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 ACTB gene ACTB Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser-Winter syndrome 1, 243310 2505231 False 3 100;0;0 1.51 False ENSG00000075624 ENSG00000075624 HGNC:132 ACTG1 gene ACTG1 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Baraitser-Winter syndrome 2, 614583 22366783 False 3 100;0;0 1.51 False ENSG00000184009 ENSG00000184009 HGNC:144 ALDH1A3 gene ALDH1A3 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Microphthalmia, isolated 8 615113 23591992;24859618 False 3 100;0;0 1.51 False ENSG00000184254 ENSG00000184254 HGNC:409 B3GLCT gene B3GLCT Expert Review;Expert Review Green Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Peters-plus syndrome, 261540 16909395 False 3 100;0;0 1.51 False ENSG00000187676 ENSG00000187676 HGNC:20207 BMP4 gene BMP4 Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia, syndromic 6, 607932 18252212, 2427285 False 3 50;0;50 1.51 False ENSG00000125378 ENSG00000125378 HGNC:1071 C12orf57 gene C12orf57 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Temtamy syndrome, 218340 23453665, 24859618 False 3 0;0;0 1.51 False ENSG00000111678 ENSG00000111678 HGNC:29521 CC2D2A gene CC2D2A Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal COACH syndrome, 216360 19574260 False 3 100;0;0 1.51 False ENSG00000048342 ENSG00000048342 HGNC:29253 CHD7 gene CHD7 Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted CHARGE syndrome, 214800 16400610 False 3 100;0;0 1.51 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000171316 ENSG00000171316 HGNC:20626 CLDN19 gene CLDN19 Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Hypomagnesemia 5, renal, with ocular involvement, 248190 17033971, 500385 False 3 0;0;0 1.51 False ENSG00000164007 ENSG00000164007 HGNC:2040 FOXE3 gene FOXE3 Emory Genetics Laboratory;Expert Review Green;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Anterior segment mesenchymal dysgenesis 107250 24859618, 19708017 False 3 0;0;0 1.51 False ENSG00000186790 ENSG00000186790 HGNC:3808 FZD5 gene FZD5 Expert Review Green;Literature Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia/coloboma 11, OMIM:620731 32737437;26908622 False 3 100;0;0 1.51 False ENSG00000163251 ENSG00000163251 HGNC:4043 HCCS gene HCCS Emory Genetics Laboratory;Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders 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 1, 309801 17033964, 24859618 False 3 100;0;0 1.51 False ENSG00000004961 ENSG00000004961 HGNC:4837 HMX1 gene HMX1 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Oculoauricular syndrome 612109 18423520;25574057;21417677;29140751 False 3 0;100;0 1.51 False ENSG00000215612 ENSG00000215612 HGNC:5017 LRP2 gene LRP2 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Donnai-Barrow syndrome, 222448 17632512;8266995;18553518 False 3 0;0;0 1.51 False ENSG00000081479 ENSG00000081479 HGNC:6694 MAB21L2 gene MAB21L2 Expert Review Green;Literature Ocular coloboma Ocular malformations Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Microphthalmia, syndromic 14 615877 PMID: 25719200;PMID: 24906020 False 3 50;0;50 1.51 False ENSG00000181541 ENSG00000181541 HGNC:6758 OTX2 gene OTX2 Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia, syndromic 5, 610125 15846561, 18781617,24859618 False 3 100;0;0 1.51 False ENSG00000165588 ENSG00000165588 HGNC:8522 PAX2 gene PAX2 Expert Review Green;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Papillorenal syndrome 120330 8589702 False 3 100;0;0 1.51 False ENSG00000075891 ENSG00000075891 HGNC:8616 PAX6 gene PAX6 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted ?Morning glory disc anomaly, 120430Aniridia, 106210Cataract with late-onset corneal dystrohpy, 106210Coloboma of optic nerve, 120430Coloboma, ocular, 120200Foveal hypoplasia 1, 136520Gillespie syndrome, 206700Keratitis, 148190Optic nerve hypoplasia, 165550Peters anomaly, 604229 12721955, 24859618 False 3 100;0;0 1.51 False ENSG00000007372 ENSG00000007372 HGNC:8620 PORCN gene PORCN Emory Genetics Laboratory;Expert Review Green;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Focal dermal hypoplasia 305600 17546030, 24859618 False 3 100;0;0 1.51 False ENSG00000102312 ENSG00000102312 HGNC:17652 PUF60 gene PUF60 Expert Review;Expert Review Green Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Verheij syndrome, 615583;VRJS;Chromosome 8q24.3 deletion syndrome;PUF60 syndrome;ocular abnormalities 28327570;27804958;24140112;19464398 False 3 100;0;0 1.51 False ENSG00000179950 ENSG00000179950 HGNC:17042 RARB gene RARB Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Microphthalmia, syndromic 12 615524 24859618 False 3 0;0;100 1.51 False ENSG00000077092 ENSG00000077092 HGNC:9865 RPGRIP1L gene RPGRIP1L Emory Genetics Laboratory;Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal COACH syndrome, 216360 19574260 False 3 100;0;0 1.51 False ENSG00000103494 ENSG00000103494 HGNC:29168 SALL4 gene SALL4 Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Duane-radial ray syndrome, 607323 12843316, 6426304 False 3 100;0;0 1.51 False ENSG00000101115 ENSG00000101115 HGNC:15924 SMO gene SMO Expert Review Green;Literature Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Curry-Jones syndrome, somatic mosaic 601707 27236920 False 3 0;0;100 1.51 False ENSG00000128602 ENSG00000128602 HGNC:11119 SOX2 gene SOX2 Emory Genetics Laboratory;Expert Review Green;Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Microphthalmia, syndromic 3 206900 12612584, 24859618 False 3 100;0;0 1.51 False ENSG00000181449 ENSG00000181449 HGNC:11195 STRA6 gene STRA6 Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Microphthalmia, syndromic 9, 601186Microphthalmia, isolated, with coloboma 8, 601186 17273977, 24859618 False 3 100;0;0 1.51 False ENSG00000137868 ENSG00000137868 HGNC:30650 TENM3 gene TENM3 Expert Review Green;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Microphthalmia, syndromic 15, OMIM:615145;?Microphthalmia, isolated, with coloboma 9, OMIM:615145;Microphthalmia, isolated, with coloboma 9, MONDO:0014059 22766609;27103084;30513139;29753094 False 3 50;0;50 1.51 False ENSG00000218336 ENSG00000218336 HGNC:29944 VSX2 gene VSX2 Emory Genetics Laboratory;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Microphthalmia/coloboma 3, OMIM:610092 10932181, 24859618 False 3 100;0;0 1.51 False ENSG00000119614 ENSG00000119614 HGNC:1975 YAP1 gene YAP1 Expert Review Green;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Coloboma, ocular, 120433;Coloboma, ocular, with or without hearing impairment, cleft lip/palate, and/or mentalretardation, 120433;isolated ocular coloboma 24462371;26209646;27267789 False 3 50;0;50 1.51 False ENSG00000137693 ENSG00000137693 HGNC:16262 C16orf62 gene C16orf62 Expert Review Amber;Literature Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal 3C/Ritscher-Schinzel-like syndrome 31712251 False 2 0;100;0 1.51 False ENSG00000103544 ENSG00000103544 HGNC:24641 IGBP1 gene IGBP1 Emory Genetics Laboratory;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders Corpus callosum, agenesis of, with mental retardation, ocular coloboma andmicrognathia, 300472 False 2 0;0;100 1.51 False ENSG00000089289 ENSG00000089289 HGNC:5461 MAF gene MAF Literature;Radboud University Medical Center, Nijmegen;UKGTN Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cataract 21, multiple types 610202 11772997 False 2 100;0;0 1.51 False ENSG00000178573 ENSG00000178573 HGNC:6776 PIGL gene PIGL Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Coloboma, Congenital Heart Disease, Ichthyosiform Dermatosis,Mental Retardation, and Ear Anomalies Syndrome;CHIME syndrome, 280000 22444671 False 2 0;100;0 1.51 False ENSG00000108474 ENSG00000108474 HGNC:8966 RBP4 gene RBP4 Emory Genetics Laboratory;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Retinal dystrophy, iris coloboma, and comedogenic acne syndrome, 615147 9888420 False 2 0;0;100 1.51 False ENSG00000138207 ENSG00000138207 HGNC:9922 SIX6 gene SIX6 Illumina TruGenome Clinical Sequencing Services;Literature;Radboud University Medical Center, Nijmegen Ocular coloboma Ocular malformations Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Optic disc anomalies with retinal and/or macular dystrophy, 212550 23167593, 24702266 False 2 0;0;100 1.51 False ENSG00000184302 ENSG00000184302 HGNC:10892 ISCA-37393-Gain region Expert Review Green;ClinGen Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown PMID 22890013: variable phenotype including developmental delay, ocular coloboma, preauricular tags/pits, cleft palate, skeletal defects, heart defects, urogenital defect, anal defect, hearing loss, clinodactyly of fifth fingers, umbilical hernia, accessory spleen, strabismus, shortening of the fifth finger. PMID 22495764: Inter and intra individual variability of phenotype, mosaic. PMID 11693792: preauricular skin tags and pits, downslanting palpebral fissures, hypertelorism, ectopic anus, hypospadias, and hypoplastic left heart syndrome;115470 11693792;22890013;22495764 False 3 0;0;0 1.51 False 22 16912063 18109094 3 60 cnv_gain 22q11.21 recurrent (Cat eye syndrome) region (includes CECR2) Gain ISCA-37396-Loss region Expert Review Green;Expert list Ocular coloboma Ocular malformations Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Chromosome 15q24 deletion syndrome, 613406;PMID: 22180641 intellectual disability, growth retardation, unusual facial morphology;developmental delay, severe speech problems;PMID:19557438 Developmental delay, short stature, hypotonia, digital abnormalities, joint laxity, genital abnormalities, characteristic facial features;PMID:614294 Developmental delay, loose connective tissue, digital and genital anomalies, distinct facial gestalt, congenital diaphragmatic hernia 22180641;19557438;19233321 False 3 100;0;0 1.51 False 15 72671374 75680568 3 60 cnv_loss 15q24 recurrent region (A-D) (includes SIN3A) Loss