The American Journal of Human Genetics

Supplemental Data

Autosomal-Recessive Hearing Impairment

due to Rare Missense Variants within S1PR2

Regie Lyn P. Santos-Cortez, Rabia Faridi, Atteeq U. Rehman, Kwanghyuk Lee,

Muhammad Ansar, Xin Wang, Robert J. Morell, Rivka Isaacson, Inna A. Belyantseva,

Hang Dai, Anushree Acharya, Tanveer A. Qaiser, Dost Muhammad, Rana Amjad Ali,

Sulaiman Shams, Muhammad Jawad Hassan, Shaheen Shahzad, Syed Irfan Raza, Zil-e-

Huma Bashir, Joshua D. Smith, Deborah A. Nickerson, Michael J. Bamshad, University

of Washington Center for Mendelian Genomics, Sheikh Riazuddin, Wasim Ahmad,

Thomas B. Friedman, and Suzanne M. Leal

1 2

I

IV

V

II

2 24 42 21 12 21 11 12 22 22 22 22 22 21 11 15 5- -2 21 12 21 11 12 11 1

2 24 42 21 12 21 21 12 22 12 12 22 22 21 21 1

01 5- T2 21 12 21 21 11 21 1

1 2

2 24 42 21 12 21 11 12 22 22 22 22 22 21 11 15 5- -2 21 12 21 11 12 21 1

2 23 4

2 21 12 21 11 12 22 22 22 22 22 21 11 15 5- -2 21 12 21 11 12 21 1

2 23 4

2 21 12 21 21 12 22 22 12 22 22 21 21 15 5- T2 11 22 21 21 12 11 2

1 3 4

4 4

5 5- -

3 3

5 5T T

2 4

4 5T -

3 4

01 5- T

52

2

76

1

5431

432

6

T -ESRRB c.690delT

)91gh( bM DI rekraM

4523401sr885S41D

8868sr975789sr429122sr482719sr

6014756sr0835517sr

377857sr4718551sr1225211sr3559984sr9613601sr7815022sr

043539sr35S41D

ESRRB762067sr660888sr214888sr

5853402sr483871sr229241sr

6673681sr

17.9622.0741.1715.1785.1747.2793.3784.3712.4703.4719.4707.5757.5748.5795.6729.67

c.690delT82.7795.7716.8779.9781.0836.0853.18

III

Figure S2. Family DEM4100 with the ESRRB c.690delT variant. Four out of five individuals with nonsyndromic hearing impairment are homozygous for the deletion. Individual IV-4 has profound hearing loss by audiometry, which may be due to other genetic or environmental cause.

Table S1. Genes within the mapped interval for family 4154 on chromosome 19p13.2-p121 with evidence for involvement in etiology of lower limb defects

Gene Gene MIM#

Limb Phenotype or Role in Limb Development Organism Reference (PMID)

ADAMTS10 608990 Brachydactyly and joint stiffness in AR Weill-Marchesani syndrome 1 (includes short stature and lens abnormalities; MIM 277600)

Human Dagoneau et al. 2004 (15368195)

PIN1 601052 In limb buds, Pin1 regulates stability of p63 which when mutated results in SHFM type IV

Mouse Restelli et al. 2014 (24569166)

SMARCA4 603254 Hypoplastic 5th toes and toenails in AD Coffin-Siris

syndrome (includes sucking or feeding difficulty, hypertrichosis, pointed chin, gastrointestinal complications, hernia, occasional hearing impairment, infection; MIM 135900)

Human Kosho et al. 2014 (25168959)

DOCK6 614194 Terminal transverse limb defects in AR Adams-Oliver syndrome 2 (includes aplasia cutis congenita and variable brain, eye and cardiovascular defects; MIM 614219)

Human Shaheen et al. 2011 (21820096)

ACP5 171640 AR spondyloenchondrodysplasia with vertebral and metaphyseal dysplasia, autoimmune disease, spasticity and cerebral calcifications (MIM 607944)

Human Lausch et al. 2011 (21217752)

MAN2B1 609458 Dysostosis multiplex which may include kyphoscoliosis, genu valgus and osteoarthritis as part of AR alpha-mannosidosis (causes immune deficiency, hearing, mental and speech impairment; MIM 248500)

Human Malm & Nilssen, 2008 (18651971)

EPS15L1 NA Deletion caused SHFM with short stature, developmental delay, hypotonia, ataxia and dysmorphic features. Deleted region also includes a few exons of CALR3 (MIM 611414) which is associated with hypertrophic cardiomyopathy.

Human Aten et al. 2009 (19353584); Bens et al. 2011 (21700002)

PIK3R2 603157 AD megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome (MIM 603387)

Human Rivière et al. 2012 (22729224)

FKBP8 604840 Spina bifida with splayed hind limbs and lower body paralysis

Mouse Wong et al. 2008 (18003640)

CRLF1 604237 Camptodactyly in AR Crisponi or cold-induced sweating syndrome (includes facial contractions, dysmorphisms, feeding and respiratory difficulties; MIM 272430)

Human Dagoneau et al. 2007 (17436251)

COMP 600310 AD pseudoachondroplasia (MIM 177170) or multiple epiphyseal dysplasia (MIM 132400) which may include hypoplasia of the distal humerus, radius or knee, coxa plana and round talar dome

Human Kawaji et al. 2002 (12483437)

AR, autosomal recessive; SHFM, split hand-foot malformation; AD, autosomal dominant

1 From exome data, all genes listed have complete coverage of the coding region, except for EPS15L1 which

was Sanger-sequenced. Rare deleterious coding variants in any of these genes were not identified.

University of Washington Center for Mendelian Genomics (UWCMG)

Michael J. Bamshad1,2, Jay Shendure1, and Deborah A. Nickerson1

Gonçalo R. Abecasis4, Peter Anderson1, Marcus Annable1, Mallory Beightol1, Brian L.

Browning1, Kati J. Buckingham1, Christina Chen1, Jennifer Chin1, Jessica X. Chong1,

Gregory M. Cooper5, Colleen Davis1, Lindsay Felker1, Christopher Frazar1, David

Hanna1, Zongxiao He3, Preti Jain5, Gail P. Jarvik1, Eric Johanson1, Goo Jun4, Martin

Kircher1, Tom Kolar1, Suzanne M. Leal3, Daniel Luksic1, Margaret J. McMillin1, Sean

McGee1, Brenton Munson1, Brian J. O'Roak1, Bryan Paeper1, Karynne Patterson1, Eric

Phillips1, Jessica Pijoan1, Christa Poel1, Peggy D. Robertson1, Regie Santos-Cortez3,

Tristan Shaffer1, Cindy Shephard1, Deborah L. Siegel1, Joshua D. Smith1, Jeffrey C.

Staples1, Holly K. Tabor1,2, Monica Tackett1, Gao Wang3, and Qian Yi1

1University of Washington

2Seattle Children’s Hospital

3Baylor College of Medicine

4University of Michigan

5HudsonAlpha Institute of Technology