Entity Name Entity type Gene Symbol Sources(; separated) Level4 Level3 Level2 Model_Of_Inheritance Phenotypes Omim Orphanet HPO Publications Description Flagged GEL_Status UserRatings_Green_amber_red version ready Mode of pathogenicity EnsemblId(GRch37) EnsemblId(GRch38) HGNC Position Chromosome Position GRCh37 Start Position GRCh37 End Position GRCh38 Start Position GRCh38 End STR Repeated Sequence STR Normal Repeats STR Pathogenic Repeats Region Haploinsufficiency Score Region Triplosensitivity Score Region Required Overlap Percentage Region Variant Type Region Verbose Name AIPL1 gene AIPL1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Cone-rod dystrophy;Leber congenital amaurosis 4, 604393;Retinitis pigmentosa, juvenile;Eye Disorders 25148430 False 2 0;100;0 4.43 False ENSG00000129221 ENSG00000129221 HGNC:359 BMP7 gene BMP7 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia, anophthalmia, systemic abnormalities, intellectual disability;None 20506283;7590254 False 2 0;100;0 4.43 False other - please provide details in the comments ENSG00000101144 ENSG00000101144 HGNC:1074 BMPR1A gene BMPR1A Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 29522511 False 2 0;100;0 4.43 False ENSG00000107779 ENSG00000107779 HGNC:1076 BRPF1 gene BRPF1 Expert list;Expert Review Amber Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Intellectual developmental disorder with dysmorphic facies and ptosis, OMIM:617333 33418956;31176769 False 2 0;100;0 4.43 False ENSG00000156983 ENSG00000156983 HGNC:14255 C16orf62 gene C16orf62 Expert Review Amber;Literature Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal 3C/Ritscher-Schinzel-like syndrome 31712251 False 2 0;100;0 4.43 False ENSG00000103544 ENSG00000103544 HGNC:24641 CDH2 gene CDH2 Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Agenesis of corpus callosum, cardiac, ocular, and genital syndrome, OMIM:618929;Agenesis of corpus callosum, cardiac, ocular, and genital syndrome, MONDO:0030065 31585109;31650526 False 2 0;100;0 4.43 False ENSG00000170558 ENSG00000170558 HGNC:1759 CDH4 gene CDH4 Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Iris coloboma, intellectual disability, and microcephaly 35034853;15918170 False 2 0;100;0 4.43 False ENSG00000179242 ENSG00000179242 HGNC:1763 CDK5RAP2 gene CDK5RAP2 Expert list;Expert Review Amber Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Microcephaly 3, primary, autosomal recessive, OMIM:604804, MONDO:0011488 31355417;32015000 False 2 0;100;0 4.43 False ENSG00000136861 ENSG00000136861 HGNC:18672 CNNM4 gene CNNM4 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Jalili syndrome, 217080;Eye Disorders 27419834 False 2 0;100;0 4.43 False ENSG00000158158 ENSG00000158158 HGNC:105 COL2A1 gene COL2A1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Epiphyseal dysplasia, multiple, with myopia and deafness;Eye Disorders;SED congenita;Kniest dysplasia, 156550;Stickler syndrome, type I, 108300;Stickler sydrome, type I, nonsyndromic ocular, 609508;Vitreoretinopathy with phalangeal epiphyseal dysplasia 18541977, 17347327 False 2 0;100;0 4.43 False ENSG00000139219 ENSG00000139219 HGNC:2200 COL6A3 gene COL6A3 Expert Review Amber;Literature Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Peters anomaly 33304895 False 2 0;100;0 4.43 False ENSG00000163359 ENSG00000163359 HGNC:2213 COX7B gene COX7B Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Linear Skin Defects with Multiple Congenital Anomalies 2, LSDMCA2, 300887 23122588 False 2 50;50;0 4.43 False ENSG00000131174 ENSG00000131174 HGNC:2291 CRB1 gene CRB1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Retinitis pigmentosa-12, autosomal recessive, 600105;Pigmented paravenous chorioretinal atrophy;Leber congenital amaurosis 8, 613835;Eye Disorders 23077403;21484995 False 2 0;100;0 4.43 False ENSG00000134376 ENSG00000134376 HGNC:2343 CRYBA4 gene CRYBA4 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cataract 23 (and microphthalmia in 1 case), 610425 16960806;20577656 False 2 0;100;0 4.43 False ENSG00000196431 ENSG00000196431 HGNC:2396 CRYBB3 gene CRYBB3 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Cataract 22, OMIM:609741 False 2 0;50;50 4.43 False ENSG00000100053 ENSG00000100053 HGNC:2400 CRYGD gene CRYGD Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cataract 4, Multiple Types, 115700 False 2 0;100;0 4.43 False ENSG00000118231 ENSG00000118231 HGNC:2411 DAG1 gene DAG1 Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 9, 613818 25934851;24052401 False 2 50;50;0 4.43 False ENSG00000173402 ENSG00000173402 HGNC:2666 EFTUD2 gene EFTUD2 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Mandibulofacial dysostosis, Guion-Almeida type, 610536 26118977 False 2 0;100;0 4.43 False ENSG00000108883 ENSG00000108883 HGNC:30858 ERCC1 gene ERCC1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Cerebrooculofacioskeletal syndrome 4, OMIM:610758 17273966 False 2 0;100;0 4.43 False ENSG00000012061 ENSG00000012061 HGNC:3433 FANCL gene FANCL Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Fanconi Anemia, Complementation Group L, FANCL, 614083 25754594 False 2 50;50;0 4.43 False ENSG00000115392 ENSG00000115392 HGNC:20748 FKRP gene FKRP Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 5, 606612 15121789;20675713;19955119;20236121 False 2 67;33;0 4.43 False ENSG00000181027 ENSG00000181027 HGNC:17997 FZD4 gene FZD4 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Exudative vitreoretinopathy 1, 133780;Eye Disorders 30882657;28413837 False 2 0;100;0 4.43 False ENSG00000174804 ENSG00000174804 HGNC:4042 GDF3 gene GDF3 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Klippel-Feil syndrome 3, autosomal dominant, OMIM:613702;Klippel-Feil syndrome 3, autosomal dominant, MONDO:0013375;Microphthalmia with coloboma 6, OMIM:613703;microphthalmia, isolated, with coloboma 6, MONDO:0013376;Microphthalmia, isolated 7, OMIM:613704;isolated microphthalmia 7, MONDO:0013377 19864492;24281366;29260090 False 2 0;80;20 4.43 False other - please provide details in the comments ENSG00000184344 ENSG00000184344 HGNC:4218 GLI2 gene GLI2 Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Holoprosencephaly 9, 610829 21204792;17096318 False 2 33;67;0 4.43 False ENSG00000074047 ENSG00000074047 HGNC:4318 HMGB3 gene HMGB3 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) ?Microphthalmia, syndromic 13, 300915 24993872 False 2 0;100;0 4.43 False ENSG00000029993 ENSG00000029993 HGNC:5004 HNRNPC gene HNRNPC Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Intellectual developmental disorder, autosomal dominant 74, OMIM:620688;microphthalmia, isolated, with coloboma, MONDO:0000170 37541189;40004505 False 2 0;100;0 4.43 False ENSG00000092199 ENSG00000092199 HGNC:5035 IGBP1 gene IGBP1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology X-LINKED: hemizygous mutation in males, biallelic mutations in females Corpus callosum, agenesis of, with mental retardation, ocular coloboma andmicrognathia, 300472 14556245 False 2 0;100;0 4.43 False ENSG00000089289 ENSG00000089289 HGNC:5461 IPO13 gene IPO13 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal 29700284 False 2 0;100;0 4.43 False ENSG00000117408 ENSG00000117408 HGNC:16853 KERA gene KERA Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Cornea plana congenita, recessive, 217300 False 2 0;100;0 4.43 False ENSG00000139330 ENSG00000139330 HGNC:6309 MYH10 gene MYH10 Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted neurodevelopmental disorder, MONDO:0700092;coloboma, MONDO:0001476 35980381;40044823 False 2 50;50;0 4.43 False ENSG00000133026 ENSG00000133026 HGNC:7568 NTN1 gene NTN1 Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted coloboma, MONDO:0001476;microphthalmia, MONDO:0021129 39648562;31162046 False 2 0;100;0 4.43 False ENSG00000065320 ENSG00000065320 HGNC:8029 OLFM2 gene OLFM2 Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Bilateral microphthalmia, short stature and facial dysmorphism;No OMIM 27844144;17122126 False 2 33;67;0 4.43 False ENSG00000105088 ENSG00000105088 HGNC:17189 PDE6D gene PDE6D Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal ?Joubert syndrome 22 (microphthalmia/optic nerve coloboma, intrauterine growth retardation, facial dysmorphism, postaxial polydactyly of feet, syndactyly, polydactyly, renal hypoplasia, extinguished electroretinogram), 615665 24166846 False 2 0;100;0 4.43 False ENSG00000156973 ENSG00000156973 HGNC:8788 PDGFRA gene PDGFRA Expert Review Amber;Literature Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Bilateral chorioretinal coloboma, microphthalmia and global developmental delay 35034853 False 2 0;100;0 4.43 False ENSG00000134853 ENSG00000134853 HGNC:8803 PLK4 gene PLK4 Expert Review Amber;Literature Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Microcephaly and chorioretinopathy, autosomal recessive, 2, OMIM:616171;microcephaly and chorioretinopathy 2, MONDO:0014516 25344692;25320347;27650967 False 2 0;100;0 4.43 False ENSG00000142731 ENSG00000142731 HGNC:11397 POMGNT2 gene POMGNT2 Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Muscular Dystrophy-Dystroglycanopathy, Type A, 8, MDDGA8, 614830 22958903 False 2 50;50;0 4.43 False ENSG00000144647 ENSG00000144647 HGNC:25902 PQBP1 gene PQBP1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology X-LINKED: hemizygous mutation in males, biallelic mutations in females Renpenning syndrome, OMIM:309500;Renpenning syndrome, MONDO:0010653 31718390;17033686 False 2 0;100;0 4.43 False ENSG00000102103 ENSG00000102103 HGNC:9330 SALL2 gene SALL2 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Coloboma, ocular, autosomal recessive, 216820 24412933 False 2 0;100;0 4.43 False ENSG00000165821 ENSG00000165821 HGNC:10526 SCLT1 gene SCLT1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Orofaciodigital syndrome IX (a severe ciliopathy phenotype featuring midline cleft, microcephaly, and colobomatous microphthalmia/anophthalmia, one case only (Adly et al 2014), variant was classified as unknown significance by OMIM);None 29450879;24285566;27894351;28486600;30425282;30237576 False 2 67;33;0 4.43 False ENSG00000151466 ENSG00000151466 HGNC:26406 SIX3 gene SIX3 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Holoprosencephaly 2 157170 21976454;21940735;10369266 False 2 0;100;0 4.43 False ENSG00000138083 ENSG00000138083 HGNC:10889 SLC16A12 gene SLC16A12 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cataract, juvenile, with microcornea and glucosuria, 612018 False 2 0;100;0 4.43 False ENSG00000152779 ENSG00000152779 HGNC:23094 SLC2A1 gene SLC2A1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted STOMATIN-DEFICIENT CRYOHYDROCYTOSIS WITH NEUROLOGIC DEFECTS, 608885 False 2 0;100;0 4.43 False ENSG00000117394 ENSG00000117394 HGNC:11005 SMAD4 gene SMAD4 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Myhre syndrome, 139210 11977156;20735985 False 2 0;100;0 4.43 False ENSG00000141646 ENSG00000141646 HGNC:6770 SMG9 gene SMG9 Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Heart and Brain Malformation Syndrome, HBMS, 616920 27018474 False 2 50;50;0 4.43 False ENSG00000105771 ENSG00000105771 HGNC:25763 TBC1D32 gene TBC1D32 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Orofaciodigital syndrome IX, OMIM:258865;orofaciodigital syndrome IX, MONDO:0009795;Alsahan-Harris syndrome, OMIM:621307;Alsahan-Harris syndrome, MONDO:0979871 32573025;31130284;32060556;24285566;35875813 False 2 0;100;0 4.43 False ENSG00000146350 ENSG00000146350 HGNC:21485 TCOF1 gene TCOF1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Treacher Collins syndrome 1 (eyelid coloboma), 154500 10888597;8741923 False 2 0;100;0 4.43 False ENSG00000070814 ENSG00000070814 HGNC:11654 TMX3 gene TMX3 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia, coloboma, micrognathia, diaphragmatic hernia;None 20485507 False 2 0;100;0 4.43 False ENSG00000166479 ENSG00000166479 HGNC:24718 TOGARAM1 gene TOGARAM1 Expert list;Expert Review Amber Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal TOGARAM1-related ciliopathy 32747439;32453716 False 2 0;100;0 4.43 False ENSG00000198718 ENSG00000198718 HGNC:19959 TSC2 gene TSC2 Expert list;Expert Review Amber Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Tuberous sclerosis-2, OMIM:613254 33110010;11264130 False 2 0;100;0 4.43 False ENSG00000103197 ENSG00000103197 HGNC:12363 TUBB gene TUBB Expert Review Amber;London North GLH;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Skin Creases, Congenital Symmetric Circumferential, 2, CSCSC2, 156610 26637975 False 2 50;50;0 4.43 False ENSG00000196230 ENSG00000196230 HGNC:20778 VAX1 gene VAX1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Microphthalmia, syndromic 11, 614402 10601035;22095910 False 2 0;100;0 4.43 False ENSG00000148704 ENSG00000148704 HGNC:12660 VSX1 gene VSX1 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Keratoconus 1, 148300;Corneal dystrophy, posterior polymorphous, 1, 122000;Craniofacial anomalies and anterior segment dysgenesis syndrome, 614195 15051220 False 2 0;100;0 4.43 False ENSG00000100987 ENSG00000100987 HGNC:12723 WNT2B gene WNT2B Expert Review Amber;Literature Structural eye disease Ophthalmology BIALLELIC, autosomal or pseudoautosomal Diarrhoea 9, OMIM:618168;microcornea;coloboma, MONDO:0001476 29909964;33526876 False 2 0;100;0 4.43 False ENSG00000134245 ENSG00000134245 HGNC:12781 ZIC2 gene ZIC2 Expert Review Amber;NHS GMS Structural eye disease Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Holoprosencephaly 5, 609637 21976454 False 2 0;100;0 4.43 False ENSG00000043355 ENSG00000043355 HGNC:12873