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 BIN1 gene BIN1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Centronuclear myopathy 2, MIM 255200 PMID 29950440 False 3 100;0;0 1.8 True ENSG00000136717 ENSG00000136717 HGNC:1052 C1QBP gene C1QBP Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Combined oxidative phosphorylation deficiency 33, MIM# 617713 PMID: 28942965 False 3 100;0;0 1.8 True ENSG00000108561 ENSG00000108561 HGNC:1243 CHAT gene CHAT Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 6, presynaptic, MIM# 254210" False 3 100;0;0 1.8 True ENSG00000070748 ENSG00000070748 HGNC:1912 CHN1 gene CHN1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Duane retraction syndrome 2, 604356 PMID 33004823;18653847;21555619 False 3 100;0;0 1.8 True ENSG00000128656 ENSG00000128656 HGNC:1943 CHRNA1 gene CHRNA1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted "Myasthenic syndrome, congenital, 1A, slow-channel, MIM# 601462" False 3 100;0;0 1.8 True ENSG00000138435 ENSG00000138435 HGNC:1955 CHRNB1 gene CHRNB1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 2A, slow-channel, MIM# 616313" False 3 100;0;0 1.8 True ENSG00000170175 ENSG00000170175 HGNC:1961 CHRND gene CHRND Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 3B, fast-channel, MIM# 616322" False 3 100;0;0 1.8 True ENSG00000135902 ENSG00000135902 HGNC:1965 CHRNE gene CHRNE Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 4B, fast-channel, MIM# 616324" False 3 100;0;0 1.8 True ENSG00000108556 ENSG00000108556 HGNC:1966 COL25A1 gene COL25A1 Expert Review Green;Genomics England PanelApp Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Fibrosis of extraocular muscles, congenital, 5, MIM# 616219 25500261;26486031;31875546;26437029 False 3 50;50;0 1.8 True ENSG00000188517 ENSG00000188517 HGNC:18603 COLQ gene COLQ Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 5, MIM# 603034" False 3 100;0;0 1.8 True ENSG00000206561 ENSG00000206561 HGNC:2226 DGUOK gene DGUOK Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 3 (hepatocerebral type), OMIM 251880;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4, OMIM 617070;portal hypertension, non cirrhotic OMIM 617068 PMID: 11687800;12205643;15887277 False 3 100;0;0 1.8 True ENSG00000114956 ENSG00000114956 HGNC:2858 GBA gene GBA Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Gaucher disease, type II, MIM# 230900" False 3 100;0;0 1.8 True ENSG00000177628 ENSG00000177628 HGNC:4177 HNRNPA2B1 gene HNRNPA2B1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted oculopharyngeal muscular dystrophy, MONDO:0008116, OMIM#620460 PMID:35484142 False 3 100;0;0 1.8 True ENSG00000122566 ENSG00000122566 HGNC:5033 HOXA1 gene HOXA1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Athabaskan brainstem dysgenesis syndrome;Bosley-Salih-Alorainy syndrome - 601536 17875913;20227628;18412118 False 3 100;0;0 1.8 True ENSG00000105991 ENSG00000105991 HGNC:5099 HPDL gene HPDL Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities, MIM# 619026" 32707086 False 3 100;0;0 1.8 True ENSG00000186603 ENSG00000186603 HGNC:28242 KIF21A gene KIF21A Expert Review Green;Genomics England PanelApp Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Fibrosis of extraocular muscles, congenital, 1/3B, MIM# 135700 15621876;15223798;15621877;18332320;28930843;27513105;26190014;24656932 False 3 100;0;0 1.8 True ENSG00000139116 ENSG00000139116 HGNC:19349 LMOD3 gene LMOD3 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Nemaline myopathy 10, MIM# 616165" 25250574 False 3 100;0;0 1.8 True ENSG00000163380 ENSG00000163380 HGNC:6649 MFF gene MFF Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Encephalopathy due to defective mitochondrial and peroxisomal fission 2, MIM# 617086" 26783368 False 3 100;0;0 1.8 True ENSG00000168958 ENSG00000168958 HGNC:24858 MGME1 gene MGME1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 11, MIM#615084 False 3 100;0;0 1.8 True ENSG00000125871 ENSG00000125871 HGNC:16205 MTM1 gene MTM1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders X-LINKED: hemizygous mutation in males, biallelic mutations in females "Myotubular myopathy, X-linked, MIM# 310400" False 3 100;0;0 1.8 True ENSG00000171100 ENSG00000171100 HGNC:7448 MUSK gene MUSK Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 9, associated with acetylcholine receptor deficiency, MIM# 616325" False 3 100;0;0 1.8 True ENSG00000030304 ENSG00000030304 HGNC:7525 MYF5 gene MYF5 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Ophthalmoplegia, external, with rib and vertebral anomalies, OMIM 61855 29887215;15386014;1423602;9268580;8918877 False 3 100;0;0 1.8 True ENSG00000111049 ENSG00000111049 HGNC:7565 MYH2 gene MYH2 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Proximal myopathy and ophthalmoplegia, MIM# 605637 PMID 24193343;32578970;11114175;23489661 False 3 100;0;0 1.8 True ENSG00000125414 ENSG00000125414 HGNC:7572 MYMK gene MYMK Expert Review Green;Other Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Carey-Fineman-Ziter syndrome, MIM 254940 28681861;29560417 False 3 100;0;0 1.8 True ENSG00000187616 ENSG00000187616 HGNC:33778 NDUFS1 gene NDUFS1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Mitochondrial complex I deficiency, nuclear type 5, MIM# 618226" False 3 100;0;0 1.8 True ENSG00000023228 ENSG00000023228 HGNC:7707 NDUFV1 gene NDUFV1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Mitochondrial complex I deficiency, nuclear type 4, MIM# 618225" False 3 100;0;0 1.8 True ENSG00000167792 ENSG00000167792 HGNC:7716 NPC1 gene NPC1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Niemann-Pick disease, type C, 257220 False 3 100;0;0 1.8 True ENSG00000141458 ENSG00000141458 HGNC:7897 OPA1 gene OPA1 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted "Optic atrophy plus syndrome, MIM# 125250" False 3 100;0;0 1.8 True ENSG00000198836 ENSG00000198836 HGNC:8140 PDHB gene PDHB Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Pyruvate dehydrogenase E1-beta deficiency, MIM# 614111" False 3 100;0;0 1.8 True ENSG00000168291 ENSG00000168291 HGNC:8808 PHOX2A gene PHOX2A Expert Review Green;Genomics England PanelApp Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Fibrosis of extraocular muscles, congenital, 2, MIM# 602078 14597037;22311481;11600883;16815872 False 3 100;0;0 1.8 True ENSG00000165462 ENSG00000165462 HGNC:691 PIEZO2 gene PIEZO2 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted "Arthrogryposis, distal, type 5, MIM# 108145;Arthrogryposis, distal, type 3, MIM# 114300" False 3 100;0;0 1.8 True ENSG00000154864 ENSG00000154864 HGNC:26270 PLXND1 gene PLXND1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted M bius syndrome PMID: 26068067 False 3 100;0;0 1.8 True ENSG00000004399 ENSG00000004399 HGNC:9107 POLG gene POLG Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 4A (Alpers type) MIM#203700;Mitochondrial DNA depletion syndrome 4B (MNGIE type) MIM#613662;Mitochondrial recessive ataxia syndrome (includes SANDO and SCAE) MIM#607459;Progressive external ophthalmoplegia, autosomal recessive 1 MIM#258450 False 3 100;0;0 1.8 True ENSG00000140521 ENSG00000140521 HGNC:9179 POLG2 gene POLG2 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 16 (hepatic type) - 618528;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 - 610131 21555342;16685652 False 3 100;0;0 1.8 True ENSG00000256525 ENSG00000256525 HGNC:9180 REV3L gene REV3L Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted M bius syndrome PMID: 26068067 False 3 100;0;0 1.8 True ENSG00000009413 ENSG00000009413 HGNC:9968 ROBO3 gene ROBO3 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Gaze palsy, familial horizontal, with progressive scoliosis, 1 (MIM#607313) PMID: 15105459;16525029 False 3 100;0;0 1.8 True ENSG00000154134 ENSG00000154134 HGNC:13433 RRM2B gene RRM2B Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 8A (encephalomyopathic type with renal tubulopathy) - 612075;Mitochondrial DNA depletion syndrome 8B (MNGIE type) - 612075;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5 - 613077 PMID: 17486094;19138848;24741716;31462754 False 3 100;0;0 1.8 True ENSG00000048392 ENSG00000048392 HGNC:17296 RYR1 gene RYR1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Minicore myopathy with external ophthalmoplegia 255320 False 3 100;0;0 1.8 True ENSG00000196218 ENSG00000196218 HGNC:10483 SALL4 gene SALL4 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Duane-radial ray syndrome, 607323 False 3 100;0;0 1.8 True ENSG00000101115 ENSG00000101115 HGNC:15924 SLC18A3 gene SLC18A3 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Myasthenic syndrome, congenital, 21, presynaptic OMIM 617239 PMID: 27590285;20123977;28188302;31059209 False 3 100;0;0 1.8 True ENSG00000187714 ENSG00000187714 HGNC:10936 SLC19A3 gene SLC19A3 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), MIM# 607483" False 3 100;0;0 1.8 True ENSG00000135917 ENSG00000135917 HGNC:16266 SLC9A6 gene SLC9A6 Expert list;Expert Review Green Congenital ophthalmoplegia Ophthalmological disorders X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) "Mental retardation, X-linked syndromic, Christianson type, MIM# 300243" False 3 100;0;0 1.8 True ENSG00000198689 ENSG00000198689 HGNC:11079 SUCLA2 gene SUCLA2 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria) OMIM 612073 PMID: 20301762 False 3 100;0;0 1.8 True ENSG00000136143 ENSG00000136143 HGNC:11448 SURF1 gene SURF1 Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial complex IV deficiency, nuclear type 1 OMIM 220110 PMID: 10746561;29933018;33134083 False 3 100;0;0 1.8 True ENSG00000148290 ENSG00000148290 HGNC:11474 TUBA1A gene TUBA1A Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Congenital fibrosis of the extraocular muscles, AD 30677308 False 3 100;0;0 1.8 True ENSG00000167552 ENSG00000167552 HGNC:20766 TUBB3 gene TUBB3 Expert Review Green;Genomics England PanelApp Congenital ophthalmoplegia Ophthalmological disorders MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Fibrosis of extraocular muscles, congenital, 3A 600638;CFEOM3A 27428177;20074521;26639658 False 3 100;0;0 1.8 True ENSG00000258947 ENSG00000258947 HGNC:20772 TWNK gene TWNK Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BOTH monoallelic and biallelic, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 7 (hepatocerebral type) 271245;Perrault syndrome 5 616138;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 609286 PMID 17921179;32234020 False 3 100;0;0 1.8 True ENSG00000107815 ENSG00000107815 HGNC:1160 TYMP gene TYMP Expert Review Green;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Mitochondrial DNA depletion syndrome 1 (MNGIE type) 603041 PMID: 21933806;30775048 False 3 100;0;0 1.8 True ENSG00000025708 ENSG00000025708 HGNC:3148 ECEL1 gene ECEL1 Expert Review Amber;Literature Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal Arthrogryposis, distal, type 5D - 615065;Congenital cranial dysinnervation disorder PMID: 25173900 False 2 0;100;0 1.8 True ENSG00000171551 ENSG00000171551 HGNC:3147 MYO9A gene MYO9A Expert list;Expert Review Amber Congenital ophthalmoplegia Ophthalmological disorders BIALLELIC, autosomal or pseudoautosomal "Myasthenic syndrome, congenital, 24, presynaptic, MIM# 618198" False 2 0;100;0 1.8 True ENSG00000066933 ENSG00000066933 HGNC:7608