Whole exome sequencing Gene package Vision disorders version 3,

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1 Whole Exome Sequencing Gene package Vision disorders, version 3, Technical information After DNA was enriched using Agilent Sureselect Clinical Research Exome (CRE) Capture, samples were run on the Illumina Hiseq platform. The aim is to obtain 50 million total reads per exome with a mapped fraction >0.98. The average coverage of the exome is ~50x. Data are demultiplexed by Illumina software bcl2fastq. Reads are mapped to the genome using BWA (reference: bwa.sourceforge.net/). Variant detection is performed by Genome Analysis Toolkit (reference: Analysis is performed in Cartagenia using The Variant Calling File (VCF) followed by filtering. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including phenotype ID(s) median depth ABCA4 Cone rod dystrophy 3, Fundus flavimaculatus, {Macular degeneration, age related, 2}, Retinal dystrophy, early onset severe, Retinitis pigmentosa 19, Stargardt disease 1, ABCB6 [Blood group, Langereis system], Dyschromatosis universalis hereditaria 3, Microphthalmia, isolated, with coloboma 7, Pseudohyperkalemia, familial, 2, due to red cell leak, ABCC6 Arterial calcification, generalized, of infancy, 2, Pseudoxanthoma elasticum, Pseudoxanthoma elasticum, forme fruste, ABHD12 Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract, ACBD5 No phenotype ACO2 Infantile cerebellar retinal degeneration, ?Optic atrophy 9, ACTB Baraitser Winter syndrome 1, ?Dystonia, juvenile onset, ACTG1 Baraitser Winter syndrome 2, Deafness 20/26,

2 Phenotype description including phenotype ID(s) median depth ADAM9 Cone rod dystrophy 9, ADAMTS10 Weill Marchesani syndrome 1, recessive, ADAMTS17 Weill Marchesani like syndrome, ADAMTS18 Microcornea, myopic chorioretinal atrophy, and telecanthus, ADAMTSL4 Ectopia lentis et pupillae, Ectopia lentis, isolated, ADGRV1?Febrile seizures, familial, 4, Usher syndrome, type 2C, Usher syndrome, type 2C, GPR98/PDZD7 digenic, ADIPOR1 No phenotype AGBL1 Corneal dystrophy, Fuchs endothelial, 8, AGBL5 Retinitis pigmentosa 75, AGK Cataract 38, Sengers syndrome, AHI1 Joubert syndrome 3, AIPL1 Cone rod dystrophy, Leber congenital amaurosis 4, Retinitis pigmentosa, juvenile, ALDH1A3 Microphthalmia, isolated 8, ALMS1 Alstrom syndrome, ALX3 Frontonasal dysplasia 1, ANTXR1 GAPO syndrome, {Hemangioma, capillary infantile, susceptibility to}, AP3B1 Hermansky Pudlak syndrome 2, ARHGEF18 Retinitis pigmentosa 78, ARL13B Joubert syndrome 8, ARL2BP Retinitis pigmentosa with or without situs inversus, ARL3 No phenotype ARL6 {Bardet Biedl syndrome 1, modifier of}, Bardet Biedl syndrome 3, ?Retinitis pigmentosa 55, ASPH Traboulsi syndrome, ASRGL1 No phenotype ATF6 Achromatopsia 7, ATOH7 Persistent hyperplastic primary vitreous, BBIP1?Bardet Biedl syndrome 18, BBS1 Bardet Biedl syndrome 1, BBS10 Bardet Biedl syndrome 10, BBS12 Bardet Biedl syndrome 12,

3 Phenotype description including phenotype ID(s) median depth BBS2 Bardet Biedl syndrome 2, Retinitis pigmentosa 74, BBS4 Bardet Biedl syndrome 4, BBS5 Bardet Biedl syndrome 5, BBS7 Bardet Biedl syndrome 7, BBS9 Bardet Biedl syndrome 9, BCOR Microphthalmia, syndromic 2, BEST1 Bestrophinopathy, Macular dystrophy, vitelliform, 2, Microcornea, rod cone dystrophy, cataract, and posterior staphyloma, Retinitis pigmentosa, concentric, Retinitis pigmentosa 50, Vitreoretinochoroidopathy, BFSP1 Cataract 33, multiple types, BFSP2 Cataract 12, multiple types, BLOC1S3 Hermansky Pudlak syndrome 8, BLOC1S6 Hermansky pudlak syndrome 9, BMP4 Microphthalmia, syndromic 6, Orofacial cleft 11, BMP7 No phenotype C12orf57 Temtamy syndrome, C19ORF12 Neurodegeneration with brain iron accumulation 4, ?Spastic paraplegia 43, C1QTNF5 Retinal degeneration, late onset, C21orf2 No phenotype C2ORF71 Retinitis pigmentosa 54, C5ORF42 Joubert syndrome 17, Orofaciodigital syndrome VI, C8ORF37 Bardet Biedl syndrome 21, Cone rod dystrophy 16, Retinitis pigmentosa 64, CA4 Retinitis pigmentosa 17, CABP4 Cone rod synaptic disorder, congenital nonprogressive, CACNA1F Aland Island eye disease, Cone rod dystrophy, 3, Night blindness, congenital stationary (incomplete), 2A, CACNA2D4 Retinal cone dystrophy 4, CAPN5 Vitreoretinopathy, neovascular inflammatory,

4 Phenotype description including phenotype ID(s) median depth CC2D2A COACH syndrome, Joubert syndrome 9, Meckel syndrome 6, CDH23 Deafness 12, Usher syndrome, type 1D, Usher syndrome, type 1D/F digenic, CDH3 Ectodermal dysplasia, ectrodactyly, and macular dystrophy, Hypotrichosis, congenital, with juvenile macular dystrophy, CDHR1 Cone rod dystrophy 15, Retinitis pigmentosa 65, CEP164 Nephronophthisis 15, CEP250 No phenotype CEP290?Bardet Biedl syndrome 14, Joubert syndrome 5, Leber congenital amaurosis 10, Meckel syndrome 4, Senior Loken syndrome 6, CEP41 Joubert syndrome 15, CEP78 Cone rod dystrophy and hearing loss, CERKL Retinitis pigmentosa 26, CFH Basal laminar drusen, Complement factor H deficiency, {Hemolytic uremic syndrome, atypical, susceptibility to, 1}, {Macular degeneration, age related, 4}, CHD7 CHARGE syndrome, Hypogonadotropic hypogonadism 5 with or without anosmia, CHM Choroideremia, CHMP4B Cataract 31, multiple types, CHST6 Macular corneal dystrophy, CIB2 Deafness 48, Usher syndrome, type IJ, CLDN19 Hypomagnesemia 5, renal, with ocular involvement, CLN3 Ceroid lipofuscinosis, neuronal, 3, CLN5 Ceroid lipofuscinosis, neuronal, 5, CLN6 Ceroid lipofuscinosis, neuronal, 6, Ceroid lipofuscinosis, neuronal, Kufs type, adult onset, CLN8 Ceroid lipofuscinosis, neuronal, 8, Ceroid lipofuscinosis, neuronal, 8, Northern epilepsy variant,

5 Phenotype description including phenotype ID(s) median depth CLRN1 Retinitis pigmentosa 61, Usher syndrome, type 3A, CLUAP1 No phenotype CNGA1 Retinitis pigmentosa 49, CNGA3 Achromatopsia 2, CNGB1 Retinitis pigmentosa 45, CNGB3 Achromatopsia 3, Macular degeneration, juvenile, CNNM4 Jalili syndrome, COL11A1 Fibrochondrogenesis 1, {Lumbar disc herniation, susceptibility to}, Marshall syndrome, Stickler syndrome, type II, COL11A2 Deafness 13, Deafness 53, Fibrochondrogenesis 2, Otospondylomegaepiphyseal dysplasia, Stickler syndrome, type III, Weissenbacher Zweymuller syndrome, COL18A1 Knobloch syndrome, type 1, COL2A1 Achondrogenesis, type II or hypochondrogenesis, Avascular necrosis of the femoral head, Czech dysplasia, Epiphyseal dysplasia, multiple, with myopia and deafness, Kniest dysplasia, Legg Calve Perthes disease, Osteoarthritis with mild chondrodysplasia, Platyspondylic skeletal dysplasia, Torrance type, SED congenita, SMED Strudwick type, Spondyloepiphyseal dysplasia, Stanescu type, Spondyloperipheral dysplasia, Stickler sydrome, type I, nonsyndromic ocular, Stickler syndrome, type I, Vitreoretinopathy with phalangeal epiphyseal dysplasia COL8A2 Corneal dystrophy, Fuchs endothelial, 1, Corneal dystrophy, posterior polymorphous 2, COL9A1?Epiphyseal dysplasia, multiple, 6, Stickler syndrome, type IV,

6 Phenotype description including phenotype ID(s) median depth COL9A2 Epiphyseal dysplasia, multiple, 2, ?Stickler syndrome, type V, CRB1 Leber congenital amaurosis 8, Pigmented paravenous chorioretinal atrophy, Retinitis pigmentosa 12, CRX Cone rod retinal dystrophy 2, Leber congenital amaurosis 7, CRYAA Cataract 9, multiple types, CRYAB Cardiomyopathy, dilated, 1II, Cataract 16, multiple types, Myopathy, myofibrillar, 2, Myopathy, myofibrillar, fatal infantile hypertrophy, alpha B crystallin related, CRYBA1 Cataract 10, multiple types, CRYBA2?Cataract 42, CRYBA4 Cataract 23, CRYBB1 Cataract 17, multiple types, CRYBB2 Cataract 3, multiple types, CRYBB3 Cataract 22, CRYGB Cataract 39, multiple types, CRYGC Cataract 2, multiple types, CRYGD Cataract 4, multiple types, CRYGS Cataract 20, multiple types, CSPP1 Joubert syndrome 21, CTDP1 Congenital cataracts, facial dysmorphism, and neuropathy, CTNNA1 Macular dystrophy, patterned, 2, CTNND1 No phenotype CWC27 Retinitis pigmentosa with or without skeletal anomalies, CYP1B1 Anterior segment dysgenesis 6, multiple subtypes, Glaucoma 3A, primary open angle, congenital, juvenile, or adult onset, CYP4V2 Bietti crystalline corneoretinal dystrophy, DCN Corneal dystrophy, congenital stromal, DFNB31 Retinitis pigmentosa 59, DHDDS Retinitis pigmentosa 59, DHX38 No phenotype DKC1 Dyskeratosis congenita, DPYD Dihydropyrimidine dehydrogenase deficiency, fluorouracil toxicity, DRAM2 Cone rod dystrophy 21, DTHD1 No phenotype

7 Phenotype description including phenotype ID(s) median depth DTNBP1 Hermansky Pudlak syndrome 7, EFEMP1 Doyne honeycomb degeneration of retina, ELOVL4 Ichthyosis, spastic quadriplegia, and mental retardation, ?Spinocerebellar ataxia 34, Stargardt disease 3, ELP4?Aniridia 2, EMC1 Cerebellar atrophy, visual impairment, and psychomotor retardation, EPG5 Vici syndrome, EPHA2 Cataract 6, multiple types, EXOSC2 No phenotype EYA1 Anterior segment anomalies with or without cataract, Branchiootic syndrome 1, Branchiootorenal syndrome 1, with or without cataracts, ?Otofaciocervical syndrome, EYS Retinitis pigmentosa 25, FA2H Spastic paraplegia 35, FAM161A Retinitis pigmentosa 28, FBN1 Acromicric dysplasia, Ectopia lentis, familial, Geleophysic dysplasia 2, MASS syndrome, Marfan lipodystrophy syndrome, Marfan syndrome, Stiff skin syndrome, Weill Marchesani syndrome 2, dominant, FLVCR1 Ataxia, posterior column, with retinitis pigmentosa, FOXC1 Anterior segment dysgenesis 3, multiple subtypes, Axenfeld Rieger syndrome, type 3, FOXE3 Anterior segment dysgenesis 2, multiple subtypes, {Aortic aneurysm, familial thoracic 11, susceptibility to}, Cataract 34, multiple types, FOXL2 Blepharophimosis, epicanthus inversus, and ptosis, type 1, Blepharophimosis, epicanthus inversus, and ptosis, type 2, Premature ovarian failure 3, FRAS1 Fraser syndrome, FREM1 Bifid nose with or without anorectal and renal anomalies, Manitoba oculotrichoanal syndrome, Trigonocephaly 2, FREM2 Fraser syndrome,

8 Phenotype description including phenotype ID(s) median depth FRMD7 Nystagmus 1, congenital, Nystagmus, infantile periodic alternating, FSCN2 Retinitis pigmentosa 30, FTL Hyperferritinemia cataract syndrome, L ferritin deficiency, dominant and recessive, Neurodegeneration with brain iron accumulation 3, FYCO1 Cataract 18, FZD4 Exudative vitreoretinopathy 1, Retinopathy of prematurity, GALK1 Galactokinase deficiency with cataracts, GALT Galactosemia, GCNT2 Adult i phenotype without cataract, [Blood group, Ii], Cataract 13 with adult i phenotype, GDF3 Klippel Feil syndrome 3, Microphthalmia with coloboma 6, Microphthalmia, isolated 7, GDF6 Klippel Feil syndrome 1, Leber congenital amaurosis 17, Microphthalmia with coloboma 6, digenic, Microphthalmia, isolated 4, GFER Myopathy progressive, with congenital cataract, hearing loss, and developmental delay, GJA1 Atrioventricular septal defect 3, Craniometaphyseal dysplasia, Erythrokeratodermia variabilis et progressiva, Hypoplastic left heart syndrome 1, Oculodentodigital dysplasia, Oculodentodigital dysplasia, Palmoplantar keratoderma with congenital alopecia, Syndactyly, type III, GJA3 Cataract 14, multiple types, GJA8 Cataract 1, multiple types, GLI2 Culler Jones syndrome, Holoprosencephaly 9, GLIS2 Nephronophthisis 7, GNAT1 Night blindness, congenital stationary 3, ?Night blindness, congenital stationary, type 1G, GNAT2 Achromatopsia 4, GNPTG Mucolipidosis III gamma,

9 Phenotype description including phenotype ID(s) median depth GPR143 Nystagmus 6, congenital, Ocular albinism, type I, Nettleship Falls type, GPR179 Night blindness, congenital stationary (complete), 1E, GRASP No phenotype No coverage data GRK1 Oguchi disease 2, GRM6 Night blindness, congenital stationary (complete), 1B, GRN Aphasia, primary progressive, Ceroid lipofuscinosis, neuronal, 11, Frontotemporal lobar degeneration with ubiquitin positive inclusions, GSN Amyloidosis, Finnish type, GUCA1A Cone dystrophy 3, Cone rod dystrophy 14, GUCA1B Retinitis pigmentosa 48, GUCY2D Cone rod dystrophy 6, Leber congenital amaurosis 1, HARS Charcot Marie Tooth disease, axonal, type 2W, Usher syndrome type 3B, HCCS Linear skin defects with multiple congenital anomalies 1, HGSNAT Mucopolysaccharidosis type IIIC (Sanfilippo C), Retinitis pigmentosa 73, HK1 Hemolytic anemia due to hexokinase deficiency, Neuropathy, hereditary motor and sensory, Russe type, Retinitis pigmentosa 79, HMGB3?Microphthalmia, syndromic 13, HMX1 Oculoauricular syndrome, HPS1 Hermansky Pudlak syndrome 1, HPS3 Hermansky Pudlak syndrome 3, HPS4 Hermansky Pudlak syndrome 4, HPS5 Hermansky Pudlak syndrome 5, HPS6 Hermansky Pudlak syndrome 6, HSF4 Cataract 5, multiple types, IDH3A No phenotype IDH3B Retinitis pigmentosa 46, IFT140 Short rib thoracic dysplasia 9 with or without polydactyly, IFT172 Retinitis pigmentosa 71, Short rib thoracic dysplasia 10 with or without polydactyly, IFT27?Bardet Biedl syndrome 19, IFT74?Bardet Biedl syndrome 20, IGBP1 Corpus callosum, agenesis of, with mental retardation, ocular coloboma and micrognathia,

10 Phenotype description including phenotype ID(s) median depth IMPDH1 Leber congenital amaurosis 11, Retinitis pigmentosa 10, IMPG1 Macular dystrophy, vitelliform, 4, IMPG2 Macular dystrophy, vitelliform, 5, Retinitis pigmentosa 56, INPP5E Joubert syndrome 1, Mental retardation, truncal obesity, retinal dystrophy, and micropenis, INVS Nephronophthisis 2, infantile, IQCB1 Senior Loken syndrome 5, JAM3 Hemorrhagic destruction of the brain, subependymal calcification, and cataracts, KCNJ13 Leber congenital amaurosis 16, Snowflake vitreoretinal degeneration, KCNV2 Retinal cone dystrophy 3B, KERA Cornea plana 2, KIF11 Microcephaly with or without chorioretinopathy, lymphedema, or mental retardation, KIF21A Fibrosis of extraocular muscles, congenital, 1, Fibrosis of extraocular muscles, congenital, 3B, KIF7 Acrocallosal syndrome, ?Al Gazali Bakalinova syndrome, ?Hydrolethalus syndrome 2, Joubert syndrome 12, KIZ Retinitis pigmentosa 69, KLHL7 Cold induced sweating syndrome 3, Retinitis pigmentosa 42, KRT12 Meesmann corneal dystrophy, KRT3 Meesmann corneal dystrophy, LAMA1 Poretti Boltshauser syndrome, LCA5 Leber congenital amaurosis 5, LEMD2 Cataract 46, juvenile onset, LIM2 Cataract 19, multiple types, LRAT Leber congenital amaurosis 14, Retinal dystrophy, early onset severe, Retinitis pigmentosa, juvenile, LRIT3 Night blindness, congenital stationary (complete), 1F, LRMDA Albinism, oculocutaneous, type VII, LRP2 Donnai Barrow syndrome,

11 Phenotype description including phenotype ID(s) median depth LRP5 [Bone mineral density variability 1], Exudative vitreoretinopathy 4, Hyperostosis, endosteal, Osteopetrosis 1, Osteoporosis pseudoglioma syndrome, {Osteoporosis}, Osteosclerosis, van Buchem disease, type 2, LSS Cataract 44, LTBP2 Glaucoma 3, primary congenital, D, Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma, Weill Marchesani syndrome 3, recessive, LYST Chediak Higashi syndrome, LZTFL1 Bardet Biedl syndrome 17, MAB21L2 Microphthalmia, syndromic 14, MAF Ayme Gripp syndrome, Cataract 21, multiple types, MAK Retinitis pigmentosa 62, MAPKAPK3?Macular dystrophy, patterned, 3, MERTK Retinitis pigmentosa 38, MFN2 Charcot Marie Tooth disease, axonal, type 2A2A, Charcot Marie Tooth disease, axonal, type 2A2B, Hereditary motor and sensory neuropathy VIA, MFRP Microphthalmia, isolated 5, Nanophthalmos 2, MFSD8 Ceroid lipofuscinosis, neuronal, 7, Macular dystrophy with central cone involvement, MIP Cataract 15, multiple types, MIR184 EDICT syndrome, No coverage data MIR204?Retinal dystrophy and iris coloboma with or without cataract, No coverage data MITF COMMAD syndrome, {Melanoma, cutaneous malignant, susceptibility to, 8}, Tietz albinism deafness syndrome, Waardenburg syndrome, type 2A, Waardenburg syndrome/ocular albinism, digenic, MKKS Bardet Biedl syndrome 6, McKusick Kaufman syndrome,

12 Phenotype description including phenotype ID(s) median depth MKS1 Bardet Biedl syndrome 13, Joubert syndrome 28, Meckel syndrome 1, MTTP Abetalipoproteinemia, {Metabolic syndrome, protection against}, MVK Hyper IgD syndrome, Mevalonic aciduria, Porokeratosis 3, multiple types, MYO7A Deafness 11, Deafness 2, Usher syndrome, type 1B, MYOC Glaucoma 1A, primary open angle, NAA10?Microphthalmia, syndromic 1, Ogden syndrome, dominant NDP Exudative vitreoretinopathy 2, Norrie disease, NEK2?Retinitis pigmentosa 67, NEK8?Nephronophthisis 9, ?Renal hepatic pancreatic dysplasia 2, NEUROD1 {Diabetes mellitus, noninsulin dependent}, Maturity onset diabetes of the young 6, NHS Cataract 40, Nance Horan syndrome, NMNAT1 Leber congenital amaurosis 9, NPHP1 Joubert syndrome 4, Nephronophthisis 1, juvenile, Senior Loken syndrome 1, NPHP3 Meckel syndrome 7, Nephronophthisis 3, Renal hepatic pancreatic dysplasia 1, NPHP4 Nephronophthisis 4, Senior Loken syndrome 4, NR2E3 Enhanced S cone syndrome, Retinitis pigmentosa 37, NR2F1 Bosch Boonstra Schaaf optic atrophy syndrome, NRL Retinal degeneration, clumped pigment type Retinitis pigmentosa 27, NYX Night blindness, congenital stationary (complete), 1A, OAT Gyrate atrophy of choroid and retina with or without ornithinemia,

13 Phenotype description including phenotype ID(s) median depth OCA2 Albinism, brown oculocutaneous, Albinism, oculocutaneous, type II, [Skin/hair/eye pigmentation 1, blond/brown hair], [Skin/hair/eye pigmentation 1, blue/nonblue eyes], OCRL Dent disease 2, Lowe syndrome, OFD1 Joubert syndrome 10, Orofaciodigital syndrome I, ?Retinitis pigmentosa 23, Simpson Golabi Behmel syndrome, type 2, OPA1 Behr syndrome, {Glaucoma, normal tension, susceptibility to}, ?Mitochondrial DNA depletion syndrome 14 (encephalocardiomyopathic type), Optic atrophy 1, Optic atrophy plus syndrome, OPA3 3 methylglutaconic aciduria, type III, Optic atrophy 3 with cataract, OPN1LW Blue cone monochromacy, Colorblindness, protan, OPN1MW Blue cone monochromacy, Colorblindness, deutan, OPN1SW Colorblindness, tritan, OPTN Amyotrophic lateral sclerosis 12, Glaucoma 1, open angle, E, {Glaucoma, normal tension, susceptibility to}, OR2W3 No phenotype OTX2 Microphthalmia, syndromic 5, Pituitary hormone deficiency, combined, 6, Retinal dystrophy, early onset, with or without pituitary dysfunction, P3H2 Myopia, high, with cataract and vitreoretinal degeneration, PANK2 HARP syndrome, Neurodegeneration with brain iron accumulation 1, PAX2 Glomerulosclerosis, focal segmental, 7, Papillorenal syndrome,

14 Phenotype description including phenotype ID(s) median depth PAX6 Aniridia, Anterior segment dysgenesis 5, multiple subtypes, Cataract with late onset corneal dystrophy, ?Coloboma of optic nerve, ?Coloboma, ocular, Foveal hypoplasia 1, Keratitis, ?Morning glory disc anomaly, Optic nerve hypoplasia, PCDH15 Deafness 23, Usher syndrome, type 1D/F digenic, Usher syndrome, type 1F, PCYT1A Spondylometaphyseal dysplasia with cone rod dystrophy, PDE6A Retinitis pigmentosa 43, PDE6B Night blindness, congenital stationary 2, Retinitis pigmentosa 40, PDE6C Cone dystrophy 4, PDE6G Retinitis pigmentosa 57, PDE6H Achromatopsia 6, Retinal cone dystrophy 3, PDZD7 {Retinal disease in Usher syndrome type IIA, modifier of}, Usher syndrome, type IIC, GPR98/PDZD7 digenic, PEX1 Heimler syndrome 1, Peroxisome biogenesis disorder 1A (Zellweger), Peroxisome biogenesis disorder 1B (NALD/IRD), PEX2 Peroxisome biogenesis disorder 5A (Zellweger), Peroxisome biogenesis disorder 5B, PEX7 Peroxisome biogenesis disorder 9B, Rhizomelic chondrodysplasia punctata, type 1, PGK1 Phosphoglycerate kinase 1 deficiency, PHYH Refsum disease, PIGL CHIME syndrome, PIK3R1?Agammaglobulinemia 7, Immunodeficiency 36, SHORT syndrome, PIKFYVE Corneal fleck dystrophy, PITPNM3 Cone rod dystrophy 5,

15 Phenotype description including phenotype ID(s) median depth PITX2 Anterior segment dysgenesis 4, Axenfeld Rieger syndrome, type 1, Ring dermoid of cornea, PITX3 Anterior segment dysgenesis 1, multiple subtypes, Cataract 11, multiple types, Cataract 11, syndromic, PLA2G5 [Fleck retina, familial benign], PLK4 Microcephaly and chorioretinopathy, 2, PNPLA6 Boucher Neuhauser syndrome, ?Laurence Moon syndrome, Oliver McFarlane syndrome, Spastic paraplegia 39, POC1B Cone rod dystrophy 20, POMGNT1 Muscular dystrophy dystroglycanopathy (congenital with brain and eye anomalies), type A, 3, Muscular dystrophy dystroglycanopathy (congenital with mental retardation), type B, 3, Muscular dystrophy dystroglycanopathy (limb girdle), type C, 3, Retinitis pigmentosa 76, PPT1 Ceroid lipofuscinosis, neuronal, 1, PRCD Retinitis pigmentosa 36, PRDM13 No phenotype PRDM5 Brittle cornea syndrome 2, PROM1 Cone rod dystrophy 12, Macular dystrophy, retinal, 2, Retinitis pigmentosa 41, Stargardt disease 4, PRPF3 Retinitis pigmentosa 18, PRPF31 Retinitis pigmentosa 11, PRPF4 Retinitis pigmentosa 70, PRPF6 Retinitis pigmentosa 60, PRPF8 Retinitis pigmentosa 13, PRPH2 Choriodal dystrophy, central areolar 2, Leber congenital amaurosis 18, Macular dystrophy, patterned, 1, Macular dystrophy, vitelliform, 3, Retinitis pigmentosa 7 and digenic, Retinitis punctata albescens, PRSS56 Microphthalmia, isolated 6, PXDN Anterior segment dysgenesis 7, with sclerocornea, RAB28 Cone rod dystrophy 18,

16 Phenotype description including phenotype ID(s) median depth RARB Microphthalmia, syndromic 12, RAX Microphthalmia, isolated 3, RAX2 Cone rod dystrophy 11, ?Macular degeneration, age related, 6, RBP3?Retinitis pigmentosa 66, RBP4 Microphthalmia, isolated, with coloboma 10, Retinal dystrophy, iris coloboma, and comedogenic acne syndrome, RCBTB1 Retinal dystrophy with or without extraocular anomalies, RD3 Leber congenital amaurosis 12, RDH11?Retinal dystrophy, juvenile cataracts, and short stature syndrome, RDH12 Leber congenital amaurosis 13, RDH5 Fundus albipunctatus, REEP6 Retinitis pigmentosa 77, RGR Retinitis pigmentosa 44, RGS9 Bradyopsia, RGS9BP Bradyopsia, RHO Night blindness, congenital stationary 1, Retinitis pigmentosa 4 or recessive, Retinitis punctata albescens, RIMS1 Cone rod dystrophy 7, RLBP1 Bothnia retinal dystrophy, Fundus albipunctatus, Newfoundland rod cone dystrophy, Retinitis punctata albescens, ROM1 Retinitis pigmentosa 7, digenic, RP1 Retinitis pigmentosa 1, RP1L1 Occult macular dystrophy, RP2 Retinitis pigmentosa 2, RP9?Retinitis pigmentosa 9, RPE65 Leber congenital amaurosis 2, Retinitis pigmentosa 20, RPGR Cone rod dystrophy, 1, Macular degeneration atrophic, Retinitis pigmentosa 3, Retinitis pigmentosa, and sinorespiratory infections, with or without deafness, RPGRIP1 Cone rod dystrophy 13, Leber congenital amaurosis 6,

17 Phenotype description including phenotype ID(s) median depth RPGRIP1L COACH syndrome, Joubert syndrome 7, Meckel syndrome 5, RS1 Retinoschisis, RTN4IP1 Optic atrophy 10 with or without ataxia, mental retardation, and seizures, SAG Oguchi disease 1, Retinitis pigmentosa 47, SALL2?Coloboma, ocular, SDCCAG8 Bardet Biedl syndrome 16, Senior Loken syndrome 7, SEMA4A Cone rod dystrophy 10, Retinitis pigmentosa 35, SHH Holoprosencephaly 3, Microphthalmia with coloboma 5, Schizencephaly, Single median maxillary central incisor, SIPA1L3?Cataract 45, SIX3 Holoprosencephaly 2, Schizencephaly, SIX6 Optic disc anomalies with retinal and/or macular dystrophy, SLC16A12 Cataract 47, juvenile, with microcornea, SLC24A1 Night blindness, congenital stationary (complete), 1D, SLC24A5 Albinism, oculocutaneous, type VI, [Skin/hair/eye pigmentation 4, fair/dark skin], SLC33A1 Congenital cataracts, hearing loss, and neurodegeneration, Spastic paraplegia 42, SLC38A8 Foveal hypoplasia 2, with or without optic nerve misrouting and/or anterior segment dysgenesis, SLC45A2 Albinism, oculocutaneous, type IV, [Skin/hair/eye pigmentation 5, black/nonblack hair], [Skin/hair/eye pigmentation 5, dark/fair skin], [Skin/hair/eye pigmentation 5, dark/light eyes], SLC4A11 Corneal dystrophy, Fuchs endothelial, 4, Corneal endothelial dystrophy and perceptive deafness, Corneal endothelial dystrophy, SLC52A2 Brown Vialetto Van Laere syndrome 2, SLC7A14 Retinitis pigmentosa 68, SMOC1 Microphthalmia with limb anomalies, SNRNP200 Retinitis pigmentosa 33,

18 Phenotype description including phenotype ID(s) median depth SOX2 Microphthalmia, syndromic 3, Optic nerve hypoplasia and abnormalities of the central nervous system, SPATA7 Leber congenital amaurosis 3, Retinitis pigmentosa, juvenile, SPP2 No phenotype SRD5A3 Congenital disorder of glycosylation, type Iq, Kahrizi syndrome, STRA6 Microphthalmia, isolated, with coloboma 8, Microphthalmia, syndromic 9, TACSTD2 Corneal dystrophy, gelatinous drop like, TCOF1 Treacher Collins syndrome 1, TCTN1 Joubert syndrome 13, TCTN3 Joubert syndrome 18, Orofaciodigital syndrome IV, TDRD7 Cataract 36, TEAD1 Sveinsson chorioretinal atrophy, TENM3 Microphthalmia, isolated, with coloboma 9, TFAP2A Branchiooculofacial syndrome, TGFBI Corneal dystrophy, Avellino type, Corneal dystrophy, Groenouw type I, Corneal dystrophy, Reis Bucklers type, Corneal dystrophy, Thiel Behnke type, Corneal dystrophy, epithelial basement membrane, Corneal dystrophy, lattice type I, Corneal dystrophy, lattice type IIIA, TGIF1 Holoprosencephaly 4, TIMM8A Mohr Tranebjaerg syndrome, TIMP3 Sorsby fundus dystrophy, TMEM126A Optic atrophy 7, TMEM138 Joubert syndrome 16, TMEM231 Joubert syndrome 20, Meckel syndrome 11, TMEM237 Joubert syndrome 14, TMEM67 {Bardet Biedl syndrome 14, modifier of}, COACH syndrome, Joubert syndrome 6, Meckel syndrome 3, Nephronophthisis 11, TOPORS Retinitis pigmentosa 31,

19 Phenotype description including phenotype ID(s) median depth TPP1 Ceroid lipofuscinosis, neuronal, 2, Spinocerebellar ataxia 7, TREX1 Aicardi Goutieres syndrome 1, dominant and recessive, Chilblain lupus, {Systemic lupus erythematosus, susceptibility to}, Vasculopathy, retinal, with cerebral leukodystrophy, TRIM32?Bardet Biedl syndrome 11, Muscular dystrophy, limb girdle, type 2H, TRNT1 Retinitis pigmentosa and erythrocytic microcytosis, Sideroblastic anemia with B cell immunodeficiency, periodic fevers, and developmental delay, TRPM1 Night blindness, congenital stationary (complete), 1C, TSPAN12 Exudative vitreoretinopathy 5, TTC8 Bardet Biedl syndrome 8, ?Retinitis pigmentosa 51, TTLL5 Cone rod dystrophy 19, TUB?Retinal dystrophy and obesity, TUBGCP4 Microcephaly and chorioretinopathy, 3, TULP1 Leber congenital amaurosis 15, Retinitis pigmentosa 14, TYR Albinism, oculocutaneous, type IA, Albinism, oculocutaneous, type IB, {Melanoma, cutaneous malignant, susceptibility to, 8}, [Skin/hair/eye pigmentation 3, blue/green eyes], [Skin/hair/eye pigmentation 3, light/dark/freckling skin], Waardenburg syndrome/albinism, digenic, TYRP1 Albinism, oculocutaneous, type III, [Skin/hair/eye pigmentation, variation in, 11 (Melanesian blond hair)], UBIAD1 Corneal dystrophy, Schnyder type, UNC119?Cone rod dystrophy ?Immunodeficiency 13, UNC45B?Cataract 43, USH1C Deafness 18A, Usher syndrome, type 1C, USH1G Usher syndrome, type 1G, USH2A Retinitis pigmentosa 39, Usher syndrome, type 2A, VAX1?Microphthalmia, syndromic 11, VCAN Wagner syndrome 1, VIM Cataract 30, pulverulent,

20 Phenotype description including phenotype ID(s) median depth VSX1?Craniofacial anomalies and anterior segment dysgenesis syndrome, Keratoconus 1, VSX2 Microphthalmia with coloboma 3, Microphthalmia, isolated 2, WASHC5 Ritscher Schinzel syndrome 1, Spastic paraplegia 8, WDPCP?Bardet Biedl syndrome 15, ?Congenital heart defects, hamartomas of tongue, and polysyndactyly, WDR19?Cranioectodermal dysplasia 4, Nephronophthisis 13, Senior Loken syndrome 8, ?Short rib thoracic dysplasia 5 with or without polydactyly, WFS1?Cataract 41, Deafness 6/14/38, {Diabetes mellitus, noninsulin dependent, association with}, Wolfram syndrome, Wolfram like syndrome, WHRN Deafness 31, Usher syndrome, type 2D, WRN Werner syndrome, YAP1 Coloboma, ocular, Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or mental retardation, YME1L1?Optic atrophy 11, ZEB2 Mowat Wilson syndrome, ZIC2 Holoprosencephaly 5, ZNF408?Exudative vitreoretinopathy 6, Retinitis pigmentosa 72, ZNF423 Joubert syndrome 19, Nephronophthisis 14, ZNF469 Brittle cornea syndrome 1, ZNF513?Retinitis pigmentosa 58, ZNF644 Myopia 21, Gene symbols according HGCN release used: "No phenotypes" indicates a gene without a current association phenotypes between "[ ]", indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values phenotypes between "{}", indicate risk factors phenotypes with a question mark, "?", before the disease name indicates an unconfirmed or possibly spurious mapping. The statistics above are based on a set of 50 samples Median depth is the median of the mean sequence depth over the protein coding exons of the transcript % Covered 10x describes the percentage of a gene s coding sequence that is covered at least 10x

21 Phenotype description including phenotype ID(s) % 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 median depth