HEARING IMPAIRMENT GENE PANEL DG 2.3.x
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1 HEARING IMPAIRMENT GENE PANEL DG 2.3.x Gene Median coverage % covered > 10x % covered > 20x Associated Phenotype description and OMIM ID ACTB 68,9 100% 94% Dystonia, juvenile-onset, Baraitser-Winter syndrome 1, ACTG1 57,8 100% 94% Deafness, autosomal dominant 20/26, Baraitser-Winter syndrome 2, ADCY1 102,4 92% 92%?Deafness, autosomal recessive 44, APOPT1 90,9 87% 80% Mitochondrial Complex IV Deficiency, ATP1A2 107,9 100% 99% Alternating hemiplegia of childhood, Migraine, familial basilar, Migraine, familial hemiplegic, 2, ATP6V1B1 108,7 100% 99% Renal tubular acidosis with deafness, BDP1 134,1 100% 99% No OMIM phenotype Hearing loss (Girotto (2013) PLoS One 8,e80323) BSND 119,6 100% 99% Bartter syndrome, type 4a, Sensorineural deafness with mild renal dysfunction, CABP2 54,2 85% 67% Deafness, autosomal recessive 93, CACNA1D 118,2 98% 98% Sinoatrial node dysfunction and deafness, CCDC50 133,9 97% 96% Deafness, autosomal dominant 44, CDH23 100,3 98% 96% Usher syndrome, type 1D, Deafness, autosomal recessive 12, Usher syndrome, type 1D/F digenic, CEACAM16 86,8 100% 98% Deafness, autosomal dominant 4B, CIB2 115,4 100% 100% Deafness, autosomal recessive 48, Usher syndrome, type IJ, CLDN14 65,5 100% 100% Deafness, autosomal recessive 29, CLIC5 106,8 96% 89%?Deafness, autosomal recessive 103, CLPP 85,9 99% 93% Perrault syndrome 3,
2 CLRN1 166,3 100% 100% Usher syndrome, type 3A, Retinitis pigmentosa 61, COCH 122,9 100% 99% Deafness, autosomal dominant 9, COL11A1 102,1 98% 98% Stickler syndrome, type II, Marshall syndrome, {Lumbar disc herniation, susceptibility to}, Fibrochondrogenesis, COL11A2 14,6 56% 21% Stickler syndrome, type III, Otospondylomegaepiphyseal dysplasia, Weissenbacher-Zweymuller syndrome, Deafness, autosomal dominant 13, Deafness, autosomal recessive 53, Fibrochondrogenesis 2, COL2A1 91,7 100% 97% Stickler syndrome, type I, Kniest dysplasia, Achondrogenesis, type II or hypochondrogenesis, SED congenita, SMED Strudwick type, Epiphyseal dysplasia, multiple, with myopia and deafness, Spondyloperipheral dysplasia, SED, Namaqualand type Osteoarthritis with mild chondrodysplasia, Vitreoretinopathy with phalangeal epiphyseal dysplasia Platyspondylic skeletal dysplasia, Torrance type, Otospondylomegaepiphyseal dysplasia, Avascular necrosis of the femoral head, Legg-Calve-Perthes disease, Stickler sydrome, type I, nonsyndromic ocular, Czech dysplasia, COL4A3 76,6 97% 93% Alport syndrome, autosomal recessive, Hematuria, benign familial, Alport syndrome, autosomal dominant, COL4A4 91,7 99% 98% Alport syndrome, autosomal recessive, Hematuria,familial benign COL4A5 73,2 99% 96% Alport syndrome,
3 COL4A6 84,5 97% 94%?Deafness,X-linked 6, COL9A1 108,9 100% 95% Epiphyseal dysplasia, multiple, 6, Stickler syndrome, type IV, COL9A2 70,6 96% 90% Epiphyseal dysplasia, multiple, 2, {Intervertebral disc disease, susceptibility to}, Stickler syndrome, type V, CRYM 72,5 99% 97% Deafness, autosomal dominant 40 DCDC2 172,8 100% 100%?Deafness,autosomal recessive 66, Nephronophthisis 19, DFNA5 102,3 100% 97% Deafness, autosomal dominant 5, DFNB31 90,6 98% 96% Deafness, autosomal recessive 31, Usher syndrome, type 2D, DFNB59 129,9 100% 100% Deafness, autosomal recessive 59, DIABLO 115,3 100% 87% Deafness, autosomal dominant 64, DIAPH1 88,6 99% 92% Deafness, autosomal dominant 1, DIAPH3 117,3 98% 97% Auditory neuropathy, autosomal dominant, 1, DSPP 154,6 99% 96% Dentinogenesis imperfecta, Shields type II, Deafness, autosomal dominant 36, with dentinogenesis, Dentinogenesis imperfecta, Shields type III, Dentin dysplasia, type II, EDN3 88,6 100% 100% Waardenburg syndrome, type 4B, Central hypoventilation syndrome, congenital, {Hirschsprung disease, susceptibility to}, EDNRB 146,4 100% 99%?{Hirschsprung disease, susceptibility to}, ABCD syndrome, Waardenburg syndrome, type 4A, ELMOD3 117,6 100% 100%?Deafness, autosomal recessive 88, EPS8 91,8 100% 99%?Deafness, autosomal recessive 102, ESPN 44,9 78% 55% Deafness, autosomal recessive 36, Deafness, neurosensory, without vestibular involvement, autosomal dominant ESRRB 59,6 95% 80% Deafness, autosomal recessive 35,
4 EYA1 109,6 100% 98% Branchiootorenal syndrome 1, with or without cataracts, Anterior segment anomalies with or without cataract, Branchiootic syndrome 1, Otofaciocervical syndrome, EYA4 126,3 100% 100% Deafness, autosomal dominant 10, Cardiomyopathy, dilated, 1J, FAM65B 96,7 100% 99%?Deafness,autosomal recessive 104, FGF3 76,7 100% 96% Deafness, congenital with inner ear agenesis, microtia, and microdontia, FOXI1 92,4 100% 100% Enlarged vestibular aqueduct, GIPC3 102,7 100% 92% Deafness, autosomal recessive 15, GJB2 178,9 100% 100% Deafness, autosomal recessive 1A, Deafness, autosomal dominant 3A, Vohwinkel syndrome, Keratoderma, palmoplantar, with deafness, Keratitis-ichthyosis-deafness syndrome, Hystrix-like ichthyosis with deafness, Bart-Pumphrey syndrome, GJB % 100% Erythrokeratodermia variabilis et progressiva, Deafness, autosomal dominant 2B, Deafness, autosomal recessive Deafness, autosomal dominant, with peripheral neuropathy Deafness, digenic, GJB2/GJB3, GJB6 172,9 100% 100% Deafness, autosomal dominant 3B, Deafness, autosomal recessive 1B, Deafness, digenic GJB2/GJB6, Ectodermal dysplasia 2, Clouston type, GPR98 121,4 100% 99% Febrile seizures, familial, 4, Usher syndrome, type 2C, Usher syndrome, type 2C, GPR98/PDZD7 digenic, GPSM2 150,6 100% 99% Chudley-McCullough syndrome, GRHL2 108,8 100% 99% Deafness, autosomal dominant 28, GRXCR1 204,8 100% 100% Deafness, autosomal recessive 25, GRXCR2 144,5 100% 100%?Deafness, autosomal recessive 101, HARS 133,7 100% 100% Usher syndrome type 3B,
5 HARS2 148,8 100% 100% Perrault syndrome 2, HGF 106,8 96% 96% Deafness, autosomal recessive 39, HSD17B % 96% D-bifunctional protein deficiency, Perrault syndrome 1, ILDR1 61,8 100% 99% Deafness, autosomal recessive 42, KARS % 100% Charcot-Marie-Tooth disease, recessive intermediate, B, Deafness, autosomal recessive 89, KCNE1 226,6 100% 100% Jervell and Lange-Nielsen syndrome 2, Long QT syndrome-5, KCNJ10 162,2 100% 100% SESAME syndrome, Enlarged vestibular aqueduct, digenic, KCNQ1 64,3 93% 83% Long QT syndrome-1, Jervell and Lange-Nielsen syndrome, Atrial fibrillation, familial, 3, Short QT syndrome-2, {Long QT syndrome 1, acquired, susceptibility to}, KCNQ4 100,3 92% 84% ness, autosomal dominant 2A, KITLG 84,3 100% 98% Hyperpigmentation with or without hypopigmentation, [Skin/hair/eye pigmentation 7], LARS2 122,7 100% 100% Perrault syndrome 4, LHFPL5 195,8 100% 100% Deafness, autosomal recessive 67, LOXHD1 110,3 100% 99% Deafness, autosomal recessive 77, LRTOMT 111,3 86% 84% Deafness, autosomal recessive 63, MARVELD2 169,9 100% 95% Deafness, autosomal recessive 49, MITF 123,9 100% 99% Waardenburg syndrome, type 2A, Waardenburg syndrome/ocular albinism, digenic, Tietz albinism-deafness syndrome, {Melanoma, cutaneous malignant, susceptibility to, 8}, MSRB3 132,2 100% 100% Deafness, autosomal recessive 74, MYH14 63,6 92% 81% Deafness, autosomal dominant 4A, Peripheral neuropathy, myopathy, hoarseness, and hearing loss,
6 MYH9 99,9 100% 98% May-Hegglin anomaly, Fechtner syndrome, Sebastian syndrome, Deafness, autosomal dominant 17, Epstein syndrome, Macrothrombocytopenia and progressive sensorineural deafness, MYO15A 89,6 97% 92% Deafness, autosomal recessive 3, MYO3A 113,4 99% 98% Deafness, autosomal recessive 30, MYO6 106,3 100% 98% Deafness,autosomal dominant 22, Deafness,autosomal dominant 22,with hypertrophic cardiomyopathy, Deafness,autosomal recessive 37, MYO7A 82,9 97% 93% Usher syndrome, type 1B, Deafness,autosomal dominant 11, Deafness,autosomal recessive 2, NARS2 117,6 100% 99% Combined oxidative phosphorylation deficiency 24, DFNB94, Simon, PLoS Genet Mar 25;11 NLRP3 122,9 100% 99% Cold-induced autoinflammatory syndrome, familial, OPA1 130,6 100% 99% Optic atrophy 1, OSBPL2 90,1 100% 99% Deafness,autosomal dominant 67, OTOA 73,4 69% 68% Deafness, autosomal recessive 22, OTOF 96,6 98% 95% Deafness, autosomal recessive 9, OTOG 96,9 99% 95% Deafness, autosomal recessive 18B, OTOGL 121,5 100% 99% Deafness, autosomal recessive 84B, P2RX % 98% Deafness, autosomal dominant 41, PAX3 128,7 100% 98% Waardenburg syndrome, type 1, Craniofacial-deafness-hand syndrome, Rhabdomyosarcoma 2,alveolar, Waardenburg syndrome,type 3, PCDH15 135,4 99% 99% Usher syndrome, type 1F, Deafness,autosomal recessive 23, Usher syndrome, type 1D/F digenic, PDZD7 83,3 97% 89% {Retinal disease in Usher syndrome type IIA, modifier of}, PET100 81,2 100% 99% Mitochondrial complex IV deficiency, PNPT1 110,2 100% 100% Combined oxidative phosphorylation deficiency 13,
7 POU3F4 149,2 100% 100% Deafness, X-linked 2, POU4F3 183,6 100% 100% Deafness, autosomal dominant 15, PRPS % 100% Arts syndrome, Charcot-Marie-Tooth disease,x-linked recessive,5, Deafness,X-linked 1, Gout,PRPS-related, Phosphoribosylpyrophosphate synthetase superactivity, PTPRQ 114,4 94% 93% Deafness, autosomal recessive 84A, RDX 56,8 90% 79% Deafness, autosomal recessive 24, SERPINB6 133,9 100% 100% Deafness, autosomal recessive 91, SIX1 77,3 95% 95% Brachiootic syndrome 3, Deafness,autosomal dominant 23, SIX5 36,4 87% 77% Branchiootorenal syndrome 2, SLC17A8 131,2 100% 100% Deafness, autosomal dominant 25, SLC26A4 99,8 99% 97% Pendred syndrome, Deafness,autosomal recessive 4,with enlarged vestibular aqueduct, SLC26A5 95,6 100% 100% Deafness, autosomal recessive 61, SLC33A1 96,6 100% 100% Spastic paraplegia 42, autosomal dominant, Congenital cataracts,hearing loss,and neurodegeneration, SLITRK6 170,1 100% 100% Deafness and myopia, SMPX 124,2 100% 99% Deafness, X-linked 4, SNAI2 86,6 100% 100% Waardenburg syndrome, type 2D, Piebaldism, SOX10 72,3 100% 100% Waardenburg syndrome, type 4C, PCWH syndrome, Waardenburg syndrome,type 2E,with/without neurologic involvement, STRC 12,8 18% 14% Deafness, autosomal recessive 16, SYNE4 88,4 100% 100% Deafness, autosomal recessive 76, TBC1D24 112,2 100% 100% Deafness,autosomal recessive 86, Deafness,autosomal dominant 65, DOOR syndrome, Epileptic encephalopathy,early infantile,16, Myoclonic epilepsy, infantile, familial,
8 TECTA % 99% Deafness, autosomal dominant 8/12, Deafness,autosomal recessive 21, TIMM8A 52,8 99% 82% Deafness, X-linked 1, progressive TJP2 89,7 100% 98% Cholestasis, progressive familial intrahepatic 4, Hypercholanemia, familial, TMC1 116,9 100% 100% Deafness, autosomal recessive 7, Deafness,autosomal dominant 36, TMEM132E 75,5 99% 96% Deafness,autosomal dominant 99 (Li et al. Hum Mutat (1) ) TMIE 59,2 99% 83% Deafness, autosomal recessive 6, TMPRSS3 92,6 100% 96% Deafness, autosomal recessive 8/10, TNC 134,1 96% 95% Deafness, autosomal dominant 56, TPRN 40,9 79% 63% Deafness, autosomal recessive 79, TRIOBP 95,4 95% 91% Deafness, autosomal recessive 28, TSPEAR 114,2 100% 99% Deafness, autosomal recessive 98, TYR 146,5 74% 74% Albinism,oculocutaneous,type IA, Albinism,oculocutaneous,type IB, Waardenburg syndrome/albinism, digenic, [Skin/hair/eye pigmentation 3], USH1C 76,7 99% 92% Deafness,autosomal recessive 18A, Usher syndrome,type 1C, USH1G 110,5 98% 88% Usher syndrome, type 1G, USH2A 122,7 100% 99% Usher syndrome, type 2A, WFS1 155,3 100% 100% Deafness,autosomal dominant 6/14/38, Wolfram syndrome, Wolfram-like syndrome,autosomal dominant, {Diabetes mellitus,noninsulin-dependent,association with}, YAP1 76,7 99% 90% Coloboma, ocular, Coloboma, ocular, with/without hearing impairment, cleft lip/palate, mental retardation, Gene symbols used follow HGCN guidelines Genomics 79(4): (2002) updated February 2014 Median Coverage describes the average number of reads seen across 50 exomes % Covered 10x describes the percentage of a gene s coding sequence that is covered at least 10x % Covered 20x describes the percentage of a gene s coding sequence that is covered at least 20x OMIM release used for OMIM disease identifiers and descriptions : June 30 th, 2015
9 This list is accurate for all panel versions starting with DG 2.3. (where x is a random number signifying a minor analysis patch without consequences for the panel composition or coverage information) Ad 1. No OMIM phenotype signifies a gene without a current OMIM association Ad 2. OMIM phenotype descriptions between {} signify risk factors
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