is probably a deletion, eliminating 1 of 3 copies and spanning ZNF415 and BAG2, thus creating a fusion gene. If splicing occurs correctly, the open reading frame would switch and terminate after 1 extra amino acid, in effect creating a truncated ZNF415. ZNF415: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53. BAG2 inhibits the chaperone activity of HSP70/HSC70 by promoting substrate release.

Probable inversion with left breakpoint in intergenic region and right breakpoint in intron 21 of ENNP1. Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.



Inversion with right breakpoint in intergenic region and right breakpoint in intron 28/29 of MLLT4. No fusion genes are created. MLLT4: Belongs to an adhesion system, probably together with the E-cadherin-catenin system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). Nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. A chromosomal aberration involving MLLT4 is associated with acute leukemias. Translocation t(6;11)(q27;q23) with MLL/HRX. The result is a rogue activator protein. No such aberration in HEK cells.

Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.




Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl esterDeletion comprising promotor region and exon 1 and 2 of SPATA13. Only one functional copy left. SPAT13 acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression.


Interchromosomal translocation with chr17 breakpoint in intron 4 of TEKT3 gene. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. TEKT3 is a structural component of ciliary and flagellar microtubules. Forms filamentous polymers in the walls of ciliary and flagellar microtubules. Required for progressive sperm mobilityInversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.


Duplication with right breakpoint in intergenic region and left breakpoint in COIL, possibly creating a truncated coil protein. It concerns one copy only probably that has a duplication. COIL: Is a component of the nuclear coiled bodies (CBS) which are involved in the function or assembly/disassembly of nucleoplasmic snRNPs. During mitosis, CBS disassemble, coinciding with a mitotic-specific phosphorylation of p80 coilin.


Deletion of 1 copy of exon 1/2/3 (depending on splice form) and a large part of upstream intron of PLCB4. Thus affected proteins all miss the aa's encoded by the first coding exon (and thus also the ATG start codon). If the first start codon available is used, proteins consisting of only 6 amino acids would be produced. PLCB4: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-4, The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.

Deletion of 1 of 4 copies of a large part of the last intron or last intron and exon, (depending on the splice form) of DIAPH2. Could be involved in oogenesis. Involved in the regulation of endosome dynamics. Implicated in a novel signal transduction pathway, in which a specific isoform and CSK are sequentially activated by RHOD to regulate the motility of early endosomes through interactions with the actin cytoskeleton.


Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.

Interchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.






Tandem duplication copmprising the last part of intron 4 of NLGN1. Splice acceptor site is not affected. Not clear what impact could be on splicing. 2 unaffected copies and 1 affected copy. LLGN1: Neuronal cell surface protein thought to be involved in cell-cell-interactions by forming intercellular junctions through binding to beta-neurexins. Seems to play role in formation or maintenance of synaptic junctions. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses, only expressed in blood vessels.


Duplication with left breakpoint in intron 22 of RASA1. No truncated gene or fusion gene created since left breakpoint is in intergenic region. RASA1, inhibitory regulator of the Ras-cyclic AMP pathway. Stimulates the GTPase of normal but not oncogenic Ras p21; this stimulation may be further increased in the presence of NCK1. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas, but SH2 is more N-terminal than the breakpoint.






Interchromosomal translocation with chr7 breakpoint in last intron of IMMP2L. Breakpoint on chr22 is inside first exon of TTC28. Several more interchromosomal translocations arise at this chr22 location. It's not clear what exactly happens here. TTC28: function unknown. IMMP2L: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.






Inversion creating FLII-LLGL1 and LLGL1-FLII fusion genes. Not clear how many copies affected, but it's a triploid region. LLGL1 is a tumor suppressor gene, and the protein is a cytoskeleton protein found in a complex involved in maintaining cell polarity and epithelial integrity. Involved in the regulation of mitotic spindle orientation, proliferation, differentiation and tissue organization of neuroepithelial cells. It's down-regulated or lost in all cell lines and in most of the tumor samples analyzed. Loss was associated with advanced stage of the disease. FLII: May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development By similarity. May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration.



Small inversion inside intron 26 of CSMD2. The inversion is also very near a breakpoint in CNV, on or near to exon 25 of the same gene. Upstream 5 copies, downstream only 2. It's not clear whether the inversion will have an impact on splicing and how many of those 5 copies are affected. CSMD2 is not well characterized, but highly similar to CSMD1, a putative tumor suppressor gene in squamous cell carcinomas. It's suggested that there might be functional overlap between these two genes. Contradictory to it's possible tumor supressor role, it's sometimes upregulated in head and neck cancer cell lines.

Interchromosomal translocation with breakpoint on chr1 in intergenic region and breakpoint on chr4 in intron 18 of SLIT2. No fusion genes created. Upstream of the breakpoint, there are 3 copies, but downstream only 2. One of these two copies is joined to chr1, so there can be only one functional copy left! SLIT2 is thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.








Tandem duplication overlapping with the largest part of SCARB1 (C-terminal part). No truncated genes or fusion genes created. SCARB1: Scavenger receptor class B member 1, receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells. Probable receptor for HDL, located in particular region of the plasma membrane, called caveolae. Facilitates the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors, such as HDL and to a lesser extent, apoB-containing lipoproteins and modified lipoproteins. Probably involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity. Receptor for hepatitis C virus glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate. Plays an important role in the uptake of HDL cholesteryl ester






Deletion ( of 3 copies) of a part of the EPHA6 gene, comprising exon 3 and parts of the flanking introns. A newly created protein skipping exon 3 would be spliced out of frame creating a truncated protein existing of only exon 1 and 2 coded parts and 23 extra amino acids coded by an out of frame exon 4, before a stop codon is encountered. EPHA4 is the ephrin type A receptor 4, a receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.


Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.Small deletion of 1/5 copies in intron 1 of PARK2. Not clear whether splicing is affected. PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

Deletion in one of 5 copies, fusing MARCH2 with HNRNPM. A fusion gene would be created with out of frame splicing causing a truncated MARCH2 with extra 3 amino acids. MARCH1: E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, downregulates their cell surface localization thus sequestering them in the intracellular endosomal system. HNRNPM: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.

Deletion of exons 3 and 4 and large part of flanking introns. In frame splicing could occur, giving rise to a protein missing amino acids encoded by exons 3 and 4, basically the same protein as isoform 6 (uniprot). PARK2 functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

>Id LeftChr LeftPosition RightChr RightPosition Inter Distance Discorda3899 chr1 10482369 chr1 10484223 N 1854 10

422 chr1 27997266 chr20 58911843 Y 203267 chr1 220699143 chr6 154179485 Y 113821 chr1 224927489 chrX 99131628 Y 94

525 chr1 234211297 chr6 114667957 Y 393754 chr2 7014439 chr2 7017433 N 2994 65

524 chr2 17110039 chr9 121845640 Y 554053 chr2 22721500 chr5 2592296 Y 261350 chr2 79970949 chr2 80021758 N 50809 523334 chr2 101343610 chr2 101346945 N 3335 231158 chr2 217716219 chr17 46221823 Y 223187 chr3 8781351 chr3 9010819 N 229468 703703 chr3 75801870 chr18 102542 Y 103132 chr3 118147530 chr3 118345751 N 198221 261313 chr3 169685856 chr3 169730430 N 44574 171312 chr3 175553075 chr3 175562478 N 9403 491306 chr4 36835833 chr4 36858979 N 23146 23

857 chr4 191179707 chr18 102542 Y 162845 chr5 4925476 chr13 112066487 Y 49

332 chr5 14418087 chr5 19787585 N 5369498 211119 chr5 16185352 chr5 16230925 N 45573 521117 chr5 20341260 chr5 20356577 N 15317 242816 chr5 24463678 chr5 24464258 N 580 632797 chr5 65539110 chr5 65562909 N 23799 352772 chr5 104748273 chr5 104793958 N 45685 272766 chr5 120253252 chr5 120495940 N 242688 382764 chr5 121952170 chr5 121955333 N 3163 1582744 chr5 164671424 chr5 165140140 N 468716 291094 chr6 62606676 chr6 62609588 N 2912 431090 chr6 101150970 chr6 101345173 N 194203 25

320 chr6 107555345 chr6 107555660 N 315 161085 chr6 138141828 chr6 138155014 N 13186 68

317 chr6 143291260 chr6 143295957 N 4697 313549 chr6 158696137 chr17 75404151 Y 432617 chr7 3315441 chr7 3322961 N 7520 182593 chr7 53309009 chr7 53311820 N 2811 381051 chr7 71284485 chr7 71374368 N 89883 362580 chr7 71533985 chr7 71541170 N 7185 132544 chr7 110392640 chr7 110517355 N 124715 312518 chr7 151795728 chr7 151796399 N 671 342508 chr7 156789004 chr7 156789828 N 824 112489 chr8 8764151 chr8 8766092 N 1941 532434 chr8 124526381 chr8 124651301 N 124920 27

832 chr8 127377384 chr19 60606504 Y 593501 chr8 128958553 chrX 73123950 Y 2321025 chr8 136785168 chr8 136787585 N 2417 96

86 chr9 75550404 chrX 72225872 Y 192367 chr9 118038697 chr9 118255720 N 217023 1232366 chr9 118266861 chr9 118270262 N 3401 127

2363 chr9 118746773 chr9 119112244 N 365471 643623 chr9 121829943 chr9 121849385 N 19442 231014 chr9 122527431 chr9 123058804 N 531373 61

3622 chr9 122733488 chr9 122775193 N 41705 94275 chr9 122734331 chr9 122743021 N 8690 161

1904 chr9 126338340 chrX 71238542 Y 1273621 chr9 129739334 chr9 129742403 N 3069 422111 chr9 130881752 chr13 84855587 Y 60

919 chr9 134379060 chr13 31015963 Y 472342 chr9 140032195 chr9 140033860 N 1665 23

269 chr10 27483457 chr10 61185535 N 33702078 40271 chr10 29017163 chr10 29018334 N 1171 24

2301 chr10 52657709 chr10 52930251 N 272542 623606 chr10 59943899 chr10 72057756 N 12113857 442291 chr10 62860591 chr10 72057866 N 9197275 172290 chr10 75474370 chr10 75754722 N 280352 142268 chr10 119189274 chr10 119191396 N 2122 832233 chr11 19708432 chr11 19714181 N 5749 55

931 chr11 122516506 chr11 122737846 N 221340 772163 chr12 6718000 chr12 6718785 N 785 172087 chr13 30094958 chr13 30095770 N 812 46

226 chr13 62024590 chr13 68619141 N 6594551 223564 chr13 89160806 chr13 89182894 N 22088 17

223 chr13 99323725 chr13 111744707 N 12420982 282054 chr13 103570461 chr13 104880997 N 1310536 26

876 chr15 23497698 chr15 23504594 N 6896 59759 chr16 20151282 chr16 20199992 N 48710 40758 chr16 24413589 chr16 24633756 N 220167 22747 chr16 76614057 chr16 76838182 N 224125 41742 chr17 37065806 chr17 37344668 N 278862 82

740 chr17 46221059 chr17 46415520 N 194461 40739 chr17 55236003 chr17 55386414 N 150411 17

1720 chr18 31924384 chr18 31927139 N 2755 33681 chr18 53340890 chr18 53511875 N 170985 19673 chr19 2058995 chr19 2200476 N 141481 53668 chr19 18851627 chr19 19064661 N 213034 121

1676 chr19 18873916 chr19 18877332 N 3416 14640 chr19 36444847 chr19 36758282 N 313435 35587 chr19 52115514 chrX 133781474 Y 25

29 chr19 60606067 chr21 33998225 Y 37633 chr19 62078571 chr19 62105475 N 26904 11

1629 chr20 14711393 chr20 14829307 N 117914 251628 chr20 14864688 chr20 14895387 N 30699 21

1579 chr20 61981505 chr20 61982265 N 760 1110 chrX 112995499 chrX 113012571 N 17072 44

1460 chrX 117905654 chrX 117907917 N 2263 29

FrequencyInBa Type RelatedJunctions Copy data to (line, Id) Notes0 deletion SG, 4630 Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.0 interchromosomal SG, 584 Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi network0 interchromosomal No annotated elements involved. Interchromosomal translocation to chr6 with both breakpoint in intergenic regions.0 interchromosomal Interchromosomal translocation with breakpoint on chr1 in the second intron of ITPKB gene and the breakpoint on chrX in intergenic region. 1 extra copy in both chromosomes starting from the breakpoints. ITPKB is Inositol-trisphosphate 3-kinase B.0 interchromosomal Interchromosomal translocation with breakpoint on chr1 in the intron 16 of NID1 and breakpoint on chr6 in intergenic region. No effect seen on copy number in chr1 in a probably pentaploid region.0 deletion SG, 3994 and eT,3707 Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known. 0 interchromosomal SG, 782 and eT,466 No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.0 interchromosomal No annotated elements involved. Interchromosomal translocation with breakpoint on both chr2 and chr5 in intergenic region.0 tandem-duplication SG, 1850 and eT, 1248 Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation0 deletion SG, 3840 and eT, 3314 Small deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.0 interchromosomal No annotated elements involved. Interchromosomal translocation with breakpoint on both chr2 and chr17 in intergenic region.0 deletion A deletion starting at the last intron of SRGAP3 and ending in the third intron of OXTR, creating a fusion gene of SRGAP3-OXTR. If splicing occurs correct and in frame (which it is likely to do, since the ORF is conserved), then the fusion gene would be an SRGAP3 missing the last 4 exons (358aa, probably comprising a coiled coil of this Rho GTPase activating protein) and replaced with the last exon of OXTR (oxitocin receptor GPCR, aa308 - 389) as the C-terminal part, comprising one TM helix and the cytoplasmic C-terminus. Only 1 copy affected probably.0 complex 857 No annotated elements involved. Related with junction Id 857, which also occurs in 293SG and SGendoT. It's possible that this is a misannotation, because there is a homologous region involving the FRG2 or FRG2C genes involved.0 deletion See Flp, 3584. No annotated elements involved. Deletion seems to be also present in SG and SGendoT judging from the CNV tracks, but not reported.0 tandem-duplication SG, 1736. duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!0 tandem-duplication SG, 1735 and eT, 1171 No annotated elements involved.0 tandem-duplication No annotated elements involved. Could have implications for the promotor region of KIAA1239, Leucine-rich repeat and WD repeat-containing protein KIAA1239 with unknown functions.0 complex 3703 SG, 1482 and eT, 1005 Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.0 interchromosomal No annotated elements involved. Interchromosomal translocation with breakpoints on both chr 5 and chr13 in intergenic region.0 probable-inversion Inversion, left side in intron 14 of the TRIO gene, and right side in intron 3 of the CDH18 gene. It thus would create both a TRIO-CDH18 fusion gene and a CDH18-TRIO fusion gene. TRIO: May regulate actin cytoskeletal organization, cell spreading and cell contraction by directly binding and stabilizing filamentous F-actin. The localized formation of TARA and TRIO complexes coordinates the amount of F-actin present in stress fibers. May also serve as a linker protein to recruit proteins required for F-actin formation and turnover. CDH18: Cadherin 18, Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.0 tandem-duplication SG, 1477 and eT, 1142 Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids0 tandem-duplication No annotated elements involved.0 deletion SG, 3331 and eT, 2899 No annotated elements involved.0 deletion SG, 3317 No annotated elements involved.0 deletion No annotated elements involved.0 deletion SG, 3283 and eT, 2745 No annotated elements involved.0 deletion SG, 3280 and eT, 2743 No annotated elements involved.0 deletion No annotated elements involved.0 tandem-duplication SG, 1440 Small tandem duplication inside intron 6 of the KHDRBS2 gene. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability 0 tandem-duplication SG, 1434 and eT, 927 Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.0 probable-inversion No annotated elements involved.0 tandem-duplication eT, 969 No annotated elements involved.0 probable-inversion SG, 375 and eT, 281 Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.0 interchromosomal Interchromosomal translocation with breakpoint on chr6 in the first intron of TUKP4 and the breakpoint on chr17 in intergenic region. Not much known about TULP4: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins 0 deletion Small deletion at the very beginning of intron 1 of SDK1. Probably only 1 of 3 copies deleted. Protein SDK1 is sidekick 1: Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy. 0 deletion No annotated elements involved.0 tandem-duplication SG, 1407 and eT, 944 duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. 0 deletion No annotated elements involved.0 deletion Deletion of almost all of intron 3 of IMMP2L. At least 1, probably 2 copies affected. IMMP2L is the Mitochondrial inner membrane protease subunit 2, Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.0 deletion SG, 3009 and eT, 2496 No annotated elements involved.0 deletion No annotated elements involved.0 deletion See Flp, 2915.0 deletion Deletion of 1 of 3 copies, comprising FBXO32. F-box only protein 32. Substrate recognition component of a (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Probably recognizes and binds to phosphorylated target proteins during skeletal muscle atrophy. Recognizes TERF1.0 complex 29 interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. 0 interchromosomal Interchromosomal translocation with breakpoint on chr8 inside PVT1, and breakpoint on chrX inside NCRNA00183. PVT1 is a known oncogen and interacts with MYC (PMID: 17503467). In plasmacytomas it's involved in translocations. NCRNA00183 seems to be involved in X chromosome inactivation.0 tandem-duplication SG, 1365 and eT, 914 No annotated elements involved.0 interchromosomal No annotated elements involved, interchromosomal translocation with breakpoints both on chr9 and X in intergenic region.0 deletion Deletion comprising a big part of PAPPA and a smaller C-terminal part of ASTN2. Probably 1 or 2 of 5 copies affected. PAPPA is a metalloproteinase which specifically cleaves IGFBP-4 and IGFBP-5, resulting in release of bound IGF. Cleavage of IGFBP-4 is dramatically enhanced by the presence of IGF, whereas cleavage of IGFBP-5 is slightly inhibited by the presence of IGF. ASTN2, astrotactin 2 isn't well characterized0 deletion Small deletion inside intron 5/19/20 (depending on splice form) of ASTN2. ASTN2, astrotactin 2 isn't well characterized

0 deletion Big deletion comprising first 6 or 7 exons of ASTN2, astrotactin 2 isn't well characterized.0 probable-inversion SG, 4369 and eT, 3558 No annotated elements involved.0 tandem-duplication SG, 1349 and eT, 901 Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.

TRAF1: Adapter molecule that regulates the activation of NF-kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.CEP110, Centriolin, Involved in cell cycle progression and cytokinesis. During the late steps of cytokinesis, anchors exocyst and SNARE complexes at the midbody, thereby allowing secretory vesicle-mediated abscission.

0 distal-duplicati 275 SG, 4395 and eT, 3557 Together with 275 a distal duplication comprising part of the C5 complement gene (C5).0 distal-duplicati 3622 SG, 317 Together with 3622 a distal duplication comprising part of the C5 complement gene (C5).0 interchromosomal Interchromosomal translocation with breakpoint on chr9 in intron 6 of NR6A1 and breakpoint on chrX in intron 1 of NHSL2. They would be fused in antisense direction, so they don't make a fusion protein. Two or one extra copy on 4 already present in chrX and 3 already present in chr9.0 probable-inversion Inversion disrupting the DPM2 gene in the second intron. Hard to tell how many copies, because it's a short inversion. DPM2 is Dolichol phosphate-mannose biosynthesis regulatory protein, Regulates the biosynthesis of dolichol phosphate-mannose. Essential for the ER localization and stable expression of DPM1.0 interchromosomal Interchromosomal translocation. Breakpoint on chr9 is in intergenic region, maybe promotor region of DOLPP1. breakpoint on chr13 is in intergenic region.0 interchromosomal SG, 1243 and eT, 819 Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.

0.06 deletion SG, 2822 Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.0 probable-inversion SG, 311 Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.0 probable-inversion No annotated elements involved.0 deletion Deletion of 1 of 4 copies of a part of the PRKG1 gene, creating a shorter form of it lacking exons 3 and 4. PRKG1 is a cGMP-dependent protein kinase 1, Phosphorylates PPP1R17 leading to its activation, Phosphorylates PPP1R12A.0 complex 2291 SG, 4375 and eT, 3546 Complex rearrangement together with 2291 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.0 complex 3606 SG, 2759 and eT, 2240 Complex rearrangement together with 3606 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.0 deletion SG, 2757 Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.0 deletion No annotated elements involved.0 deletion SG, 2701 and eT, 2185 Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. 0 tandem-duplication SG, 1257 and eT, 826 Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.0 deletion No annotated elements involved.0 deletion See Flp line.0 probable-inversion No annotated elements involved in breakpoints.0 probable-inversion No annotated elements involved in breakpoints.0 probable-inversion First breakpoint of this inversion in intron 7 of CLYBL. Other breakpoint in intergenic region. This trims off the last two exons (part of CDS and 3' UTR.0 deletion No annotated elements involved in breakpoints.0 tandem-duplication SG, 1208 and eT, 770 Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VA0 tandem-duplication SG, 1195 and eT, 754 No annotated elements involved in breakpoints.0 tandem-duplication SG, 1194 and eT, 753 Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.0 tandem-duplication SG, 1043 and eT, 669 Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. 0 tandem-duplication Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below.

eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.

0 tandem-duplication Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).0 tandem-duplication SG, 1033 and eT, 662 Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. 0 deletion SG, 2077 and eT, 1605 No annotated elements involved in breakpoints.0 tandem-duplication SG, 961 Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.0 tandem-duplication Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. 0 tandem-duplication Duplication fusing SLC45A42 and GDF1/LASS1 in a strand inconsistent way, thus not creating fusion genes. Relevant genes inside duplication, see below.

SFRS14: May play a role in mRNA splicing0 deletion Deletion of exons 4/5 and 5/6 and 7 of COPE in 1 of 3 copies. COPE: Coatomer subunit epsilon, The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. 0 tandem-duplication SG, 919 and eT, 566 Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). 0 interchromosomal Interchromosomal translocation with the breakpoint on chr19 inside the first exon of GRLF1 (Represses transcription of the glucocorticoid receptor by binding to the cis-acting regulatory sequence 5'-GAGAAAAGAAACTGGAGAAACTC-3'. May participate in the regulation of retinal development and degeneration. May transduce signals from p21-ras to the nucleus, acting via the ras GTPase-activating protein (GAP). May also act as a tumor suppressor), going upstream. The second breakpoint on chrX is inside intron 2/3 of FAM122C (function unknown). A functional fusion gene is not created. GRFL1 is in a triploid region. And 1 copy extra exists due to this translocation.0 complex 8320 tandem-duplication No annotated elements involved in breakpoints.0 deletion 2 or 3 of 3 copies deleted of intron 5 of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.0 deletion 2 or 3 of 3 copies deleted of intron 5 of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.

Interchromosomal translocation with breakpoint on chr19 in intron of UBE2S and breakpoint on chr21 in intron of 1 of ITSN1.

0.1 deletion see Flp, 2250 probable-inversion SG, 8 No annotated elements involved in breakpoints.0 deletion see Flp, 109

Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi networkNo annotated elements involved. Interchromosomal translocation to chr6 with both breakpoint in intergenic regions.Interchromosomal translocation with breakpoint on chr1 in the second intron of ITPKB gene and the breakpoint on chrX in intergenic region. 1 extra copy in both chromosomes starting from the breakpoints. ITPKB is Inositol-trisphosphate 3-kinase B.Interchromosomal translocation with breakpoint on chr1 in the intron 16 of NID1 and breakpoint on chr6 in intergenic region. No effect seen on copy number in chr1 in a probably pentaploid region.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known. No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.No annotated elements involved. Interchromosomal translocation with breakpoint on both chr2 and chr5 in intergenic region.Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulationSmall deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.No annotated elements involved. Interchromosomal translocation with breakpoint on both chr2 and chr17 in intergenic region.A deletion starting at the last intron of SRGAP3 and ending in the third intron of OXTR, creating a fusion gene of SRGAP3-OXTR. If splicing occurs correct and in frame (which it is likely to do, since the ORF is conserved), then the fusion gene would be an SRGAP3 missing the last 4 exons (358aa, probably comprising a coiled coil of this Rho GTPase activating protein) and replaced with the last exon of OXTR (oxitocin receptor GPCR, aa308 - 389) as the C-terminal part, comprising one TM helix and the cytoplasmic C-terminus. Only 1 copy affected probably.No annotated elements involved. Related with junction Id 857, which also occurs in 293SG and SGendoT. It's possible that this is a misannotation, because there is a homologous region involving the FRG2 or FRG2C genes involved.No annotated elements involved. Deletion seems to be also present in SG and SGendoT judging from the CNV tracks, but not reported.duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!No annotated elements involved.No annotated elements involved. Could have implications for the promotor region of KIAA1239, Leucine-rich repeat and WD repeat-containing protein KIAA1239 with unknown functions.Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.No annotated elements involved. Interchromosomal translocation with breakpoints on both chr 5 and chr13 in intergenic region.Inversion, left side in intron 14 of the TRIO gene, and right side in intron 3 of the CDH18 gene. It thus would create both a TRIO-CDH18 fusion gene and a CDH18-TRIO fusion gene. TRIO: May regulate actin cytoskeletal organization, cell spreading and cell contraction by directly binding and stabilizing filamentous F-actin. The localized formation of TARA and TRIO complexes coordinates the amount of F-actin present in stress fibers. May also serve as a linker protein to recruit proteins required for F-actin formation and turnover. CDH18: Cadherin 18, Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatidsNo annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.No annotated elements involved.Small tandem duplication inside intron 6 of the KHDRBS2 gene. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.No annotated elements involved.No annotated elements involved.Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Interchromosomal translocation with breakpoint on chr6 in the first intron of TUKP4 and the breakpoint on chr17 in intergenic region. Not much known about TULP4: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins Small deletion at the very beginning of intron 1 of SDK1. Probably only 1 of 3 copies deleted. Protein SDK1 is sidekick 1: Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy. No annotated elements involved.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. No annotated elements involved.Deletion of almost all of intron 3 of IMMP2L. At least 1, probably 2 copies affected. IMMP2L is the Mitochondrial inner membrane protease subunit 2, Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.No annotated elements involved.No annotated elements involved.

Deletion of 1 of 3 copies, comprising FBXO32. F-box only protein 32. Substrate recognition component of a (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Probably recognizes and binds to phosphorylated target proteins during skeletal muscle atrophy. Recognizes TERF1.interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. Interchromosomal translocation with breakpoint on chr8 inside PVT1, and breakpoint on chrX inside NCRNA00183. PVT1 is a known oncogen and interacts with MYC (PMID: 17503467). In plasmacytomas it's involved in translocations. NCRNA00183 seems to be involved in X chromosome inactivation.No annotated elements involved.No annotated elements involved, interchromosomal translocation with breakpoints both on chr9 and X in intergenic region.Deletion comprising a big part of PAPPA and a smaller C-terminal part of ASTN2. Probably 1 or 2 of 5 copies affected. PAPPA is a metalloproteinase which specifically cleaves IGFBP-4 and IGFBP-5, resulting in release of bound IGF. Cleavage of IGFBP-4 is dramatically enhanced by the presence of IGF, whereas cleavage of IGFBP-5 is slightly inhibited by the presence of IGF. ASTN2, astrotactin 2 isn't well characterizedSmall deletion inside intron 5/19/20 (depending on splice form) of ASTN2. ASTN2, astrotactin 2 isn't well characterized

Big deletion comprising first 6 or 7 exons of ASTN2, astrotactin 2 isn't well characterized.No annotated elements involved.Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.TRAF1: Adapter molecule that regulates the activation of NF-kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.CEP110, Centriolin, Involved in cell cycle progression and cytokinesis. During the late steps of cytokinesis, anchors exocyst and SNARE complexes at the midbody, thereby allowing secretory vesicle-mediated abscission.Together with 275 a distal duplication comprising part of the C5 complement gene (C5).Together with 3622 a distal duplication comprising part of the C5 complement gene (C5).Interchromosomal translocation with breakpoint on chr9 in intron 6 of NR6A1 and breakpoint on chrX in intron 1 of NHSL2. They would be fused in antisense direction, so they don't make a fusion protein. Two or one extra copy on 4 already present in chrX and 3 already present in chr9.Inversion disrupting the DPM2 gene in the second intron. Hard to tell how many copies, because it's a short inversion. DPM2 is Dolichol phosphate-mannose biosynthesis regulatory protein, Regulates the biosynthesis of dolichol phosphate-mannose. Essential for the ER localization and stable expression of DPM1.Interchromosomal translocation. Breakpoint on chr9 is in intergenic region, maybe promotor region of DOLPP1. breakpoint on chr13 is in intergenic region.Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.No annotated elements involved.Deletion of 1 of 4 copies of a part of the PRKG1 gene, creating a shorter form of it lacking exons 3 and 4. PRKG1 is a cGMP-dependent protein kinase 1, Phosphorylates PPP1R17 leading to its activation, Phosphorylates PPP1R12A.Complex rearrangement together with 2291 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.Complex rearrangement together with 3606 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.No annotated elements involved.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.No annotated elements involved.

No annotated elements involved in breakpoints.No annotated elements involved in breakpoints.First breakpoint of this inversion in intron 7 of CLYBL. Other breakpoint in intergenic region. This trims off the last two exons (part of CDS and 3' UTR.No annotated elements involved in breakpoints.Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VANo annotated elements involved in breakpoints.Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. No annotated elements involved in breakpoints.Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication fusing SLC45A42 and GDF1/LASS1 in a strand inconsistent way, thus not creating fusion genes. Relevant genes inside duplication, see below.SFRS14: May play a role in mRNA splicingDeletion of exons 4/5 and 5/6 and 7 of COPE in 1 of 3 copies. COPE: Coatomer subunit epsilon, The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Interchromosomal translocation with the breakpoint on chr19 inside the first exon of GRLF1 (Represses transcription of the glucocorticoid receptor by binding to the cis-acting regulatory sequence 5'-GAGAAAAGAAACTGGAGAAACTC-3'. May participate in the regulation of retinal development and degeneration. May transduce signals from p21-ras to the nucleus, acting via the ras GTPase-activating protein (GAP). May also act as a tumor suppressor), going upstream. The second breakpoint on chrX is inside intron 2/3 of FAM122C (function unknown). A functional fusion gene is not created. GRFL1 is in a triploid region. And 1 copy extra exists due to this translocation.

No annotated elements involved in breakpoints.2 or 3 of 3 copies deleted of intron 5 of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.2 or 3 of 3 copies deleted of intron 5 of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer.

Interchromosomal translocation with breakpoint on chr19 in intron of UBE2S and breakpoint on chr21 in intron of 1 of ITSN1. UBE2S

No annotated elements involved in breakpoints.

Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi network

Interchromosomal translocation with breakpoint on chr1 in the second intron of ITPKB gene and the breakpoint on chrX in intergenic region. 1 extra copy in both chromosomes starting from the breakpoints. ITPKB is Inositol-trisphosphate 3-kinase B.Interchromosomal translocation with breakpoint on chr1 in the intron 16 of NID1 and breakpoint on chr6 in intergenic region. No effect seen on copy number in chr1 in a probably pentaploid region.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known. No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.

Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulationSmall deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.

A deletion starting at the last intron of SRGAP3 and ending in the third intron of OXTR, creating a fusion gene of SRGAP3-OXTR. If splicing occurs correct and in frame (which it is likely to do, since the ORF is conserved), then the fusion gene would be an SRGAP3 missing the last 4 exons (358aa, probably comprising a coiled coil of this Rho GTPase activating protein) and replaced with the last exon of OXTR (oxitocin receptor GPCR, aa308 - 389) as the C-terminal part, comprising one TM helix and the cytoplasmic C-terminus. Only 1 copy affected probably.No annotated elements involved. Related with junction Id 857, which also occurs in 293SG and SGendoT. It's possible that this is a misannotation, because there is a homologous region involving the FRG2 or FRG2C genes involved.No annotated elements involved. Deletion seems to be also present in SG and SGendoT judging from the CNV tracks, but not reported.duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!

No annotated elements involved. Could have implications for the promotor region of KIAA1239, Leucine-rich repeat and WD repeat-containing protein KIAA1239 with unknown functions.

Inversion, left side in intron 14 of the TRIO gene, and right side in intron 3 of the CDH18 gene. It thus would create both a TRIO-CDH18 fusion gene and a CDH18-TRIO fusion gene. TRIO: May regulate actin cytoskeletal organization, cell spreading and cell contraction by directly binding and stabilizing filamentous F-actin. The localized formation of TARA and TRIO complexes coordinates the amount of F-actin present in stress fibers. May also serve as a linker protein to recruit proteins required for F-actin formation and turnover. CDH18: Cadherin 18, Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids

Small tandem duplication inside intron 6 of the KHDRBS2 gene. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.

Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Interchromosomal translocation with breakpoint on chr6 in the first intron of TUKP4 and the breakpoint on chr17 in intergenic region. Not much known about TULP4: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins Small deletion at the very beginning of intron 1 of SDK1. Probably only 1 of 3 copies deleted. Protein SDK1 is sidekick 1: Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.

duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning.

Deletion of almost all of intron 3 of IMMP2L. At least 1, probably 2 copies affected. IMMP2L is the Mitochondrial inner membrane protease subunit 2, Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Deletion of 1 of 3 copies, comprising FBXO32. F-box only protein 32. Substrate recognition component of a (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Probably recognizes and binds to phosphorylated target proteins during skeletal muscle atrophy. Recognizes TERF1.interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. Interchromosomal translocation with breakpoint on chr8 inside PVT1, and breakpoint on chrX inside NCRNA00183. PVT1 is a known oncogen and interacts with MYC (PMID: 17503467). In plasmacytomas it's involved in translocations. NCRNA00183 seems to be involved in X chromosome inactivation.

Deletion comprising a big part of PAPPA and a smaller C-terminal part of ASTN2. Probably 1 or 2 of 5 copies affected. PAPPA is a metalloproteinase which specifically cleaves IGFBP-4 and IGFBP-5, resulting in release of bound IGF. Cleavage of IGFBP-4 is dramatically enhanced by the presence of IGF, whereas cleavage of IGFBP-5 is slightly inhibited by the presence of IGF. ASTN2, astrotactin 2 isn't well characterized


Interchromosomal translocation with breakpoint on chr9 in intron 6 of NR6A1 and breakpoint on chrX in intron 1 of NHSL2. They would be fused in antisense direction, so they don't make a fusion protein. Two or one extra copy on 4 already present in chrX and 3 already present in chr9.Inversion disrupting the DPM2 gene in the second intron. Hard to tell how many copies, because it's a short inversion. DPM2 is Dolichol phosphate-mannose biosynthesis regulatory protein, Regulates the biosynthesis of dolichol phosphate-mannose. Essential for the ER localization and stable expression of DPM1.Interchromosomal translocation. Breakpoint on chr9 is in intergenic region, maybe promotor region of DOLPP1. breakpoint on chr13 is in intergenic region.Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.

Deletion of 1 of 4 copies of a part of the PRKG1 gene, creating a shorter form of it lacking exons 3 and 4. PRKG1 is a cGMP-dependent protein kinase 1, Phosphorylates PPP1R17 leading to its activation, Phosphorylates PPP1R12A.Complex rearrangement together with 2291 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.Complex rearrangement together with 3606 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.

Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

First breakpoint of this inversion in intron 7 of CLYBL. Other breakpoint in intergenic region. This trims off the last two exons (part of CDS and 3' UTR.

Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VA

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.

ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated.

Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication fusing SLC45A42 and GDF1/LASS1 in a strand inconsistent way, thus not creating fusion genes. Relevant genes inside duplication, see below.

Deletion of exons 4/5 and 5/6 and 7 of COPE in 1 of 3 copies. COPE: Coatomer subunit epsilon, The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Interchromosomal translocation with the breakpoint on chr19 inside the first exon of GRLF1 (Represses transcription of the glucocorticoid receptor by binding to the cis-acting regulatory sequence 5'-GAGAAAAGAAACTGGAGAAACTC-3'. May participate in the regulation of retinal development and degeneration. May transduce signals from p21-ras to the nucleus, acting via the ras GTPase-activating protein (GAP). May also act as a tumor suppressor), going upstream. The second breakpoint on chrX is inside intron 2/3 of FAM122C (function unknown). A functional fusion gene is not created. GRFL1 is in a triploid region. And 1 copy extra exists due to this translocation.Interchromosomal translocation with breakpoint on chr19 in intron of UBE2S and breakpoint on chr21 in intron of 1 of ITSN1.UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. ITSN1 is a adapter protein that may provide indirect link between the endocytic membrane traffic and the actin assembly machinery. May regulate the formation of clathrin-coated vesicles. Isoform 1 could be involved in brain-specific synaptic vesicle recycling. Inhibits ARHGAP31 activity toward RAC1.

Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi network

Interchromosomal translocation with breakpoint on chr1 in the second intron of ITPKB gene and the breakpoint on chrX in intergenic region. 1 extra copy in both chromosomes starting from the breakpoints. ITPKB is Inositol-trisphosphate 3-kinase B.

Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known.

Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation

A deletion starting at the last intron of SRGAP3 and ending in the third intron of OXTR, creating a fusion gene of SRGAP3-OXTR. If splicing occurs correct and in frame (which it is likely to do, since the ORF is conserved), then the fusion gene would be an SRGAP3 missing the last 4 exons (358aa, probably comprising a coiled coil of this Rho GTPase activating protein) and replaced with the last exon of OXTR (oxitocin receptor GPCR, aa308 - 389) as the C-terminal part, comprising one TM helix and the cytoplasmic C-terminus. Only 1 copy affected probably.


Small tandem duplication inside intron 6 of the KHDRBS2 gene. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability

Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Interchromosomal translocation with breakpoint on chr6 in the first intron of TUKP4 and the breakpoint on chr17 in intergenic region. Not much known about TULP4: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins Small deletion at the very beginning of intron 1 of SDK1. Probably only 1 of 3 copies deleted. Protein SDK1 is sidekick 1: Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV-associated nephropathy.

duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning.


Deletion of 1 of 3 copies, comprising FBXO32. F-box only protein 32. Substrate recognition component of a (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Probably recognizes and binds to phosphorylated target proteins during skeletal muscle atrophy. Recognizes TERF1.interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. Interchromosomal translocation with breakpoint on chr8 inside PVT1, and breakpoint on chrX inside NCRNA00183. PVT1 is a known oncogen and interacts with MYC (PMID: 17503467). In plasmacytomas it's involved in translocations. NCRNA00183 seems to be involved in X chromosome inactivation.


TRAF1: Adapter molecule that regulates the activation of NF-kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.

Interchromosomal translocation with breakpoint on chr9 in intron 6 of NR6A1 and breakpoint on chrX in intron 1 of NHSL2. They would be fused in antisense direction, so they don't make a fusion protein. Two or one extra copy on 4 already present in chrX and 3 already present in chr9.Inversion disrupting the DPM2 gene in the second intron. Hard to tell how many copies, because it's a short inversion. DPM2 is Dolichol phosphate-mannose biosynthesis regulatory protein, Regulates the biosynthesis of dolichol phosphate-mannose. Essential for the ER localization and stable expression of DPM1.


Complex rearrangement together with 3606 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm.


Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated.

Deletion of exons 4/5 and 5/6 and 7 of COPE in 1 of 3 copies. COPE: Coatomer subunit epsilon, The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Interchromosomal translocation with the breakpoint on chr19 inside the first exon of GRLF1 (Represses transcription of the glucocorticoid receptor by binding to the cis-acting regulatory sequence 5'-GAGAAAAGAAACTGGAGAAACTC-3'. May participate in the regulation of retinal development and degeneration. May transduce signals from p21-ras to the nucleus, acting via the ras GTPase-activating protein (GAP). May also act as a tumor suppressor), going upstream. The second breakpoint on chrX is inside intron 2/3 of FAM122C (function unknown). A functional fusion gene is not created. GRFL1 is in a triploid region. And 1 copy extra exists due to this translocation.

accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. ITSN1 is a adapter protein that may provide indirect link between the endocytic membrane traffic and the actin assembly machinery. May regulate the formation of clathrin-coated vesicles. Isoform 1 could be involved in brain-specific synaptic vesicle recycling. Inhibits ARHGAP31 activity toward RAC1.





Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Interchromosomal translocation with breakpoint on chr6 in the first intron of TUKP4 and the breakpoint on chr17 in intergenic region. Not much known about TULP4: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins


Deletion of 1 of 3 copies, comprising FBXO32. F-box only protein 32. Substrate recognition component of a (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Probably recognizes and binds to phosphorylated target proteins during skeletal muscle atrophy. Recognizes TERF1.interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination.




Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.


Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated.


Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Interchromosomal translocation with the breakpoint on chr19 inside the first exon of GRLF1 (Represses transcription of the glucocorticoid receptor by binding to the cis-acting regulatory sequence 5'-GAGAAAAGAAACTGGAGAAACTC-3'. May participate in the regulation of retinal development and degeneration. May transduce signals from p21-ras to the nucleus, acting via the ras GTPase-activating protein (GAP). May also act as a tumor suppressor), going upstream. The second breakpoint on chrX is inside intron 2/3 of FAM122C (function unknown). A functional fusion gene is not created. GRFL1 is in a triploid region. And 1 copy extra exists due to this translocation.




Inversion, left side in intron 14 of the TRIO gene, and right side in intron 3 of the CDH18 gene. It thus would create both a TRIO-CDH18 fusion gene and a CDH18-TRIO fusion gene. TRIO: May regulate actin cytoskeletal organization, cell spreading and cell contraction by directly binding and stabilizing filamentous F-actin. The localized formation of TARA and TRIO complexes coordinates the amount of F-actin present in stress fibers. May also serve as a linker protein to recruit proteins required for F-actin formation and turnover. CDH18: Cadherin 18, Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.


Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.

interchromosomal translocation with breakpoint on chr8 in intergenic region, and breakpoint on chr19 in intron 3 of UBE2S. Immediately linked to interchromosomal translocation Id29 (see further down). UBE2S accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes 'Lys-11'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as a E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination.



Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm.

Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated.







Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter).


>Id LeftChr LeftPosition RightChr RightPosition StrandConsiste Type4630 chr1 10482363 chr1 10484217 Y deletion

862 chr1 15422806 chr1 25362531 N probable-inversion4913 chr1 15616806 chr1 25365520 N probable-inversion

584 chr1 27997266 chr20 58911843 N interchromosomal4864 chr1 148200908 chr5 1616581 N interchromosomal3994 chr2 7014439 chr2 7017433 Y deletion3990 chr2 14595272 chr2 14687503 Y deletion

782 chr2 17110039 chr9 121845640 N interchromosomal4887 chr2 17112030 chr2 17113246 N probable-inversion1850 chr2 79970949 chr2 80021758 Y tandem-duplication3840 chr2 101343610 chr2 101346945 Y deletion4664 chr2 132747167 chr16 33863532 N interchromosomal1761 chr2 184040004 chr2 184045815 Y tandem-duplication4805 chr2 239732680 chr2 239749389 N probable-inversion1755 chr3 3198211 chr3 3557169 Y tandem-duplication1753 chr3 31908327 chr3 32331754 Y tandem-duplication1736 chr3 169685856 chr3 169730430 Y tandem-duplication1735 chr3 175553075 chr3 175562478 Y tandem-duplication

756 chr4 185742332 chr4 185964343 N probable-inversion

3557 chr4 186576504 chr4 186577558 Y deletion1482 chr4 191179805 chr18 102542 Y interchromosomal1477 chr5 16185352 chr5 16230925 Y tandem-duplication3331 chr5 24463678 chr5 24464258 Y deletion3317 chr5 65539110 chr5 65562909 Y deletion


3222 chr5 104388037 chr10 59071734 Y interchromosomal1474 chr5 113075321 chr5 128695457 Y tandem-duplication1473 chr5 116211166 chr5 163407056 Y tandem-duplication3283 chr5 120253252 chr5 120495940 Y deletion3280 chr5 121952170 chr5 121955333 Y deletion3276 chr5 129523564 chr5 129917097 Y deletion3264 chr5 133458702 chr5 179587691 Y deletion


3038 chr5 156527451 chr10 133957281 Y interchromosomal3259 chr5 165104041 chr5 165236386 Y deletion4454 chr5 179718847 chr5 179720864 N probable-inversion1440 chr6 62606676 chr6 62609588 Y tandem-duplication

377 chr6 82135227 chr6 82147560 N probable-inversion1434 chr6 101150970 chr6 101345173 Y tandem-duplication

375 chr6 143291260 chr6 143295957 N probable-inversion1407 chr7 71284485 chr7 71374368 Y tandem-duplication1137 chr7 132648851 chr19 48238737 Y interchromosomal3009 chr7 151795880 chr7 151796549 Y deletion

2980 chr8 8764151 chr8 8766092 Y deletion4409 chr8 90909091 chr8 90914794 N complex2939 chr8 90914794 chr8 91965062 Y complex2937 chr8 94209883 chr8 94211891 Y complex4407 chr8 94211774 chr8 94212776 N complex1365 chr8 136785168 chr8 136787585 Y tandem-duplication4396 chr9 121829943 chr9 121849385 N probable-inversion1349 chr9 122527431 chr9 123058804 Y tandem-duplication

4395 chr9 122733488 chr9 122775193 N distal-duplicati317 chr9 122734331 chr9 122743021 N distal-duplicati

1243 chr9 134379060 chr13 31015963 Y interchromosomal2822 chr9 140032287 chr9 140033878 Y deletion2334 chr10 5854594 chr16 33858444 Y interchromosomal

311 chr10 27483457 chr10 61185535 N probable-inversion4375 chr10 59943899 chr10 72057756 N complex2759 chr10 62860591 chr10 72057866 Y complex4374 chr10 63508026 chr10 63508237 N probable-inversion2757 chr10 75474370 chr10 75754722 Y deletion1298 chr10 78863822 chr10 78886302 Y tandem-duplication2751 chr10 84422076 chr10 84623549 Y deletion4371 chr10 84424587 chr10 84631678 N probable-inversion2701 chr11 19708432 chr11 19714181 Y deletion1282 chr11 30393285 chr11 30410818 Y tandem-duplication1268 chr11 84129465 chr11 84258079 Y tandem-duplication1257 chr11 122516385 chr11 122737894 Y tandem-duplication2616 chr12 6718000 chr12 6718785 Y deletion2523 chr13 30094958 chr13 30095770 Y deletion2504 chr13 68813467 chr13 68815641 Y deletion2427 chr15 22884267 chr15 22885409 Y deletion1208 chr15 23497702 chr15 23504598 Y tandem-duplication1207 chr15 23538771 chr15 23542711 Y tandem-duplication1195 chr16 20151282 chr16 20199992 Y tandem-duplication1194 chr16 24413574 chr16 24633741 Y tandem-duplication1043 chr16 76614057 chr16 76838182 Y tandem-duplication1035 chr17 37065806 chr17 37344668 Y tandem-duplication

1033 chr17 55236003 chr17 55386414 Y tandem-duplication2102 chr18 98927 chr18 101079 Y deletion2077 chr18 31924384 chr18 31927139 Y deletion

961 chr18 53340890 chr18 53511875 Y tandem-duplication951 chr19 2058995 chr19 2200476 Y tandem-duplication919 chr19 36444847 chr19 36758282 Y tandem-duplication

1973 chr20 14547213 chr20 14811306 Y deletion1918 chr20 61981503 chr20 61982263 Y deletion

549 chrX 7077182 chrX 7100680 Y deletion

522 chrX 93233376 chrX 93236393 Y deletion8 chrX 112995499 chrX 113012571 N probable-inversion

514 chrX 117718981 chrX 117720311 Y deletion

RelatedJunction Also present in othNotesSmall deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.

probable-inversion SGendoT, 1060 No annotated elements involved. Large inversion with both breakpoints in intergenic region.probable-inversion SGendoT, 4061 Inversion largely overlapping with inversion 862, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance interchromosomal Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi networkinterchromosomal SGendoT, 4020 Interchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.

Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known. SGendoT, 3703 No annotated elements involved.

interchromosomal No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.probable-inversion No annotated elements involved.tandem-duplication Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation

Small deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.interchromosomal See Flp, 4461tandem-duplication SGendoT, 1195 No annotated elements involved.probable-inversion SGendoT, 3976 Small deletion inside HDAC4 gene, comprising most of introns 6 and 7 and exon 7. It's hard to say how many alleles have been hit from the CNV data. Probaby at least 2 copies intact. HDAC4 is Histone deacetylase 4, responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.tandem-duplication SGendoT, 1187 No annotated elements involved.tandem-duplication SGendoT, 1185 Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.tandem-duplication duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!tandem-duplication No annotated elements involved.probable-inversion SGendoT, 445 Inversion with left breakpoint in intergenic region and right breakpoint in ACSL1 gene. A loss of 1 copy in this inversion seems to be the case, 2 instead of 3 copies in SG, but not in SGendoT (overall only 2 copies in this region. Affected genes: CASP3, CCDC111, MLF1IP and ACSL1.

CASP3, caspase 3 is involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9.CCDC111, function unknown.MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').

SGendoT, 2937 Small deletion, comprising exons 3 and 4 of the UFSP2 gene. It is a thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, an ubiquitin-like modifier protein bound to a number of target proteins. Not clear how many copies have been deleted, but most prabably not all.interchromosomal Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.tandem-duplication Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids

No annotated elements involved.No annotated elements involved.

probable-inversion See separate word docprobable-inversion See separate word docinterchromosomal See separate word doctandem-duplication See separate word doctandem-duplication See separate word doc

No annotated elements involved.No annotated elements involved.See separate word docSee separate word doc

probable-inversion See separate word docprobable-inversion See separate word docinterchromosomal See separate word doc

See separate word docprobable-inversion See separate word doctandem-duplication Small tandem duplication inside intron 6 of the KHDRBS2 gene. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability probable-inversion SGendoT, 283 No annotated elements involved.tandem-duplication Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.probable-inversion Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.tandem-duplication duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. interchromosomal Interchromosomal translocation with breakpoint on chr7 in intron 4 of the EXOC4 gene. The breakpoint on chr19 is in intergenic region, but in the PSG gene cluster, close to where the adenoviral DNA has integrated. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.

No annotated elements involved.

SGendoT, 2452 Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised. 2939 No annotated elements involved.4409 SGendoT, 2409 Left breakpoint is intergenic region, right breakpoint is inside NECAB1. It seems to concern a deletion of 1 of 4 copies. NECAB1 is N-terminal EF-hand calcium-binding protein 1, but not much is known about it. Inside this deletion are OSGIN2, DECR1, NBN, CALB1 and TMEM64. But thery are all still present in three copies.4407 SGendoT, 3570 No annotated elements involved.2937 SGendoT, 2408 No annotated elements involved.

tandem-duplication No annotated elements involved.probable-inversion No annotated elements involved.tandem-duplication Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.


317 Together with 315 a distal duplication comprising part of the C5 complement gene (C5). This Id 4395 event is probably an inversion.4395 Together with 4395 a distal duplication comprising part of the C5 complement gene (C5). This Id 317 event is probably a duplication.

interchromosomal Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.

interchromosomal Interchromosomal rearrangement with breakpoint on chr10 in intron 7/8 of GDI2 and breakpoint on chr16 in intergenic region. GDI2 is Rab GDP dissociation inhibitor beta, Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them.probable-inversion Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.

2759 Complex rearrangement together with 2795 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.4375 Complex rearrangement together with 4375 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.

probable-inversion SGendoT, 3545 Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.

tandem-duplication Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.SGendoT, 2232 Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.

probable-inversion SGendoT, 3541 Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs.

tandem-duplication SGendoT, 839 Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemtandem-duplication SGendoT, 829 Small duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses tandem-duplication Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

See Flp, 2608See Flp, 2530SGendoT, 1985 No annotated elements involved.

Deletion comprising SNORD116-21. Homo sapiens small nucleolar RNA, C/D box 116-21 (SNORD116-21), small nucleolar RNA. Not clear how many copies deleted.tandem-duplication Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VAtandem-duplication SGendoT, 769 Small duplication inside intron 2 of ATP10A. Not clear whether wplicing is affected. Probable phospholipid-transporting ATPase VA. Not many details known.tandem-duplication No annotated elements involved.tandem-duplication Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.tandem-duplication Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. tandem-duplication SGendoT, 664 Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.

eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).

tandem-duplication Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. No annotated elements involved.No annotated elements involved.

tandem-duplication Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.tandem-duplication SGendoT, 589 Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. tandem-duplication Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter).

SGendoT, 1502 Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.See Flp, 1579

Deletion of 1 of 3 copies overlapping with promotor region of HDHD1. Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.

SG, 1315 No annotated elements involved.probable-inversion No annotated elements involved.

No annotated elements involved.

Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.No annotated elements involved. Large inversion with both breakpoints in intergenic region.Inversion largely overlapping with inversion 862, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi networkInterchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known.

No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.

Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulationSmall deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.

Small deletion inside HDAC4 gene, comprising most of introns 6 and 7 and exon 7. It's hard to say how many alleles have been hit from the CNV data. Probaby at least 2 copies intact. HDAC4 is Histone deacetylase 4, responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.

Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!

Inversion with left breakpoint in intergenic region and right breakpoint in ACSL1 gene. A loss of 1 copy in this inversion seems to be the case, 2 instead of 3 copies in SG, but not in SGendoT (overall only 2 copies in this region. Affected genes: CASP3, CCDC111, MLF1IP and ACSL1. CASP3, caspase 3 is involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9.

MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').Small deletion, comprising exons 3 and 4 of the UFSP2 gene. It is a thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, an ubiquitin-like modifier protein bound to a number of target proteins. Not clear how many copies have been deleted, but most prabably not all.Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids


Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. Interchromosomal translocation with breakpoint on chr7 in intron 4 of the EXOC4 gene. The breakpoint on chr19 is in intergenic region, but in the PSG gene cluster, close to where the adenoviral DNA has integrated. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.

Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised.

Left breakpoint is intergenic region, right breakpoint is inside NECAB1. It seems to concern a deletion of 1 of 4 copies. NECAB1 is N-terminal EF-hand calcium-binding protein 1, but not much is known about it. Inside this deletion are OSGIN2, DECR1, NBN, CALB1 and TMEM64. But thery are all still present in three copies.

Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.TRAF1: Adapter molecule that regulates the activation of NF-kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.CEP110, Centriolin, Involved in cell cycle progression and cytokinesis. During the late steps of cytokinesis, anchors exocyst and SNARE complexes at the midbody, thereby allowing secretory vesicle-mediated abscission.Together with 315 a distal duplication comprising part of the C5 complement gene (C5). This Id 4395 event is probably an inversion.Together with 4395 a distal duplication comprising part of the C5 complement gene (C5). This Id 317 event is probably a duplication.Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.Interchromosomal rearrangement with breakpoint on chr10 in intron 7/8 of GDI2 and breakpoint on chr16 in intergenic region. GDI2 is Rab GDP dissociation inhibitor beta, Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them.Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.Complex rearrangement together with 2795 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.Complex rearrangement together with 4375 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

Deletion comprising SNORD116-21. Homo sapiens small nucleolar RNA, C/D box 116-21 (SNORD116-21), small nucleolar RNA. Not clear how many copies deleted.Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VASmall duplication inside intron 2 of ATP10A. Not clear whether wplicing is affected. Probable phospholipid-transporting ATPase VA. Not many details known.

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated.

Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.


Small deletion in intron 2 of PEX14, probably impacts 1 of 3 copies. PEX14 is a component of the peroxisomal translocation machinery with PEX13 and PEX17. Interacts with both the PTS1 and PTS2 receptors. Binds directly to PEX17.

Inversion largely overlapping with inversion 862, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi networkInterchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known.

No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.



Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.duplication inside intron of C3orf50. seems to be also present in 293SGendoT line, but not annotated. C3orf50 is a EGF-like and EMI domain-containing protein 1, but could be a pseudogene!


MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').Small deletion, comprising exons 3 and 4 of the UFSP2 gene. It is a thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, an ubiquitin-like modifier protein bound to a number of target proteins. Not clear how many copies have been deleted, but most prabably not all.

Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids


Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. Interchromosomal translocation with breakpoint on chr7 in intron 4 of the EXOC4 gene. The breakpoint on chr19 is in intergenic region, but in the PSG gene cluster, close to where the adenoviral DNA has integrated. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.



Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.Interchromosomal rearrangement with breakpoint on chr10 in intron 7/8 of GDI2 and breakpoint on chr16 in intergenic region. GDI2 is Rab GDP dissociation inhibitor beta, Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them.Inversion disrupting YMEL1 in the first intron and intergenic region at the other breakpoint. YML1 is a putative ATP-dependent protease which plays a role in mitochondrial protein metabolism. Seems to act in the processing of OPA1.

Complex rearrangement together with 4375 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.


Tandem duplication with breakpoint in intergenic region, and the othe rin ATP8B1. NARS (Asparaginyl-tRNA synthetase, cytoplasmic) and FECH (Catalyzes the ferrous insertion into protoporphyrin IX.) are duplicated.Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.


Inversion largely overlapping with inversion 862, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance Interchromosomal translocation with breakpoint on chr1 in intron 3 of STX12 and an intergenic region on chr20. Both breakpoints have one extra copy starting from the breakpoint. STX12 is a SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi networkInterchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known.



Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.

CASP3, caspase 3 is involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9.




Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. Interchromosomal translocation with breakpoint on chr7 in intron 4 of the EXOC4 gene. The breakpoint on chr19 is in intergenic region, but in the PSG gene cluster, close to where the adenoviral DNA has integrated. EXOC4 is a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.



Deletion inside intron 18 of CACNA1B.Voltage-dependent N-type calcium channel subunit alpha-1B, Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by omega-conotoxin-GVIA (omega-CTx-GVIA) and by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), and omega-agatoxin-IVA (omega-Aga-IVA). Calcium channels containing alpha-1B subunit may play a role in directed migration of immature neurons.Interchromosomal rearrangement with breakpoint on chr10 in intron 7/8 of GDI2 and breakpoint on chr16 in intergenic region. GDI2 is Rab GDP dissociation inhibitor beta, Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them.

Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.

Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses



Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter).

Inversion largely overlapping with inversion 862, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance

Interchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.





MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').



Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.



Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion of 1 of 3 copies spanning 3 genes, creating a fusion gene of VCL and ADK, but if splicing occurs correctly, it's out of frame and immediately terminated. VCL or vinculin is an actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. ADK is adenosine kinase, ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.

Small duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses






MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.



Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.

Small duplication inside intron 1 of KCNMA1. Not clear whether splicing if affected. KCNMA1 is a calcium-activated potassium channel subunit alpha-1. Potassium channel activated by both membrane depolarization or increase in cytosolic Ca2+ that mediates export of K+. It is also activated by the concentration of cytosolic Mg2+. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity.



>Id LeftChr LeftPosition RightChr RightPosition StrandConsiste Type1060 chr1 15422806 chr1 25362531 N probable-inversion4061 chr1 15616806 chr1 25365520 N probable-inversion3863 chr1 43613227 chr1 43613833 Y deletion4020 chr1 148200908 chr5 1616581 N interchromosomal3707 chr2 7014439 chr2 7017433 Y deletion3703 chr2 14595273 chr2 14687504 Y deletion

466 chr2 17110039 chr9 121845640 N interchromosomal1248 chr2 79970949 chr2 80021758 Y tandem-duplication3314 chr2 101343610 chr2 101346945 Y deletion3670 chr2 132747163 chr16 33863532 N interchromosomal3223 chr2 141530911 chr2 141535899 Y deletion1195 chr2 184040004 chr2 184045815 Y tandem-duplication3976 chr2 239732680 chr2 239749389 N probable-inversion1187 chr3 3198211 chr3 3557169 Y tandem-duplication1185 chr3 31908327 chr3 32331754 Y tandem-duplication3139 chr3 32877419 chr3 32877977 Y deletion3125 chr3 53258062 chr3 53258639 Y deletion1183 chr3 53746648 chr3 53907380 Y tandem-duplication

3063 chr3 157438519 chr3 157442174 Y deletion3061 chr3 162162965 chr3 162168702 Y deletion1171 chr3 175553075 chr3 175562478 Y tandem-duplication3057 chr3 175781833 chr3 175804340 Y deletion1154 chr4 91221327 chr4 91766481 Y tandem-duplication2945 chr4 181852936 chr4 182128860 Y deletion

445 chr4 185742332 chr4 185964343 N probable-inversion

2937 chr4 186576504 chr4 186577558 Y deletion1005 chr4 191179790 chr18 102542 Y interchromosomal1142 chr5 16185352 chr5 16230925 Y tandem-duplication2899 chr5 24463678 chr5 24464258 Y deletion

304 chr5 58472099 chr5 58568016 N probable-inversion3633 chr5 58550632 chr5 59365648 N probable-inversion3631 chr5 91151582 chr5 91172716 N probable-inversion1787 chr5 92857497 chrX 10023488 Y interchromosomal

301 chr5 93735869 chr5 93738713 N probable-inversion1824 chr5 95657489 chr17 54648511 Y interchromosomal

298 chr5 107230463 chr5 166031020 N complex2740 chr5 107230627 chr5 163382944 Y complex

182 chr5 107269272 chr16 70044674 N interchromosomal997 chr5 116211166 chr5 163407056 Y tandem-duplication

2745 chr5 120253252 chr5 120495940 Y deletion2743 chr5 121952170 chr5 121955333 Y deletion2731 chr5 133458702 chr5 179587691 Y deletion

993 chr5 155347893 chr5 155505348 Y tandem-duplication292 chr5 156513349 chr5 169341706 N probable-inversion

2477 chr5 156527451 chr10 133957281 Y interchromosomal992 chr5 162966905 chr5 166048108 Y tandem-duplication290 chr5 163382944 chr5 166031020 N complex

2715 chr5 165104041 chr5 165236386 Y deletion3618 chr5 171414553 chr5 175274688 N probable-inversion3617 chr5 179718847 chr5 179720687 N probable-inversion

283 chr6 82135227 chr6 82147560 N probable-inversion973 chr6 84647694 chr6 84660140 Y tandem-duplication972 chr6 101150970 chr6 101345173 Y tandem-duplication969 chr6 138141828 chr6 138155014 Y tandem-duplication281 chr6 143291260 chr6 143295957 N probable-inversion967 chr6 157288728 chr6 157305797 Y tandem-duplication

2606 chr6 161561694 chr6 162146100 Y deletion

951 chr7 18091940 chr7 18149879 Y tandem-duplication1821 chr7 47974703 chr17 44224376 Y interchromosomal

944 chr7 71284485 chr7 71374368 Y tandem-duplication2496 chr7 151795880 chr7 151796549 Y deletion2452 chr8 8764151 chr8 8766092 Y deletion2409 chr8 90914794 chr8 91965062 Y deletion2408 chr8 94209883 chr8 94211891 Y complex3570 chr8 94211774 chr8 94212776 N complex

914 chr8 136785168 chr8 136787585 Y tandem-duplication913 chr8 141740921 chr8 141751457 Y tandem-duplication

2343 chr9 73121629 chr9 73291697 Y deletion101 chr9 119456103 chr21 14091937 N interchromosomal

3558 chr9 121829943 chr9 121849385 N probable-inversion901 chr9 122527431 chr9 123058804 Y tandem-duplication

3557 chr9 122733488 chr9 122775193 N probable-inversion819 chr9 134379060 chr13 31015963 Y interchromosomal859 chr10 46548420 chr10 46569521 Y tandem-duplication

3546 chr10 59943899 chr10 72057756 N complex2240 chr10 62860591 chr10 72057866 Y complex3545 chr10 63508026 chr10 63508237 N probable-inversion2232 chr10 84422076 chr10 84623549 Y deletion3541 chr10 84424587 chr10 84631678 N probable-inversion

152 chr10 135349718 chr18 101377 N interchromosomal2185 chr11 19708432 chr11 19714181 Y deletion


826 chr11 122516385 chr11 122737894 Y tandem-duplication2101 chr12 6718000 chr12 6718785 Y deletion2041 chr12 120630979 chr12 120632071 Y deletion2017 chr13 30094958 chr13 30095770 Y deletion1985 chr13 68813467 chr13 68815641 Y deletion

770 chr15 23497698 chr15 23504594 Y tandem-duplication769 chr15 23538771 chr15 23542711 Y tandem-duplication754 chr16 20151282 chr16 20199992 Y tandem-duplication753 chr16 24413589 chr16 24633756 Y tandem-duplication669 chr16 76614057 chr16 76838182 Y tandem-duplication664 chr17 37065806 chr17 37344668 Y tandem-duplication


1605 chr18 31924384 chr18 31927139 Y deletion589 chr19 2058995 chr19 2200476 Y tandem-duplication566 chr19 36444847 chr19 36758282 Y tandem-duplication

1502 chr20 14547213 chr20 14811306 Y deletion1501 chr20 14991805 chr20 15632692 Y deletion1460 chr20 61981514 chr20 61982274 Y deletion1346 chrX 12388664 chrX 13756544 Y deletion1315 chrX 93233376 chrX 93236393 Y deletion1310 chrX 117719016 chrX 117720346 Y deletion1309 chrX 117905654 chrX 117907917 Y deletion

RelatedJunctio Also present in other li Notesprobable-inversion No annotated elements involved. Large inversion with both breakpoints in intergenic region.probable-inversion Inversion largely overlapping with inversion 1060, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance

No annotated elements involved.interchromosomal Interchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.

Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known. No annotated elements involved.

interchromosomal No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.tandem-duplication Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation

Small deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.interchromosomal See Flp, 4461

Partial deletion of LRP1B, 1 of 3 copies deleted at exons 8-14 and a big part of intron 7. Around exons 8 and 9 probably two copies deleted. LRP1B: tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.tandem-duplication No annotated elements involved.probable-inversion Small deletion inside HDAC4 gene, comprising most of introns 6 and 7 and exon 7. It's hard to say how many alleles have been hit from the CNV data. Probaby at least 2 copies intact. HDAC4 is Histone deacetylase 4, responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.tandem-duplication No annotated elements involved.tandem-duplication Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.

Small deletion inside intron 1 of TRIM71 gene. Since it's smaller than 2kb it cannot be deduced how many copies are affected. Not known whether splicing is affected. TRIM71: putative role, may be involved in controlling the timing of organ formation during development.Small deletion in the middle of intron 1 of TKT. Not known whether splicing is affected. TKT: transketolase, an enzyme from the pentose phosphate pathway to make precursor sugars for nucleotides. Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.

tandem-duplication Tandem duplication with left breakpoint in CACNA1D. No fusion genes are created. Duplicated genes: CHDH, IL17RB, ACTR8, SELK.CACNA1D: Voltage-dependent L-type calcium channel subunit alpha-1D. Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1D gives rise to L-type calcium currents. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group. CHDH: Choline dehydrogenase, mitochondrial. IL17RB, Interleukin-17 receptor B, Receptor for the proinflammatory cytokines IL17B and IL17E. May play a role in controlling the growth and/or differentiation of hematopoietic cells. ACTR8, Actin-related protein 8, Plays an important role in the functional organization of mitotic chromosomes. Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage. SELK, Selenoprotein K, further details not known.Small deletion inside intron 1 of the two longest isoforms of KCNAB1: Voltage-gated potassium channel subunit beta-1. Accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. All three isoforms alter the functional properties of Kv1.4 and Kv1.5. Isoform KvB1.2 has no effect on Kv1.1, Kv1.2 or Kv2.1.Small deletion comprising exon 1 and small parts of flanking introns of PPM1L. Not clear how many copies affected but comparing to SG it is probably 1 of 3. PPM1L is a protein phosphatase 1L, Acts as a suppressor of the SAPK signaling pathways by associating with and dephosphorylating MAP3K7/TAK1 and MAP3K5, and by attenuating the association between MAP3K7/TAK1 and MAP2K4 or MAP2K6.

tandem-duplication No annotated elements involved.No annotated elements involved.

tandem-duplication Tandem duplication comprising the first part of FAM190A. Function unknown.No annotated elements involved.

probable-inversion Inversion with left breakpoint in intergenic region and right breakpoint in ACSL1 gene. A loss of 1 copy in this inversion seems to be the case, 2 instead of 3 copies in SG, but not in SGendoT (overall only 2 copies in this region. Affected genes: CASP3, CCDC111, MLF1IP and ACSL1. CASP3, caspase 3 is involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9.CCDC111, function unknown.MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').Small deletion, comprising exons 3 and 4 of the UFSP2 gene. It is a thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, an ubiquitin-like modifier protein bound to a number of target proteins. Not clear how many copies have been deleted, but most prabably not all.

interchromosomal Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.tandem-duplication Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids

No annotated elements involved.probable-inversion See separate word documentprobable-inversion See separate word documentprobable-inversion See separate word documentinterchromosomal See separate word documentprobable-inversion See separate word documentinterchromosomal See separate word document

290;2740 See separate word document290;298 See separate word document

interchromosomal See separate word documenttandem-duplication See separate word document

No annotated elements involved.No annotated elements involved.See separate word document

tandem-duplication See separate word documentprobable-inversion See separate word documentinterchromosomal See separate word documenttandem-duplication See separate word document

298;2740 See separate word documentSee separate word document

probable-inversion See separate word documentprobable-inversion See separate word documentprobable-inversion No annotated elements involved.tandem-duplication Tandem duplication inside CYB5R4 gene, involving exon 3 and parts of the flanking introns. Probably 2 unaffected copies and one duplicated copy. CYB5R4 is Cytochrome b5 reductase 4, NADH-cytochrome b5 reductase involved in endolasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.tandem-duplication Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.tandem-duplication No annotated elements involved.probable-inversion Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.tandem-duplication Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.

Deletion creating a PARK2-AGPAT4 fusion gene, joining intron 3/5/6 (depending on splice form) of PARK2 to intron 2 of AGPAT4. This creates a fusion gene with out of frame joining and subsequently the resulting protein would terminate with about 40 extra amino acids after PARK2 exon 3/5/6/, but not the same as AGPAT4. Also, at least 3 intact copies remain. PARK2: Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.AGPAT4: 1-acyl-sn-glycerol-3-phosphate acyltransferase delta, Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone.

tandem-duplication No annotated elements involved.interchromosomal Interchromosomal rearrangement with breakpoint on chr7 in intron 6 of HUS1 and breakpoint on chr17 in intron 1/8 of TTLL6, thus creating a strand consistent TTLL6-HUS1 fusion gene, containing the 5' TTLL6 and the 3' HUS1 ends. The fusion gene is joined out of frame creating a truncated TTLL6 in effect, with 1 extra amino acid before termination.

TTLL6 is a putative polyglutamylase which preferentially modifies alpha-tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation stepHUS1: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase.

tandem-duplication duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning. No annotated elements involved.Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised. Left breakpoint is intergenic region, right breakpoint is inside NECAB1. It seems to concern a deletion of 1 of 4 copies. NECAB1 is N-terminal EF-hand calcium-binding protein 1, but not much is known about it. Inside this deletion are OSGIN2, DECR1, NBN, CALB1 and TMEM64. But thery are all still present in three copies.

3570 No annotated elements involved.2408 No annotated elements involved.

tandem-duplication No annotated elements involved.tandem-duplication Duplication comprising exon 29 and 30 and parts of the flanking introns of PTK2. Copy number from 2 to 3, so probably one intact copy and one affected copy. PTK2 is Focal adhesion kinase 1. Non-receptor protein-tyrosine kinase implicated in signaling pathways involved in cell motility, proliferation and apoptosis. Activated by tyrosine-phosphorylation in response to either integrin clustering induced by cell adhesion or antibody cross-linking, or via G-protein coupled receptor (GPCR) occupancy by ligands such as bombesin or lysophosphatidic acid, or via LDL receptor occupancy. Microtubule-induced dephosphorylation at Tyr-397 is crucial for the induction of focal adhesion disassembly. Plays a potential role in oncogenic transformations resulting in increased kinase activity.

No annotated elements involved.interchromosomal No annotated elements involved. Interchromosomal rearrangement with both breakpoint on chr9 and chr21 in intergenic region.probable-inversion No annotated elements involved.tandem-duplication Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.


probable-inversion A probable inversion comprising part of the C5 complement gene (C5). It's a region with 4 copies.interchromosomal Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.tandem-duplication Tandem duplication generating a 6 or 7 copy island inside a 3 or 4 copy region. The LOC728643 gene is involved. It's a gene with unknown function.

2240 Complex rearrangement together with 2240 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.3546 Complex rearrangement together with 3546 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.

probable-inversion Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.

probable-inversion Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.interchromosomal No annotated elements invloved. Interchromosomal rearrangement with breakpoint on chr10 at the very telomeric end of the q arm, in intergenic region. The breakpoint on chr18 is also in the telomeric region, but on the p arm. It's also in intergenic region.

Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. tandem-duplication Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemtandem-duplication Small duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses

tandem-duplication Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.See Flp, 2608.

No annotated elements involved.See Flp, 2530

No annotated elements involved.tandem-duplication Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VAtandem-duplication Small duplication inside intron 2 of ATP10A. Not clear whether wplicing is affected. Probable phospholipid-transporting ATPase VA. Not many details known.tandem-duplication No annotated elements involved.tandem-duplication Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.tandem-duplication Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. tandem-duplication Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.

eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).

tandem-duplication Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. tandem-duplication Tandem duplication with left breakpoint inside intron 10 of CCDC57 and right breakpoint inside intron 5 of C17orf101 thus creating a C17orf101-CCDC57 fusion gene. If splicing occurs correctly, it happens in frame! It would contain the cytoplasmic, transmembrane and a short part of the lumenal domain of C17orf101 and the second but not the first coiled coil domain of CCDC57 and its C-terminal domain.

CCDC57 is a Coiled-coil domain-containing protein 57 for which no further information is known.C17orf101 is PKHD domain-containing transmembrane protein C17orf101No annotated elements involved.

tandem-duplication Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. tandem-duplication Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter).

Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.Deletion comprising exons 6-8 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left.

See Flp, 225Deletion joining FRMPD4 and GPM6B in a strand inconsistent way, so no functional fusion gene is created. One of three copies deleted.No annotated elements involved.No annotated elements involved.No annotated elements involved.

No annotated elements involved. Large inversion with both breakpoints in intergenic region.Inversion largely overlapping with inversion 1060, left breakpoint in first intron of EFHD2 gene. There are probably 4 copies before and 3 copies after the breakpoint. EFHD2 is a protein that may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis (putative activity). Plays a role as negative regulator of the canonical NF-kappa-B-activating branch (putative activity). Controls spontaneous apoptosis through the regulation of BCL2L1 abundance

Interchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.Small deletion inside intron 2 of the RNF144A gene. RNF144A is a ring finger protein, E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Further no details known.

No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulationSmall deletion inside intron 2 of the CREG2 gene. It's a gene with unknown function, and a putative secreted glycoprotein with brain-specific expression.

Partial deletion of LRP1B, 1 of 3 copies deleted at exons 8-14 and a big part of intron 7. Around exons 8 and 9 probably two copies deleted. LRP1B: tumor suppressor gene LRP1B, potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis. Gene is known to be partially deleted in non small cell lung carcinoma.


Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.Small deletion inside intron 1 of TRIM71 gene. Since it's smaller than 2kb it cannot be deduced how many copies are affected. Not known whether splicing is affected. TRIM71: putative role, may be involved in controlling the timing of organ formation during development.Small deletion in the middle of intron 1 of TKT. Not known whether splicing is affected. TKT: transketolase, an enzyme from the pentose phosphate pathway to make precursor sugars for nucleotides. Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.Tandem duplication with left breakpoint in CACNA1D. No fusion genes are created. Duplicated genes: CHDH, IL17RB, ACTR8, SELK.CACNA1D: Voltage-dependent L-type calcium channel subunit alpha-1D. Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1D gives rise to L-type calcium currents. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group.

IL17RB, Interleukin-17 receptor B, Receptor for the proinflammatory cytokines IL17B and IL17E. May play a role in controlling the growth and/or differentiation of hematopoietic cells. ACTR8, Actin-related protein 8, Plays an important role in the functional organization of mitotic chromosomes. Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage.

Small deletion inside intron 1 of the two longest isoforms of KCNAB1: Voltage-gated potassium channel subunit beta-1. Accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. All three isoforms alter the functional properties of Kv1.4 and Kv1.5. Isoform KvB1.2 has no effect on Kv1.1, Kv1.2 or Kv2.1.Small deletion comprising exon 1 and small parts of flanking introns of PPM1L. Not clear how many copies affected but comparing to SG it is probably 1 of 3. PPM1L is a protein phosphatase 1L, Acts as a suppressor of the SAPK signaling pathways by associating with and dephosphorylating MAP3K7/TAK1 and MAP3K5, and by attenuating the association between MAP3K7/TAK1 and MAP2K4 or MAP2K6.

Tandem duplication comprising the first part of FAM190A. Function unknown.


MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').Small deletion, comprising exons 3 and 4 of the UFSP2 gene. It is a thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, an ubiquitin-like modifier protein bound to a number of target proteins. Not clear how many copies have been deleted, but most prabably not all.Interchromosomal translocation, breakpoint on chr4 in intergenic region and on chr18 in ROCK1P1 a pseudogene.Duplication comprising part of exon 2, and part of intron 2 of MARCH11. E3 ubiquitin-protein ligase that mediates polyubiquitination of CD4. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. May play a role in ubuquitin-dependent protein sorting in developmenting spermatids

Tandem duplication inside CYB5R4 gene, involving exon 3 and parts of the flanking introns. Probably 2 unaffected copies and one duplicated copy. CYB5R4 is Cytochrome b5 reductase 4, NADH-cytochrome b5 reductase involved in endolasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.Tandem duplication of part of ASCC3, breakpoints in intron 8 and intron 34. ASCC3 enhances NF-kappa-B, SRF and AP1 transactivation.

Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. Deletion creating a PARK2-AGPAT4 fusion gene, joining intron 3/5/6 (depending on splice form) of PARK2 to intron 2 of AGPAT4. This creates a fusion gene with out of frame joining and subsequently the resulting protein would terminate with about 40 extra amino acids after PARK2 exon 3/5/6/, but not the same as AGPAT4. Also, at least 3 intact copies remain. PARK2: Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.AGPAT4: 1-acyl-sn-glycerol-3-phosphate acyltransferase delta, Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone.

Interchromosomal rearrangement with breakpoint on chr7 in intron 6 of HUS1 and breakpoint on chr17 in intron 1/8 of TTLL6, thus creating a strand consistent TTLL6-HUS1 fusion gene, containing the 5' TTLL6 and the 3' HUS1 ends. The fusion gene is joined out of frame creating a truncated TTLL6 in effect, with 1 extra amino acid before termination.TTLL6 is a putative polyglutamylase which preferentially modifies alpha-tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation stepHUS1: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning.

Small deletion inside intron 1 of MFHAS1. Hard to tell how many copies affected, probably all. Not sure whether splicing is compromised. Left breakpoint is intergenic region, right breakpoint is inside NECAB1. It seems to concern a deletion of 1 of 4 copies. NECAB1 is N-terminal EF-hand calcium-binding protein 1, but not much is known about it. Inside this deletion are OSGIN2, DECR1, NBN, CALB1 and TMEM64. But thery are all still present in three copies.

Duplication comprising exon 29 and 30 and parts of the flanking introns of PTK2. Copy number from 2 to 3, so probably one intact copy and one affected copy. PTK2 is Focal adhesion kinase 1. Non-receptor protein-tyrosine kinase implicated in signaling pathways involved in cell motility, proliferation and apoptosis. Activated by tyrosine-phosphorylation in response to either integrin clustering induced by cell adhesion or antibody cross-linking, or via G-protein coupled receptor (GPCR) occupancy by ligands such as bombesin or lysophosphatidic acid, or via LDL receptor occupancy. Microtubule-induced dephosphorylation at Tyr-397 is crucial for the induction of focal adhesion disassembly. Plays a potential role in oncogenic transformations resulting in increased kinase activity.

No annotated elements involved. Interchromosomal rearrangement with both breakpoint on chr9 and chr21 in intergenic region.

Duplication with breakpoints in intergenic region, comprising many genes. Relevant ones are shown below.TRAF1: Adapter molecule that regulates the activation of NF-kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.CEP110, Centriolin, Involved in cell cycle progression and cytokinesis. During the late steps of cytokinesis, anchors exocyst and SNARE complexes at the midbody, thereby allowing secretory vesicle-mediated abscission.A probable inversion comprising part of the C5 complement gene (C5). It's a region with 4 copies.Interchromosomal translocation. Breakpoint on chr9 is in third intron of C9orf171, breakpoint on chr13 is in intergenic region. C9orf171 is an uncharacterized protein.Tandem duplication generating a 6 or 7 copy island inside a 3 or 4 copy region. The LOC728643 gene is involved. It's a gene with unknown function.Complex rearrangement together with 2240 comprising many genes. Breakpoints are at TMEM26 and intergenic region. TMEM26: unknown function.Complex rearrangement together with 3546 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.No annotated elements invloved. Interchromosomal rearrangement with breakpoint on chr10 at the very telomeric end of the q arm, in intergenic region. The breakpoint on chr18 is also in the telomeric region, but on the p arm. It's also in intergenic region.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses

Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

Tandem duplication comprising exons 11, 12 and 13 of ATP10A. Probably 1 extra copy on 3 present. ATP10A is Probable phospholipid-transporting ATPase VASmall duplication inside intron 2 of ATP10A. Not clear whether wplicing is affected. Probable phospholipid-transporting ATPase VA. Not many details known.

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.FKBP10: Peptidyl prolyl cis-trans isomerase, accelerates the folding of proteins during protein synthesis.ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. Tandem duplication with left breakpoint inside intron 10 of CCDC57 and right breakpoint inside intron 5 of C17orf101 thus creating a C17orf101-CCDC57 fusion gene. If splicing occurs correctly, it happens in frame! It would contain the cytoplasmic, transmembrane and a short part of the lumenal domain of C17orf101 and the second but not the first coiled coil domain of CCDC57 and its C-terminal domain.CCDC57 is a Coiled-coil domain-containing protein 57 for which no further information is known.C17orf101 is PKHD domain-containing transmembrane protein C17orf101

Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.Deletion comprising exons 6-8 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left.

Deletion joining FRMPD4 and GPM6B in a strand inconsistent way, so no functional fusion gene is created. One of three copies deleted.



No annotated elements involved. Interchromosomal translocation with breakpoint on chr2 in intergenic region and breakpoint on chr9 also in intergenic region, but inside a probable inversion.Tandem duplication comprising exon 7 and a part of up- and downstream introns of CTNNA2 gene. Copy number probably from 3 to 4. CTNNA2 is catenin alpha-2. May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system. Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation



Tandem duplication with left breakpoint in the OSBPL10 gene and right breakpoint in CMTM8 gene. Since both genes are on the opposite strands, no fusion gene is formed. GPD1L is duplicated from 3 to 4 copies. GPD1L is Glycerol-3-phosphate dehydrogenase 1-like protein, which plays a role in regulating cardiac sodium current; decreased enzymatic activity with resulting increased levels of glycerol 3-phosphate activating the DPD1L-dependent SCN5A phosphorylation pathway, may ultimately lead to decreased sodium current; cardiac sodium current may also be reduced due to alterations of NAD(H) balance induced by DPD1L.Small deletion inside intron 1 of TRIM71 gene. Since it's smaller than 2kb it cannot be deduced how many copies are affected. Not known whether splicing is affected. TRIM71: putative role, may be involved in controlling the timing of organ formation during development.Small deletion in the middle of intron 1 of TKT. Not known whether splicing is affected. TKT: transketolase, an enzyme from the pentose phosphate pathway to make precursor sugars for nucleotides. Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.

CACNA1D: Voltage-dependent L-type calcium channel subunit alpha-1D. Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1D gives rise to L-type calcium currents. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group.

IL17RB, Interleukin-17 receptor B, Receptor for the proinflammatory cytokines IL17B and IL17E. May play a role in controlling the growth and/or differentiation of hematopoietic cells. ACTR8, Actin-related protein 8, Plays an important role in the functional organization of mitotic chromosomes. Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage.





Tandem duplication inside CYB5R4 gene, involving exon 3 and parts of the flanking introns. Probably 2 unaffected copies and one duplicated copy. CYB5R4 is Cytochrome b5 reductase 4, NADH-cytochrome b5 reductase involved in endolasmic reticulum stress response pathway. Plays a critical role in protecting pancreatic beta-cells against oxidant stress, possibly by protecting the cell from excess buildup of reactive oxygen species (ROS). Reduces a variety of substrates in vitro, such as cytochrome c, feericyanide and methemoglobin.

Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. Deletion creating a PARK2-AGPAT4 fusion gene, joining intron 3/5/6 (depending on splice form) of PARK2 to intron 2 of AGPAT4. This creates a fusion gene with out of frame joining and subsequently the resulting protein would terminate with about 40 extra amino acids after PARK2 exon 3/5/6/, but not the same as AGPAT4. Also, at least 3 intact copies remain. PARK2: Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.AGPAT4: 1-acyl-sn-glycerol-3-phosphate acyltransferase delta, Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone.

Interchromosomal rearrangement with breakpoint on chr7 in intron 6 of HUS1 and breakpoint on chr17 in intron 1/8 of TTLL6, thus creating a strand consistent TTLL6-HUS1 fusion gene, containing the 5' TTLL6 and the 3' HUS1 ends. The fusion gene is joined out of frame creating a truncated TTLL6 in effect, with 1 extra amino acid before termination.TTLL6 is a putative polyglutamylase which preferentially modifies alpha-tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation stepHUS1: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning.




Complex rearrangement together with 3546 comprising many genes. Breakpoints are at the very beginning of BICC1 and intergenic region. BICC1: Putative RNA-binding protein. May be involved in regulating gene expression during embryonic development.Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.No annotated elements invloved. Interchromosomal rearrangement with breakpoint on chr10 at the very telomeric end of the q arm, in intergenic region. The breakpoint on chr18 is also in the telomeric region, but on the p arm. It's also in intergenic region.Small deletion inside intron 1 of NAV2. Probably 1 of 3 copies deleted. Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses

Tandem duplication with the first breakpoint inside the first intron of ASAM, May be involved in cell-cell adhesion of adipocytes. May play a role in adipocyte differentiation and development of obesity.

Tandem duplication with no annotated elements on the breakpoints. RBBP6 lies inside. Probably one extra copy on 3 already present. RBBP6 is an E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth.Tandem duplication with left breakpoint right before the first exon of CLEC3A and the left breakpoint inside intron 6 of WWOX. Thus not creating any fusion genes. Duplication of CLEC3A, but doubtful if the second copy has an operational promotor. CLEC3A is: C-type lectin domain family 3 member A, Promotes cell adhesion to laminin-332 and fibronectin. WWOX is: Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. Required for normal bone development By similarity. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. May also play a role in tumor necrosis factor (TNF)-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm. Large tandem duplication not creating any fusion genes. Right breakpoint is inside first intron of TTC25. Relevant duplicated genes shown below. TTC25 gene: function unknown.eIF1: translation factor 1. Necessary for scanning and involved in initiation site selection. Promotes the assembly of 48S ribosomal complexes at the authentic initiation codon of a conventional capped mRNA.

ATP-citrate synthase, ATP citrate-lyase is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues. Has a central role in de novo lipid synthesis. In nervous tissue it may be involved in the biosynthesis of acetylcholine.Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. Tandem duplication with left breakpoint inside intron 10 of CCDC57 and right breakpoint inside intron 5 of C17orf101 thus creating a C17orf101-CCDC57 fusion gene. If splicing occurs correctly, it happens in frame! It would contain the cytoplasmic, transmembrane and a short part of the lumenal domain of C17orf101 and the second but not the first coiled coil domain of CCDC57 and its C-terminal domain.

Tandem duplication joining AP3D1 and AMH, but in a strand inconsistent way, thus not creating a functional fusion gene. DOT1L (Histone methyltransferase. Methylates 'Lys-79' of histone H3. Nucleosomes are preferred as substrate compared to free histones. Binds to DNA), PLEKHJ1 (function unknown) and SF3A2 (Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. ) are duplicated. Duplication comprising TSHZ3 gene (Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s). Regulates the development of neurons involved in both respiratory rythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter). Deletion comprising exon 5 and parts of flanking introns of MACROD2. It's a O-acetyl-ADP-ribose deacetylases, might be involved in cancer. Only one copy is left. Further down the gene are more parts deleted.







Small deletion in the middle of intron 1 of TKT. Not known whether splicing is affected. TKT: transketolase, an enzyme from the pentose phosphate pathway to make precursor sugars for nucleotides. Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.


ACTR8, Actin-related protein 8, Plays an important role in the functional organization of mitotic chromosomes. Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage.






Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. Deletion creating a PARK2-AGPAT4 fusion gene, joining intron 3/5/6 (depending on splice form) of PARK2 to intron 2 of AGPAT4. This creates a fusion gene with out of frame joining and subsequently the resulting protein would terminate with about 40 extra amino acids after PARK2 exon 3/5/6/, but not the same as AGPAT4. Also, at least 3 intact copies remain. PARK2: Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

Interchromosomal rearrangement with breakpoint on chr7 in intron 6 of HUS1 and breakpoint on chr17 in intron 1/8 of TTLL6, thus creating a strand consistent TTLL6-HUS1 fusion gene, containing the 5' TTLL6 and the 3' HUS1 ends. The fusion gene is joined out of frame creating a truncated TTLL6 in effect, with 1 extra amino acid before termination.

HUS1: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase.duplication inside intron 2/3 (depends on splice form) of CALN1. No exons or splice sites hit. CALN1 is a protein that negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity By similarity. May play a role in the physiology of neurons and is potentially important in memory and learning.




Small inversion inside intron 8 of ARID5B. Doubtful whether it affects splicing. ARID5B is a transcription coactivator that binds to the 5'-AATA[CT]-3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.Deletion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.Inversion comprising exon 3/4 and 4/5 of NRG3 (depending on splice form) and parts of the flanking introns. Direct ligand for the ERBB4 tyrosine kinase receptor. Binding results in ligand-stimulated tyrosine phosphorylation and activation of the receptor. Does not bind to the EGF receptor, ERBB2 or ERBB3 receptors. May be a survival factor for oligodendrocytes.

Small tandem duplication comprising exon 4/5 and 5/6 of MPPED2, in effect doubling the C-terminal part of the protein, except the last exon. 4 copies in this duplication. Metallophosphoesterase MPPED2 displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous systemSmall duplication inside intron 1/7 (depending on splice form) of DLG2. Not clear whether splicing is affected. DLG2 is required for perception of chronic pain through NMDA receptor signaling. Regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord. Interacts with the cytoplasmic tail of NMDA receptor subunits as well as inward rectifying potassium channels. Involved in regulation of synaptic stability at cholinergic synapses. Part of the postsynaptic protein scaffold of excitatory synapses


Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. Tandem duplication with left breakpoint inside intron 10 of CCDC57 and right breakpoint inside intron 5 of C17orf101 thus creating a C17orf101-CCDC57 fusion gene. If splicing occurs correctly, it happens in frame! It would contain the cytoplasmic, transmembrane and a short part of the lumenal domain of C17orf101 and the second but not the first coiled coil domain of CCDC57 and its C-terminal domain.



Interchromosomal translocation with breakpoint on chr1 in intron 6 of OTUD7B and breakpoint on chr5 in intergenic region. Thus no fusion genes are created. Copy number in chr1 probably from 3 to 4 at breakpoint. OTUD7B is a protein with deubiquitinating activity that is directed towards 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. Hydrolyzes both linear and branched forms of polyubiquitin. Negative regulator of nuclear factor NF-kappa-B.





ACTR8, Actin-related protein 8, Plays an important role in the functional organization of mitotic chromosomes. Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage.

Small deletion comprising exon 1 and small parts of flanking introns of PPM1L. Not clear how many copies affected but comparing to SG it is probably 1 of 3. PPM1L is a protein phosphatase 1L, Acts as a suppressor of the SAPK signaling pathways by associating with and dephosphorylating MAP3K7/TAK1 and MAP3K5, and by attenuating the association between MAP3K7/TAK1 and MAP2K4 or MAP2K6.


MLF1IP or Centromere protein U, Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression.ASCL1 or Achaete-scute homolog 1 is a transcriptional regulator. May play a role at early stages of development of specific neural lineages in most regions of the CNS, and of several lineages in the PNS. Essential for the generation of olfactory and autonomic neurons. Involved in the initiation of neuronal differentiation. Mediates transcription activation by binding to the E box (5'-CANNTG-3').



Small inversion inside first intron of HIVEP2. This protein specifically binds to the DNA sequence 5'-GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, somatostatin receptor II, and interferon-beta genes. It may act in T-cell activation.Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.

PARK2: Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene.

HUS1: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of C12orf32/RHINO to sites of double-stranded breaks (DSB) occurring during the S phase.






Tandem duplication with left breakpoint in intergenic region, and right breakpoint in SPAG9, thus not creating any fusion genes. Duplicated genes inside: WFIKKN2 (Protease-inhibitor that contains multiple distinct protease inhibitor domains. Probably has serine protease- and metalloprotease-inhibitor activity. Inhibits the biological activity of mature myostatin, but not activin)and TOB1 (Anti-proliferative protein that interacts with the erbB-2 receptor tyrosine kinase. May physically and/or functionally interact with protein-tyrosine kinase receptors.).Tandem duplication fusing RNFT1 and TMEM49, but in a strand inconsistend way, so not creating any functional fusion genes. TUBD1 (tubulin delta chain, In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head) and RPS6K1 (Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. ) are duplicated. Tandem duplication with left breakpoint inside intron 10 of CCDC57 and right breakpoint inside intron 5 of C17orf101 thus creating a C17orf101-CCDC57 fusion gene. If splicing occurs correctly, it happens in frame! It would contain the cytoplasmic, transmembrane and a short part of the lumenal domain of C17orf101 and the second but not the first coiled coil domain of CCDC57 and its C-terminal domain.



Tandem duplication comprising exon 4/5 and parts of the flanking introns of ARID1B. Probably 1 of 4 copies affected. ARID1B is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.






SymbolABL1ABL2ACSL3AF15Q14 (CASC5)AF1Q (MLLT11)AF3p21 ( NCKIPSD)AF5q31 (AFF4)AKAP9AKT1AKT2ALDH2ALKALO17 (RNF213)APCARHGEF12ARHH (RHOH)ARID1AARID2ARNTASPSCR1ASXL1ATF1ATICATMATRXBAP1BCL10BCL11ABCL11BBCL2BCL3BCL5 (BCL6)BCL6BCL7ABCL9BCRBHDBIRC3BLMBMPR1ABRAFBRCA1BRCA2BRD3BRD4

BRIP1BTG1BUB1BC12orf9C15orf21C15orf55C16orf75CANT1CARD11CARSCBFA2T1 (runx1t1)CBFA2T3CBFBCBL CBLBCBLCCCNB1IP1CCND1CCND2CCND3CCNE1CD273 (PDCD1LG2)CD274CD74CD79ACD79BCDH1CDH11CDK12CDK4CDK6CDKN2A -p16(INK4a) CDKN2A- p14ARFCDKN2CCDX2CEBPACEP1 (CEP110)CHCHD7CHEK2CHIC2CHN1CICCIITACLTCCLTCL1CMKOR1 (CXCR7)COL1A1COPEBCOX6CCREB1

CREB3L1CREB3L2CREBBPCRLF2CRTC3CTNNB1CYLDD10S170 (CCDC6)DAXXDDB2DDIT3DDX10DDX5DDX6DEKDICER1DNMT3ADUX4EBF1EGFREIF4A2ELF4ELK4ELKS (ERC1)ELLELNEML4EP300EPS15ERBB2ERCC2ERCC3ERCC4ERCC5ERG ETV1ETV4ETV5ETV6EVI1EWSR1EXT1EXT2EZH2FACL6 (ACSL6)FANCAFANCCFANCD2FANCEFANCF

FANCGFBXW7FCGR2BFEVFGFR1FGFR1OPFGFR2FGFR3FHFHITFIP1L1FLI1FLJ27352FLT3FNBP1FOXL2FOXO1A (FOXO1)FOXO3AFOXP1FSTL3FUBP1FUSFVT1 (KDSR)GAS7GATA1GATA2GATA3GMPSGNA11GNAQGNASGOLGA5GOPCGPC3GPHNGRAF (ARHGAP26)HCMOGT-1 (CYTSB)HEAB (CLP1)HEI10 (CCNB1IP1)HERPUD1HIP1HIST1H4IHLFHLXB9 (MNX1)HMGA1HMGA2HNRNPA2B1HOOK3HOXA11

HOXA13HOXA9HOXC11HOXC13HOXD11HOXD13HRASHRPT2HSPCA (HSP90AA1)HSPCB (HSP90AB1)IDH1IDH2IGH@IGK@IGL@IKZF1IL2IL21RIL6STIL7RIRF4IRTA1 (FCRL4)ITKJAK1JAK2JAK3JAZF1JUNKDM5AKDM5CKDM6AKDRKIAA1549KITKLK2KRASKTN1LAF4 (AFF3)LASP1LCKLCP1LCX (TET1)LHFPLIFRLMO1LMO2LPPLYL1MADH4 (SMAD4)MAF

MAFBMALT1MAML2MAP2K4MDM2MDM4MDS1 (MECOM)MDS2MECT1 (CRTC1)MED12MEN1METMHC2TA (CIITA)MITFMKL1MLF1MLH1MLLMLL2MLL3MLLT1MLLT10MLLT2 (AFF1)MLLT3MLLT4MLLT6MLLT7 (FOXO4)MN1MPLMSF (SEPT9)MSH2MSH6MSI2MSNMTCP1MUC1MUTYHMYBMYCMYCL1MYCNMYD88MYH11MYH9MYST4NACANBS1NCOA1NCOA2NCOA4

NDRG1NF1NF2NFE2L2NFIBNFKB2NINNKX2-1NONONOTCH1NOTCH2NPM1NR4A3NRASNSD1NTRK1NTRK3NUMA1NUP214NUP98NUTOLIG2OMDP2RY8PAFAH1B2PALB2PAX3PAX5PAX7PAX8PBRM1PBX1PCM1PCSK7PDE4DIPPDGFBPDGFRAPDGFRBPER1PHOX2BPICALMPIK3CAPIK3R1PIM1PLAG1PMLPMS1PMS2PMX1 (PRRX1)

PNUTL1 (SEPT5)POU2AF1POU5F1PPARGPPP2R1APRCCPRDM1PRDM16PRF1PRKAR1APRO1073 (CCNL1)PSIP2 (PSIP1)PTCHPTENPTPN11RAB5EP (RABEP1)RAD51L1RAF1RALGDSRANBP17RAP1GDS1RARARB1RBM15RECQL4RELRETROS1RPL22RPN1RUNDC2ARUNX1RUNXBP2 (MYST3)SBDSSDH5SDHBSDHCSDHDSEPT6SETSETD2SF3B1SFPQSFRS3SH3GL1SIL (STIL)SLC45A3SMARCA4SMARCB1SMO

SOCS1SOX2SRGAP3SS18SS18L1SSH3BP1 (ABI1)SSX1 SSX2SSX4STK11STLSUFUSUZ12SYKTAF15TAL1TAL2TCEA1TCF1TCF12TCF3TCF7L2TCL1ATCL6TET2TFE3TFEBTFGTFPTTFRCTHRAP3TIF1 (TRIM24)TLX1TLX3TMPRSS2TNFAIP3TNFRSF14TNFRSF17TNFRSF6TOP1TP53TPM3TPM4TPRTRA@TRB@TRD@TRIM27TRIM33TRIP11

TSC1TSC2TSHRTTLUSP6VHLVTI1AWASWHSC1WHSC1L1WIF1WRNWT1WTX (fam123b)XPAXPCXPO1ZNF145 (ZBTB16)ZNF198 (ZMYM2)ZNF278 (PATZ1)ZNF331ZNF384ZNF521ZNF9 (CNBP)ZNFN1A1 (ikzf1)

Name Mutation Type v-abl Abelson murine leukemia viral oncogene homolog 1 T, Misv-abl Abelson murine leukemia viral oncogene homolog 2 Tacyl-CoA synthetase long-chain family member 3 TAF15q14 protein TALL1-fused gene from chromosome 1q TSH3 protein interacting with Nck, 90 kDa (ALL1 fused gene from 3p21) TALL1 fused gene from 5q31 TA kinase (PRKA) anchor protein (yotiao) 9 Tv-akt murine thymoma viral oncogene homolog 1 Misv-akt murine thymoma viral oncogene homolog 2 Aaldehyde dehydrogenase 2 family (mitochondrial) Tanaplastic lymphoma kinase (Ki-1) T, Mis, AKIAA1618 protein Tadenomatous polyposis of the colon gene D, Mis, N, F, SRHO guanine nucleotide exchange factor (GEF) 12 (LARG) TRAS homolog gene family, member H (TTF) TAT rich interactive domain 1A (SWI-like) Mis, N, F, S, DAT rich interactive domain 2 N, S, Faryl hydrocarbon receptor nuclear translocator Talveolar soft part sarcoma chromosome region, candidate 1 Tadditional sex combs like 1 F, N, Misactivating transcription factor 1 T5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase Tataxia telangiectasia mutated D, Mis, N, F, Salpha thalassemia/mental retardation syndrome X-linked Mis, F, NBRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) N, Mis, F, S, OB-cell CLL/lymphoma 10 TB-cell CLL/lymphoma 11A TB-cell CLL/lymphoma 11B (CTIP2) TB-cell CLL/lymphoma 2 TB-cell CLL/lymphoma 3 TB-cell CLL/lymphoma 5 TB-cell CLL/lymphoma 6 T, MisB-cell CLL/lymphoma 7A TB-cell CLL/lymphoma 9 Tbreakpoint cluster region Tfolliculin, Birt-Hogg-Dube syndrome Mis. N, Fbaculoviral IAP repeat-containing 3 TBloom Syndrome Mis, N, Fbone morphogenetic protein receptor, type IA Mis, N, Fv-raf murine sarcoma viral oncogene homolog B1 Mis, T, Ofamilial breast/ovarian cancer gene 1 D, Mis, N, F, Sfamilial breast/ovarian cancer gene 2 D, Mis, N, F, Sbromodomain containing 3 Tbromodomain containing 4 T

BRCA1 interacting protein C-terminal helicase 1 F, N, MisB-cell translocation gene 1, anti-proliferative TBUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) Mis, N, F, Schromosome 12 open reading frame 9 Tchromosome 15 open reading frame 21 Tchromosome 15 open reading frame 55 Tchromosome 16 open reading frame 75 Tcalcium activated nucleotidase 1 Tcaspase recruitment domain family, member 11 Miscysteinyl-tRNA synthetase Tcore-binding factor, runt domain, alpha subunit 2;translocated to, 1 (ETO) Tcore-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16) Tcore-binding factor, beta subunit TCas-Br-M (murine) ecotropic retroviral transforming T, Mis S, OCas-Br-M (murine) ecotropic retroviral transforming sequence b Mis SCas-Br-M (murine) ecotropic retroviral transforming sequence c Mcyclin B1 interacting protein 1, E3 ubiquitin protein ligase Tcyclin D1 Tcyclin D2 Tcyclin D3 Tcyclin E1 Aprogrammed cell death 1 ligand 2 TCD274 molecule TCD74 molecule, major histocompatibility complex, class II invariant chain TCD79a molecule, immunoglobulin-associated alpha O, SCD79b molecule, immunoglobulin-associated beta Mis, Ocadherin 1, type 1, E-cadherin (epithelial) (ECAD) Mis, N, F, Scadherin 11, type 2, OB-cadherin (osteoblast) Tcyclin-dependent kinase 12 Mis, N, Fcyclin-dependent kinase 4 Miscyclin-dependent kinase 6 Tcyclin-dependent kinase inhibitor 2A (p16(INK4a)) gene D, Mis, N, F, Scyclin-dependent kinase inhibitor 2A-- p14ARF protein D, Scyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) Dcaudal type homeo box transcription factor 2 TCCAAT/enhancer binding protein (C/EBP), alpha Mis, N, Fcentrosomal protein 1 Tcoiled-coil-helix-coiled-coil-helix domain containing 7 TCHK2 checkpoint homolog (S. pombe) Fcysteine-rich hydrophobic domain 2 Tchimerin (chimaerin) 1 Tcapicua homolog Mis, F, Sclass II, major histocompatibility complex, transactivator Tclathrin, heavy polypeptide (Hc) Tclathrin, heavy polypeptide-like 1 Tchemokine orphan receptor 1 Tcollagen, type I, alpha 1 Tcore promoter element binding protein (KLF6) Mis, N cytochrome c oxidase subunit VIc TcAMP responsive element binding protein 1 T

cAMP responsive element binding protein 3-like 1 TcAMP responsive element binding protein 3-like 2 TCREB binding protein (CBP) T, N, F, Mis, Ocytokine receptor-like factor 2 Mis, TCREB regulated transcription coactivator 3 Tcatenin (cadherin-associated protein), beta 1 H, Mis, Tfamilial cylindromatosis gene Mis, N, F, SDNA segment on chromosome 10 (unique) 170, H4 gene (PTC1) Tdeath-domain associated protein Mis, F, Ndamage-specific DNA binding protein 2 Mis, NDNA-damage-inducible transcript 3 TDEAD (Asp-Glu-Ala-Asp) box polypeptide 10 TDEAD (Asp-Glu-Ala-Asp) box polypeptide 5 TDEAD (Asp-Glu-Ala-Asp) box polypeptide 6 TDEK oncogene (DNA binding) Tdicer 1, ribonuclease type III Mis F, NDNA (cytosine-5-)-methyltransferase 3 alpha Mis, F, N, Sdouble homeobox, 4 Tearly B-cell factor 1 Tepidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolA, O, Miseukaryotic translation initiation factor 4A, isoform 2 TE74-like factor 4 (ets domain transcription factor) TELK4, ETS-domain protein (SRF accessory protein 1) TELKS protein TELL gene (11-19 lysine-rich leukemia gene) Telastin Techinoderm microtubule associated protein like 4 T300 kd E1A-Binding protein gene T, N, F, Mis, Oepidermal growth factor receptor pathway substrate 15 (AF1p) Tv-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived A, Mis, Oexcision repair cross-complementing rodent repair deficiency, complementation group Mis, N, F, Sexcision repair cross-complementing rodent repair deficiency, complementation group Mis, Sexcision repair cross-complementing rodent repair deficiency, complementation group 4 Mis, N, Fexcision repair cross-complementing rodent repair deficiency, complementation grou Mis, N, Fv-ets erythroblastosis virus E26 oncogene like (avian) Tets variant gene 1 Tets variant gene 4 (E1A enhancer binding protein, E1AF) Tets variant gene 5 Tets variant gene 6 (TEL oncogene) Tecotropic viral integration site 1 TEwing sarcoma breakpoint region 1 (EWS) Tmultiple exostoses type 1 gene Mis, N, F, Smultiple exostoses type 2 gene Mis, N, F, Senhancer of zeste homolog 2 Misfatty-acid-coenzyme A ligase, long-chain 6 TFanconi anemia, complementation group A D, Mis, N, F, SFanconi anemia, complementation group C D, Mis, N, F, SFanconi anemia, complementation group D2 D, Mis, N, FFanconi anemia, complementation group E N, F, SFanconi anemia, complementation group F N, F

Fanconi anemia, complementation group G Mis, N, F, SF-box and WD-40 domain protein 7 (archipelago homolog, Drosophila) Mis, N, D, FFc fragment of IgG, low affinity IIb, receptor for (CD32) TFEV protein - (HSRNAFEV) Tfibroblast growth factor receptor 1 TFGFR1 oncogene partner (FOP) Tfibroblast growth factor receptor 2 Misfibroblast growth factor receptor 3 Mis, Tfumarate hydratase Mis, N, Ffragile histidine triad gene TFIP1 like 1 (S. cerevisiae) TFriend leukemia virus integration 1 TBX648577, FLJ27352 hypothetical LOC145788 Tfms-related tyrosine kinase 3 Mis, Oformin binding protein 1 (FBP17) Tforkhead box L2 Misforkhead box O1A (FKHR) Tforkhead box O3A Tforkhead box P1 Tfollistatin-like 3 (secreted glycoprotein) Tfar upstream element (FUSE) binding protein 1 F, Nfusion, derived from t(12;16) malignant liposarcoma Tfollicular lymphoma variant translocation 1 Tgrowth arrest-specific 7 TGATA binding protein 1 (globin transcription factor 1) Mis, FGATA binding protein 2 MisGATA binding protein 3 F, N, Sguanine monphosphate synthetase Tguanine nucleotide binding protein (G protein), alpha 11 (Gq class) Misguanine nucleotide binding protein (G protein), q polypeptide Misguanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 Misgolgi autoantigen, golgin subfamily a, 5 (PTC5) Tgolgi associated PDZ and coiled-coil motif containing Oglypican 3 T, D, Mis, N, F, Sgephyrin (GPH) TGTPase regulator associated with focal adhesion kinase pp125(FAK) T, F, Ssperm antigen HCMOGT-1 TATP_GTP binding protein Tenhancer of invasion 10 - fused to HMGA2 Thomocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain Thuntingtin interacting protein 1 Thistone 1, H4i (H4FM) Thepatic leukemia factor Thomeo box HB9 Thigh mobility group AT-hook 1 Thigh mobility group AT-hook 2 (HMGIC) Theterogeneous nuclear ribonucleoprotein A2/B1 Thook homolog 3 Thomeo box A11 T

homeo box A13 Thomeo box A9 Thomeo box C11 Thomeo box C13 Thomeo box D11 Thomeo box D13 Tv-Ha-ras Harvey rat sarcoma viral oncogene homolog Mishyperparathyroidism 2 Mis, N, Fheat shock 90kDa protein 1, alpha Theat shock 90kDa protein 1, beta Tisocitrate dehydrogenase 1 (NADP+), soluble Missocitrate dehydrogenase 2 (NADP+), mitochondrial Mimmunoglobulin heavy locus Timmunoglobulin kappa locus Timmunoglobulin lambda locus TIKAROS family zinc finger 1 Dinterleukin 2 Tinterleukin 21 receptor Tinterleukin 6 signal transducer (gp130, oncostatin M receptor) Ointerleukin 7 receptor Mis, Ointerferon regulatory factor 4 Timmunoglobulin superfamily receptor translocation associated 1 TIL2-inducible T-cell kinase TJanus kinase 1 MisJanus kinase 2 T, Mis, OJanus kinase 3 Misjuxtaposed with another zinc finger gene 1 Tjun oncogene Alysine (K)-specific demethylase 5A, JARID1A T

N, F, SD, N, F, S

vascular endothelial growth factor receptor 2 MisKIAA1549 Ov-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Mis, Okallikrein-related peptidase 2 Tv-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog Miskinectin 1 (kinesin receptor) Tlymphoid nuclear protein related to AF4 TLIM and SH3 protein 1 Tlymphocyte-specific protein tyrosine kinase Tlymphocyte cytosolic protein 1 (L-plastin) Tleukemia-associated protein with a CXXC domain Tlipoma HMGIC fusion partner Tleukemia inhibitory factor receptor TLIM domain only 1 (rhombotin 1) (RBTN1) T, ALIM domain only 2 (rhombotin-like 1) (RBTN2) TLIM domain containing preferred translocation partner in lipoma Tlymphoblastic leukemia derived sequence 1 THomolog of Drosophila Mothers Against Decapentaplegic 4 gene D, Mis, N, Fv-maf musculoaponeurotic fibrosarcoma oncogene homolog T

lysine (K)-specific demethylase 5C (JARID1C)lysine (K)-specific demethylase 6A, UTX

v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian) Tmucosa associated lymphoid tissue lymphoma translocation gene 1 Tmastermind-like 2 (Drosophila) Tmitogen-activated protein kinase kinase 4 D, Mis, NMdm2 p53 binding protein homolog AMdm4 p53 binding protein homolog Amyelodysplasia syndrome 1 Tmyelodysplastic syndrome 2 Tmucoepidermoid translocated 1 Tmediator complex subunit 12 M, Smultiple endocrine neoplasia type 1 gene D, Mis, N, F, Smet proto-oncogene (hepatocyte growth factor receptor) MisMHC class II transactivator Tmicrophthalmia-associated transcription factor Amegakaryoblastic leukemia (translocation) 1 Tmyeloid leukemia factor 1 TE.coli MutL homolog gene D, Mis, N, F, Smyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) T, Omyeloid/lymphoid or mixed-lineage leukemia 2 N, F, Mismyeloid/lymphoid or mixed-lineage leukemia 3 Nmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateTmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateT myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocat Tmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateTmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateTmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateTmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocateTmeningioma (disrupted in balanced translocation) 1 Tmyeloproliferative leukemia virus oncogene, thrombopoietin receptor MisMLL septin-like fusion TmutS homolog 2 (E. coli) D, Mis, N, F, SmutS homolog 6 (E. coli) Mis, N, F, Smusashi homolog 2 (Drosophila) Tmoesin Tmature T-cell proliferation 1 Tmucin 1, transmembrane TmutY homolog (E. coli) Misv-myb myeloblastosis viral oncogene homolog Tv-myc myelocytomatosis viral oncogene homolog (avian) A, Tv-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) Av-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) Amyeloid differentiation primary response gene (88) Mis myosin, heavy polypeptide 11, smooth muscle Tmyosin, heavy polypeptide 9, non-muscle TMYST histone acetyltransferase (monocytic leukemia) 4 (MORF) Tnascent-polypeptide-associated complex alpha polypeptide TNijmegen breakage syndrome 1 (nibrin) Mis, N, Fnuclear receptor coactivator 1 Tnuclear receptor coactivator 2 (TIF2) Tnuclear receptor coactivator 4 - PTC3 (ELE1) T

N-myc downstream regulated 1 Tneurofibromatosis type 1 gene D, Mis, N, F, S, Oneurofibromatosis type 2 gene D, Mis, N, F, S, Onuclear factor (erythroid-derived 2)-like 2 (NRF2) Misnuclear factor I/B Tnuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) Tninein (GSK3B interacting protein) TNK2 homeobox 1 Anon-POU domain containing, octamer-binding TNotch homolog 1, translocation-associated (Drosophila) (TAN1) T, Mis, ONotch homolog 2 N, F, Misnucleophosmin (nucleolar phosphoprotein B23, numatrin) T, F nuclear receptor subfamily 4, group A, member 3 (NOR1) Tneuroblastoma RAS viral (v-ras) oncogene homolog Misnuclear receptor binding SET domain protein 1 Tneurotrophic tyrosine kinase, receptor, type 1 Tneurotrophic tyrosine kinase, receptor, type 3 Tnuclear mitotic apparatus protein 1 Tnucleoporin 214kDa (CAN) Tnucleoporin 98kDa Tnuclear protien in testis Toligodendrocyte lineage transcription factor 2 (BHLHB1) Tosteomodulin Tpurinergic receptor P2Y, G-protein coupled, 8 Tplatelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa Tpartner and localizer of BRCA2 F, N, Mispaired box gene 3 Tpaired box gene 5 (B-cell lineage specific activator protein) T, Mis, D, F, Spaired box gene 7 Tpaired box gene 8 Tpolybromo 1 Mis, N, F, S, D, Opre-B-cell leukemia transcription factor 1 Tpericentriolar material 1 (PTC4) Tproprotein convertase subtilisin/kexin type 7 Tphosphodiesterase 4D interacting protein (myomegalin) Tplatelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene Tplatelet-derived growth factor, alpha-receptor Mis, O, Tplatelet-derived growth factor receptor, beta polypeptide Tperiod homolog 1 (Drosophila) Tpaired-like homeobox 2b Mis, Fphosphatidylinositol binding clathrin assembly protein (CALM) Tphosphoinositide-3-kinase, catalytic, alpha polypeptide Misphosphoinositide-3-kinase, regulatory subunit 1 (alpha) Mis, F, Opim-1 oncogene Tpleiomorphic adenoma gene 1 Tpromyelocytic leukemia TPMS1 postmeiotic segregation increased 1 (S. cerevisiae) Mis, NPMS2 postmeiotic segregation increased 2 (S. cerevisiae) Mis, N, Fpaired mesoderm homeo box 1 T

peanut-like 1 (Drosophila) TPOU domain, class 2, associating factor 1 (OBF1) TPOU domain, class 5, transcription factor 1 Tperoxisome proliferative activated receptor, gamma Tprotein phosphatase 2, regulatory subunit A, alpha Mispapillary renal cell carcinoma (translocation-associated) TPR domain containing 1, with ZNF domain D, N, Mis, F, SPR domain containing 16 Tperforin 1 (pore forming protein) Mprotein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1 T, Mis, N, F, SPRO1073 protein (ALPHA) TPC4 and SFRS1 interacting protein 2 (LEDGF) THomolog of Drosophila Patched gene Mis, N, F, Sphosphatase and tensin homolog gene D, Mis, N, F, Sprotein tyrosine phosphatase, non-receptor type 11 Misrabaptin, RAB GTPase binding effector protein 1 (RABPT5) TRAD51-like 1 (S. cerevisiae) (RAD51B) Tv-raf-1 murine leukemia viral oncogene homolog 1 Tral guanine nucleotide dissociation stimulator TRAN binding protein 17 TRAP1, GTP-GDP dissociation stimulator 1 Tretinoic acid receptor, alpha Tretinoblastoma gene D, Mis, N, F, SRNA binding motif protein 15 TRecQ protein-like 4 N, F, Sv-rel reticuloendotheliosis viral oncogene homolog (avian) Aret proto-oncogene T, Mis, N, Fv-ros UR2 sarcoma virus oncogene homolog 1 (avian) Tribosomal protein L22 (EAP) Tribophorin I TRUN domain containing 2A T runt-related transcription factor 1 (AML1) Trunt-related transcription factor binding protein 2 (MOZ/ZNF220) TShwachman-Bodian-Diamond syndrome protein Gene Conversionchromosome 11 open reading frame 79 Msuccinate dehydrogenase complex, subunit B, iron sulfur (Ip) Mis, N, Fsuccinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa Mis, N, Fsuccinate dehydrogenase complex, subunit D, integral membrane protein Mis, N, F, Sseptin 6 TSET translocation TSET domain containing 2 N, F, S, Missplicing factor 3b, subunit 1, 155kDa Missplicing factor proline/glutamine rich(polypyrimidine tract binding protein associated) Tsplicing factor, arginine/serine-rich 3 TSH3-domain GRB2-like 1 (EEN) TTAL1 (SCL) interrupting locus Tsolute carrier family 45, member 3 TSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily F, N, MisSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily D, N, F, Ssmoothened homolog (Drosophila) Mis

F, OSRY (sex determining region Y)-box 2 ASLIT-ROBO Rho GTPase activating protein 3 Tsynovial sarcoma translocation, chromosome 18 Tsynovial sarcoma translocation gene on chromosome 18-like 1 Tspectrin SH3 domain binding protein 1 Tsynovial sarcoma, X breakpoint 1 Tsynovial sarcoma, X breakpoint 2 Tsynovial sarcoma, X breakpoint 4 Tserine/threonine kinase 11 gene (LKB1) D, Mis, N, F, SSix-twelve leukemia gene Tsuppressor of fused homolog (Drosophila) D, F, Ssuppressor of zeste 12 homolog (Drosophila) Tspleen tyrosine kinase TTAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa TT-cell acute lymphocytic leukemia 1 (SCL) TT-cell acute lymphocytic leukemia 2 Ttranscription elongation factor A (SII), 1 Ttranscription factor 1, hepatic (HNF1) Mis, Ftranscription factor 12 (HTF4, helix-loop-helix transcription factors 4) Ttranscription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47) Ttranscription factor 7-like 2 TT-cell leukemia/lymphoma 1A TT-cell leukemia/lymphoma 6 Ttet oncogene family member 2 Mis N, Ftranscription factor binding to IGHM enhancer 3 Ttranscription factor EB TTRK-fused gene TTCF3 (E2A) fusion partner (in childhood Leukemia) Ttransferrin receptor (p90, CD71) Tthyroid hormone receptor associated protein 3 (TRAP150) Ttranscriptional intermediary factor 1 (PTC6,TIF1A) T T-cell leukemia, homeobox 1 (HOX11) TT-cell leukemia, homeobox 3 (HOX11L2) Ttransmembrane protease, serine 2 Ttumor necrosis factor, alpha-induced protein 3 D, N, Ftumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator) Mis, N, Ftumor necrosis factor receptor superfamily, member 17 Ttumor necrosis factor receptor superfamily, member 6 (FAS) Mis topoisomerase (DNA) I Ttumor protein p53 Mis, N, Ftropomyosin 3 Ttropomyosin 4 Ttranslocated promoter region TT cell receptor alpha locus TT cell receptor beta locus TT cell receptor delta locus Ttripartite motif-containing 27 T tripartite motif-containing 33 (PTC7,TIF1G) Tthyroid hormone receptor interactor 11 T

suppressor of cytokine signaling 1

tuberous sclerosis 1 gene D, Mis, N, F, Stuberous sclerosis 2 gene D, Mis, N, F, Sthyroid stimulating hormone receptor Mistubulin tyrosine ligase Tubiquitin specific peptidase 6 (Tre-2 oncogene) Tvon Hippel-Lindau syndrome gene D, Mis, N, F, Svesicle transport through interaction with t-SNAREs homolog 1A TWiskott-Aldrich syndrome Mis, N, F, SWolf-Hirschhorn syndrome candidate 1(MMSET) TWolf-Hirschhorn syndrome candidate 1-like 1 (NSD3) TWNT inhibitory factor 1 TWerner syndrome (RECQL2) Mis, N, F, SWilms tumour 1 gene D, Mis, N, F, S, Tfamily with sequence similarity 123B (FAM123B) F, D, N, Misxeroderma pigmentosum, complementation group A Mis, N, F, Sxeroderma pigmentosum, complementation group C Mis, N, F, Sexportin 1 (CRM1 homolog, yeast) Miszinc finger protein 145 (PLZF) Tzinc finger protein 198 Tzinc finger protein 278 (ZSG) Tzinc finger protein 331 Tzinc finger protein 384 (CIZ/NMP4) Tzinc finger protein 521 Tzinc finger protein 9 (a cellular retroviral nucleic acid binding protein) Tzinc finger protein, subfamily 1A, 1 (Ikaros) T

Translocation Partner Chr Chr BandBCR, ETV6, NUP214 9 9q34.1 No -ETV6 1 1q24-q25 No -ETV1 2 2q36 No -MLL 15 15q14 No -MLL 1 1q21 No -MLL 3 3p21 No -MLL 5 5q31 No -BRAF 7 7q21-q22 No, but 1 of 3 copies o -

14 14q32.32 - -19 19q13.1-q13.2 - Has 7 copies in Flp,

HMGA2 12 12q24.2 No -NPM1, TPM3, TFG, TPM4, 2 2p23 No, but there is a small Has 3 copies in each ALK 17 17q25.3 No -

5 5q21 - -MLL 11 11q23.3 No -BCL6 4 4p13 No -

1 1p35.3 - -12 12q12 - -

ETV6 1 1q21 No -TFE3 17 17q25 No -

20 20q11.1 - -EWSR1, FUS 12 12q13 No -ALK 2 2q35 No -

11 11q22.3 - -X Xq21.1 - -

3 3p21.31-p21.2 - -IGH@ (Ig Heavy locus, ch 1 1p22 No rearrangements in he-IGH@ 2 2p13 No -TLX3 14 14q32.1 No -IGH@ 18 18q21.3 No -IGH@ 19 19q13 No -MYC 17 17q22 No -IG loci, ZNFN1A1(ikzf1 3 3q27 No -MYC 12 12q24.1 No -IGH@, IGL@ (2p11 and 2p1 1 1q21 No -ABL1, FGFR1, JAK2 22 22q11.21 No -

17 17p11.2 - -MALT1 11 11q22-q23 No -

15 15q26.1 - -10 10q22.3 - -

KIAA1549 7 7q34 No -17 17q21 - -13 13q12 - -

NUT (C15orf55) 9 9q34 No -NUT (C15orf55) 19 19p13.1 No -

Evidence for fusion genes in SV files? (AvsNA19238 and all lines vsA)

Evidence for amplification of gene (Snp array or CG CNV data)

17 17q22 - -MYC 12 12q22 No -

15 15q15 - -LPP 12 12q14.3 C12orf9 is not known in-ETV1 15 15q21.1 No -BRD3, BRD4 15 15q14 No -CIITA 16 16p13.13 No -ETV4 17 17q25 No -

7 7p22 - -ALK 11 11p15.5 No -MLL, RUNX1 8 8q22 No -RUNX1 16 16q24 No -MYH11 16 16q22 No -MLL 11 11q23.3 No -

3 3q13.11 - -19 19q13.2 - -

HMGA2 14 14q11.2 No -IGH@, FSTL3 11 11q13 No -IGL@ 12 12p13 No -IGH@ 6 6p21 No -

19 19q12 - Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. CIITA 9 9p24.2 No -CIITA 9 9p24 No -ROS1 5 5q32 No -

19 19q13.2 - -17 17q23 - -16 16q22.1 - -

USP6 16 16q22.1 No -17 17q12 - -12 12q14 - -

MLLT10 7 7q21-q22 No -9 9p21 - -9 9p21 - -1 1p32 - -

ETV6 13 13q12.3 No -19 19q13.1 - -

FGFR1 9 9q33 No -PLAG1 8 8q11.2 No -

22 22q12.1 - -ETV6 4 4q11-q12 No -TAF15 2 2q31-q32.1 No -DUX4 19 19q13.2 - -FLJ27352, CD274, CD27 16 16p13 No, FLJ27352 not known-ALK, TFE3 17 17q11-qter No -? 22 22q11.21 No -HMGA2 2 2q37.3 No -PDGFB, USP6 17 17q21.31-q22 No -

10 10p15 - -HMGA2 8 8q22-q23 No -EWSR1 2 2q34 No -

FUS 11 11p11.2 No -FUS 7 7q34 No -MLL, MORF (MYST4), R 16 16p13.3 No -P2RY8, IGH@ X,Y Xp22.3; Yp11.3 No, P2RY8 is on tht Y -MAML2 15 15q26.1 No -PLAG1 3 3p22-p21.3 No -

16 16q12-q13 - -RET, PDGFRB 10 10q21 No -

6 6p21.3 - -11 11p12 - -

FUS 12 12q13.1-q13.2 No -NUP98 11 11q22-q23 No -ETV4 17 17q21 No -IGH@ 11 11q23.3 No -NUP214 6 6p23 No -

14 14q32.13 - -2 2p23 - -

CIC 4 4q35 - -HMGA2 5 5q34 No -

7 7p12.3-p12.1 - 2 or 3 copies in all lBCL6 3 3q27.3 No -ERG X Xq26 No -SLC45A3 1 1q32 No -RET 12 12p13.3 No, but there is a small -MLL 19 19p13.1 No -PAX5 7 7q11.23 No -ALK 2 2p21 No -MLL, RUNXBP2 22 22q13 No -MLL 1 1p32 No -

17 17q21.1 - 293T 2 copies, Flp 319 19q13.2-q13.3 - -

2 2q21 - -16 16p13.3-p13.13 - -13 13q33 - -

EWSR1, TMPRSS2, ELF4 21 21q22.3 No -EWSR1, TMPRSS2, SLC4 7 7p22 No -EWSR1, TMPRSS2, DDX5 17 17q21 No -TMPRSS2, SCL45A3 3 3q28 No -NTRK3, RUNX1, PDGFRB, 12 12p13 No -RUNX1, ETV6, PRDM16, 3 3q26 No -FLI1, ERG, ZNF278, NR4 22 22q12 No -

8 8q24.11-q24.13 - -11 11p12-p11 - -

7 7q35-q36 - -ETV6 5 5q31 No -

16 16q24.3 - -9 9q22.3 - -3 3p26 - -6 6p21-p22 - -

11 11p15 - -

9 9p13 - -4 4q31.3 - -

? 1 1q23 No -EWSR1, FUS 2 2q36 No -BCR, FGFR1OP, ZNF198 8 8p11.2-p11.1 No -FGFR1 6 6q27 No -

10 10q26 - -IGH@, ETV6 4 4p16.3 No -

1 1q42.1 - -HMGA2 3 3p14.2 No, but some deletions -PDGFRA 4 4q12 No -EWSR1 11 11q24 No -CIITA 15 15q21.3 No -

13 13q12 - -MLL 9 9q23 No -

3 3q23 - -PAX3 13 13q14.1 No -MLL 6 6q21 No -PAX5 3 3p14.1 No -CCND1 19 19p13 No -

1 1p13.1 - -DDIT3, ERG, FEV, ATF1 16 16p11.2 No -IGK@ 18 18q21.3 No -MLL 17 17p No -

X Xp11.23 - -3 3q21.3 - -

10 10p15 - -MLL 3 3q24 No -

19 19p13.3 - -9 9q21 - -

20 20q13.2 - -RET 14 14q No -ROS1 6 6q21 No -

X Xq26.1 No -MLL 14 14q24 No -MLL 5 5q31 No -PDGFRB 17 17p11.2 No -MLL 11 11q12 No -HMGA2 14 14q11.1 No -ERG 16 16q12.2-q13 No -PDGFRB 7 7q11.23 No -BCL6 6 6p21.3 No -TCF3 17 17q22 No -ETV6 7 7q36 No -? 6 6p21 No -LHFP, RAD51L1, LPP, HE 12 12q15 No, but refer to NFIB. -ETV1 7 7p15 No -RET 8 8p11.21 No -NUP98 7 7p15-p14.2 No -

NUP98 7 7p15-p14.2 No -NUP98, MSI2 7 7p15-p14.2 No -NUP98 12 12q13.3 No -NUP98 12 12q13.3 No -NUP98 2 2q31-q32 No -NUP98 2 2q31-q32 No -

11 11p15.5 - -1 1q21-q31 - -

BCL6 14 14q32.31 No -BCL6 6 6p12 No -

2 2q33.3 - -15 15q26.1 - -

MYC, FGFR3,PAX5, IRTA1 14 14q32.33 No -MYC, FVT1 2 2p12 No -BCL9, MYC, CCND2 22 22q11.1-q11.2 No -

7 7p12.2 - -TNFRSF17 4 4q26-q27 No -BCL6 16 16p11 No -

5 5q11 - -5 5p13 - -

IGH@ 6 6p25-p23 No -IGH@ 1 1q21 No -SYK 5 5q31-q32 No -

1 1p32.3-p31.3 - -ETV6, PCM1, BCR 9 9p24 No -

19 19p13.1 - -SUZ12 7 7p15.2-p15.1 No -

1 1p32-p31 - 3 copies in Flp and NUP98 12 12p11 No -

X Xp11.22-p11.21 - -X Xp11.2 - -

4 4q11-q12 - -BRAF 7 7q34 - -

4 4q12 - -ETV4 19 19q13.41 No -

12 12p12.1 - -RET 14 14q22.1 No -MLL, RUNX1 2 2q11.2-q12 No -MLL 17 17q11-q21.3 No -TRB@ 1 1p35-p34.3 No -BCL6 13 13q14.1-q14.3 Fused to ADARB1 in Flp -MLL 10 10q21 No -HMGA2 13 13q12 No -PLAG1 5 5p13-p12 No -TRD@ 11 11p15 No 4 copies in 293A, 2 TRD@ 11 11p13 No -HMGA2, MLL, C12orf9 3 3q28 No -TRB@ 19 19p13.2-p13.1 No -

18 18q21.1 - -IGH@ 16 16q22-q23 No -

IGH@ 20 20q11.2-q13.1 No -BIRC3 18 18q21 No -MECT1, CRTC3 11 11q22-q23 No -

17 17p11.2 - -12 12q15 - 3 copies in all lines.

1 1q32 - 5 copies in 293S, 4 RUNX1 3 3q26 No -ETV6 1 1p36 No -MAML2 19 19p13 Not with MAML2, but the-

X Xq13 - -11 11q13 - -

7 7q31 - -BCL6 16 16p13 No -

3 3p14.1 - 2 copies in Flp, 4 inRBM15 22 22q13 No -NPM1 3 3q25.1 No -

3 3p21.3 - -MLL, MLLT1, MLLT2, ML 11 11q23 No -

12 12q12-q14 - -7 7q36.1 - -

MLL 19 19p13.3 No -MLL, PICALM, CDK6 10 10p12 No -MLL 4 4q21 No -MLL 9 9p22 No -MLL 6 6q27 Not with MLL, but in 293-MLL 17 17q21 No -MLL X Xq13.1 No -ETV6 22 22q13 No -

1 p34 - -MLL 17 17q25 No -

2 2p22-p21 - -2 2p16 - -

HOXA9 17 17q23.2 No -ALK X Xq11.2-q12 No -TRA@ X Xq28 No -IGH@ 1 1q21 No -

1 1p34.3-1p32.1 - -NFIB 6 6q22-23 No, but check NFIB -IGK@, BCL5, BCL7A , B 8 8q24.12-q24.13 No 5 copies in 293S, 2 i

1 1p34.3 - 3 copies in 293A, 42 2p24.1 - 2 copies for 293Flp, 3 3p22 - -

CBFB 16 16p13.13-p13.12 No -ALK 22 22q13.1 No -CREBBP 10 10q22 No -BCL6 12 12q23-q24.1 No -

8 8q21 - -PAX3 2 2p23 No -RUNXBP2 8 8q13.1 No -RET 10 10q11.2 No -

ERG 8 8q24.3 No -17 17q12 - -22 22q12.2 - -

2 2q31 - -MYB, HGMA2 9 9p24.1 Not with any of these t -IGH@ 10 10q24 No -PDGFRB 14 14q24 no -

14 14q13 - 2 copies in 293T, 3 TFE3 X Xq13.1 No -TRB@ 9 9q34.3 No -

1 1p13-p11 - -ALK, RARA, MLF1 5 5q35 No -EWSR1 9 9q22 No -

1 1p13.2 - -NUP98 5 5q35 No -TPM3, TPR, TFG 1 1q21-q22 No -ETV6 15 15q25 No -RARA 11 11q13 No -DEK, SET, ABL1 9 9q34.1 No -HOXA9, NSD1, WHSC1L1 11 11p15 No -BRD4, BRD3 15 q13 No -TRA@ 21 21q22.11 No -USP6 9 9q22.31 No -CRLF2 X,Y Xp22.3; Yp11.3 No, P2RY8 is on the Y -IGH@ 11 11q23 No -

16 16p12.1 - -FOXO1A, NCOA1 2 2q35 No -IGH@, ETV6, PML, FOXP 9 9p13 No -FOXO1A 1 1p36.2-p36.12 No -PPARG 2 2q12-q14 No -

3 3p21 - -TCF3, EWSR1 1 1q23 No -RET, JAK2 8 8p22-p21.3 No -IGH@ 11 11q23.3 No -PDGFRB 1 1q12 No -COL1A1 22 22q12.3-q13.1 No -FIP1L1 4 4q11-q13 No -ETV6, TRIP11, HIP1, RA 5 5q31-q32 No, H4 is not an existin -ETV6 17 17p13.1-17p12 No -

4 4p12 - -MLLT10, MLL 11 11q14 No -

3 3q26.3 - -5 5q13.1 - -

BCL6 6 6p21.2 No -TCEA1, LIFR, CTNNB1, 8 8q12 No -RARA, PAX5 15 15q22 No -

2 2q31-q33 - -7 7p22 - -

NUP98 1 1q24 No -

MLL 22 22q11.2 No -BCL6 11 11q23.1 No -EWSR1 6 6p21.31 No -PAX8 3 3p25 No -

19 19q13.41 - -TFE3 1 1q21.1 No -

6 6q21 - -EVI1 1 1p36.23-p33 No -

10 10q22 - -RET 17 17q23-q24 No -TFEB 11 11q31.1 No -NUP98 9 9p22.2 No -

9 9q22.3 - -10 10q23.3 - -12 12q24.1 - -

PDGFRB 17 17p13 No -HMGA2 14 14q23-q24.2 No -SRGAP3 3 3p25 No -CIITA 9 9q34.3 No -TRD@ 5 5q34 No -NUP98 4 4q21-q25 No -PML, ZNF145, TIF1, NU 17 17q12 No -

13 13q14 - -MKL1 1 1p13 No -

8 8q24.3 - -2 2p13-p12 - 2 copies in 293Flp, 3

H4, PRKAR1A, NCOA4, P 10 10q11.2 No -GOPC, ROS1 6 6q22 No -RUNX1 1 1p36.31 No -EVI1 3 3q21.3-q25.2 No -CIITA 16 16p13.13 No -RPL22, MDS1, EVI1, CBF 21 21q22.3 No -CREBBP, NCOA2, EP300 8 8p11 No -

7 7q11 No -11 11q12.2 - -

1 1p36.1-p35 - -1 1q21 - -

11 11q23 - -MLL X Xq24 No -NUP214 9 9q34 No -

3 3p21.31 - -2 2q33.1 - -

TFE3 1 1p34.3 No -BCL6 6 6p21 No -MLL 19 19p13.3 No -TAL1 1 1p32 No -ETV1, ETV5, ELK4, ERG 1 1q32 No -

19 19p13.2 - -22 22q11 - -

7 7q31-q32 - -

16 16p13.13 - -3 3q26.3-q27 - 2 copies 293T and F

RAF1 3 3p25.3 Not with RAF1, but in 2-SSX1, SSX2 18 18q11.2 No -SSX1 20 20q13.3 No -MLL 10 10p11.2 No -SS18 X Xp11.23-p11.22 No -SS18 X Xp11.23-p11.22 No -SS18 X Xp11.23 No -

19 19p13.3 - -ETV6 6 6q23 No -

10 10q24.32 - -JAZF1 17 17q11.2 No -ETV6, ITK 9 9q22 No -TEC, CHN1, ZNF384 17 17q11.1-q11.2 No -TRD@, SIL 1 1p32 No -TRB@ 9 9q31 No -PLAG1 8 8q11.2 No -

12 12q24.2 - -TEC 15 15q21 No -PBX1, HLF, TFPT 19 19p13.3 No -VTI1A 10 10q25.3 No -TRA@ 14 14q32.1 No -TRA@ 14 14q32.1 No -

4 4q24 - -SFPQ, ASPSCR1, PRCC,X Xp11.22 No -ALPHA 6 6p21 ALPHA is not an existin -NTRK1, ALK 3 3q11-q12 No -TCF3 19 19q13 No -BCL6 3 3q29 No -USP6 1 1p34.3 No -RARA 7 7q32-q34 No -TRB@, TRD@ 10 10q24 No -BCL11B 5 5q35.1 No -ERG, ETV1, ETV4, ETV5 21 21q22.3 No -

6 6q23 - -1 1p36.32 - -

IL2 16 16p13.1 No -10 10q24.1 - -

NUP98 20 20q12-q13.1 No -17 17p13 - -

NTRK1, ALK 1 1q22-q23 No -ALK 19 19p13.1 No -NTRK1 1 1q25 No -ATL,OLIG2, MYC, TCL1A 14 14q11.2 No rearrangements at 1-HOX11, LCK, NOTCH1, T 7 7q35 No rearrangements at 7-TAL1, HOX11, TLX1, LM 14 14q11 No rearrangements at 14-RET 6 6p22 No -RET 1 1p13 No -PDGFRB 14 14q31-q32 No -

9 9q34 - -16 16p13.3 - -14 14q31 - -

ETV6 2 2q13 No -COL1A1, CDH11, ZNF9, 17 17p13 No -

3 3p25 - -TCF7L2 10 10q25.2 No -

X Xp11.23-p11.22 - -IGH@ 4 4p16.3 No -NUP98 8 8p12 No -HMGA2 12 12q14.3 No -

8 8p12-p11.2 - -EWSR1 11 11p13 No -

X Xq11.1 - -9 9q22.3 - -3 3p25 - -2 2p15 - -

RARA 11 11q23.1 No -FGFR1 13 13q11-q12 No -EWSR1 22 22q12-q14 No -? 19 19q13.3-q13.4 No -EWSR1, TAF15 12 12p13 No -PAX5 18 18q11.2 No -USP6 3 3q21 No -BCL6 7 7p12 No -

-------------No, has at least 3 copies in all lines. --No, has at least 3 copies in all lines. ------No, 2 copies in Flp and 3 in others.-----------------Only 2 copies in 293T according to snp array data. Not confirmed by CG CNV (3 copies), 3 or 4 in others.Only 2 copies in 293A and 293Flp, 3 or 4 in other lines.--

Evidence for deletion of gene or part of gene (Snp array or CG CNV data)

--------------------

Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies. ----------2 copies in 293 Flp, 3 in others.2 copies in 293 Flp, 3 in others.At least 3 copies in all lines.----------------

---------------------------------------------Only 2 copies in 293S and 293Flp, 3 or 4 in others.2 copies in Flp, 3 in others.At least 3 copies in all lines.--

-2 copies in 293A and Flp, 3 in others.-------------------------------At least 3 copies in all lines.---------------

---------------2 copies in 293Flp, 293SG and 293SgendoT, 3 copies in others, no data in a large part of intron 3 of IKZF1. Is this a deletion??--------------2 copies in 293Flp, at least 3 copies in others.-----------------3 copies in A, 4 copies in Flp, only 2 copies in other lines.-

---At least 3 copies in all lines.------At least 3 copies in all lines.-----2 copies in Flp, at least 3 copies in other lines.-------------2 copies in 293Flp, 3 in all others.-------------------

-Only 2 copies in 293T, at least 3 in all others.At least 3 copies in all lines.-

----------------------Only 2 copies in 293S, at least 3 in all others.--2 copies in Flp, at least 3 copies in other lines.------------------

------At least 3 copies in all lines.------Only 2 copies in 293SG and SGendoT, 3 in others.--------1 or 2 copies in 293S, 2 in 293A. Seems to be 3 in others-------------------------At least 3 copies in all lines.-

---------At least 3 copies in all lines.-At least 3 copies in all lines.-----------------------At least 3 copies in all lines.--------------

At least 3 copies in all lines.At least 3 copies in all lines.---At least 3 copies in all lines.------2 copies in Flp, 3 in others.At least 3 copies in all lines.-----------

Lies inside a tandem duplication in 293T, with probably 4 copies inside a 3 copies area, the duplication also contains c19orf2 and c19orf12. In the Flp lines, there are 7 copies according to snp array data. Other lines, 3 copies.

2 copies in 293Flp, 293SG and 293SgendoT, 3 copies in others, no data in a large part of intron 3 of IKZF1. Is this a deletion??

[xls]media.nature.com · web view16p13.3-p13.13 xeroderma pigmentosum (f) ercc5 excision repair...

Documents