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 ACO2 gene ACO2 Expert Review Green;London North GLH;NHS GMS;Other Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Infantile cerebellar-retinal degeneration, OMIM:614559;Infantile cerebellar-retinal degeneration, MONDO:0013802;?Optic atrophy 9, OMIM:616289;Optic atrophy 9, MONDO:0014571 25351951;22405087;34056600 False 3 100;0;0 5.54 False ENSG00000100412 ENSG00000100412 HGNC:118 AFG3L2 gene AFG3L2 Expert Review Green;London North GLH Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Optic atrophy 12, OMIM:618977 (AD);Spastic ataxia 5, autosomal recessive, OMIM:614487 (AR) 29181157;26539208;30544562;30252181;30389403;32600459;32219868;32548275 False 3 75;25;0 5.54 False ENSG00000141385 ENSG00000141385 HGNC:315 ALPK1 gene ALPK1 Expert Review Green;Literature;Other;Research Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted ROSAH syndrome, OMIM:614979 30967659;31053777;31939038;34159509;35868845 False 3 100;0;0 5.54 False Other ENSG00000073331 ENSG00000073331 HGNC:20917 ATG7 gene ATG7 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Spinocerebellar ataxia, autosomal recessive 31, OMIM:619422 34161705 False 3 100;0;0 5.54 False ENSG00000197548 ENSG00000197548 HGNC:16935 BORCS8 gene BORCS8 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Neurodegeneration, infantile-onset, with optic atrophy and brain abnormalities, OMIM:620987 38128568 False 3 100;0;0 5.54 False ENSG00000254901 ENSG00000254901 HGNC:37247 BTD gene BTD Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Biotinidase deficiency, OMIM:253260;optic atrophy, MONDO:0003608 26203071;29025919;32235217;33364171 False 3 100;0;0 5.54 False ENSG00000169814 ENSG00000169814 HGNC:1122 C12orf65 gene C12orf65 Expert Review Green;London North GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Combined oxidative phosphorylation deficiency 7, OMIM:613559;Spastic paraplegia 55, autosomal recessive, OMIM:615035 20598281;23188110;24080142;24198383;24284555;24424123;25995486;26380172;28091420;31753091 False 3 100;0;0 5.54 False ENSG00000130921 ENSG00000130921 HGNC:26784 C19orf12 gene C19orf12 Expert Review Green;London North GLH;NHS GMS Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal ?Spastic paraplegia 43, autosomal recessive, OMIM:615043;Neurodegeneration with brain iron accumulation 4, OMIM: 614298 27772766;26187298;24209434;22584950;23269600;21981780;29295770;31087512 False 3 100;0;0 5.54 False ENSG00000131943 ENSG00000131943 HGNC:25443 CISD2 gene CISD2 Expert Review Green;London North GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal WOLFRAM SYNDROME 2, 604928 25056293;25371195;28335035 False 3 100;0;0 5.54 False ENSG00000145354 ENSG00000145354 HGNC:24212 DNAJC30 gene DNAJC30 Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Leber-like hereditary optic neuropathy, autosomal recessive 1, MONDO:0958183;Leber-like hereditary optic neuropathy, autosomal recessive 1, OMIM:619382 33465056;35091433;38107630 False 3 100;0;0 5.54 False ENSG00000176410 ENSG00000176410 HGNC:16410 DNM1L gene DNM1L Expert Review Green;London North GLH Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted OPTIC ATROPHY 5, 610708 28969390;17460227 False 3 100;0;0 5.54 False ENSG00000087470 ENSG00000087470 HGNC:2973 EPRS gene EPRS Expert list;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal "Leukodystrophy, hypomyelinating, 15, MIM# 617951" 29576217;33805425 False 3 100;0;0 5.54 False ENSG00000136628 ENSG00000136628 HGNC:3418 FDXR gene FDXR Expert list;Expert Review Green Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Auditory neuropathy and optic atrophy, OMIM:617717;Multiple mitochondrial dysfunctions syndrome 9B, OMIM:620887 30250212;28965846;29040572;32499495;33348459 False 3 100;0;0 5.54 False ENSG00000161513 ENSG00000161513 HGNC:3642 HIKESHI gene HIKESHI Expert list;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Leukodystrophy, hypomyelinating, 13, OMIM:616881 26545878;28000699;34111619 False 3 100;0;0 5.54 False ENSG00000149196 ENSG00000149196 HGNC:26938 HK1 gene HK1 BRIDGE study SPEED NEURO Tier1 Gene;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Neurodevelopmental disorder with visual defects and brain anomalies, OMIM:618547 30778173;28135719 False 3 100;0;0 5.54 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000156515 ENSG00000156515 HGNC:4922 HSD17B10 gene HSD17B10 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) HSD10 mitochondrial disease, OMIM:300438 22132097;26950678;27295195 False 3 100;0;0 5.54 False ENSG00000072506 ENSG00000072506 HGNC:4800 ISCA2 gene ISCA2 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Multiple mitochondrial dysfunctions syndrome 4, OMIM:616370;optic atrophy, MONDO:0003608 25539947;29297947;29122497;29359243 False 3 100;0;0 5.54 False ENSG00000165898 ENSG00000165898 HGNC:19857 LETM1 gene LETM1 Expert Review;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 36055214;33815143 False 3 100;0;0 5.54 False ENSG00000168924 ENSG00000168924 HGNC:6556 LHX2 gene LHX2 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown neurodevelopmental disorder 37057675 False 3 100;0;0 5.54 False ENSG00000106689 ENSG00000106689 HGNC:6594 MAG gene MAG Expert Review Green;Literature;London North GLH;NHS GMS;Yorkshire and North East GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 75, autosomal recessive, OMIM:616680 24482476;26179919;31402626;32629324;32340215 False 3 60;40;0 5.54 False ENSG00000105695 ENSG00000105695 HGNC:6783 MECR gene MECR Expert list;Expert Review Green Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities, 617282 27817865;31137067 False 3 100;0;0 5.54 False ENSG00000116353 ENSG00000116353 HGNC:19691 MFF gene MFF Expert Review Green;London North GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Encephalopathy due to defective mitochondrial and peroxisomal fission 2, 617086 30581454;26783368;22499341 False 3 100;0;0 5.54 False ENSG00000168958 ENSG00000168958 HGNC:24858 MFN2 gene MFN2 Emory Genetics Laboratory;Expert;Expert Review Green;London North GLH Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Charcot-Marie-Tooth disease, axonal, type 2A2A, OMIM:609260;Charcot-Marie-Tooth disease, axonal, type 2A2B, OMIM:617087;Hereditary motor and sensory neuropathy VIA, OMIM:601152 26955893;26306937;21715711 False 3 100;0;0 5.54 False ENSG00000116688 ENSG00000116688 HGNC:16877 MIEF1 gene MIEF1 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Optic atrophy 14, OMIM:620550;optic atrophy 14, MONDO:0957824 33632269 False 3 67;33;0 5.54 False ENSG00000100335 ENSG00000100335 HGNC:25979 MT-ATP6 gene MT-ATP6 Expert Review Green;London North GLH;UKGTN Optic neuropathy Ophthalmology MITOCHONDRIAL Leber optic atrophy;535000;neurogenic weakness, ataxia, and retinitis pigmentosa;retinopathy 7726182;10676807;26448634;26252090;24118886 (functional evidence);23266623 False 3 100;0;0 5.54 False ENSG00000198899 ENSG00000198899 HGNC:7414 MT-ND1 gene MT-ND1 Expert Review Green;London North GLH;UKGTN Optic neuropathy Ophthalmology MITOCHONDRIAL Optic neuropathy and nystagmus;External ophthalmoplegia;Leber's hereditary optic neuropathy 26448634;27449621;20301353;27177320;24884847;24800637;23665487 False 3 100;0;0 5.54 False ENSG00000198888 ENSG00000198888 HGNC:7455 MT-ND4 gene MT-ND4 Expert Review Green;London North GLH;UKGTN Optic neuropathy Ophthalmology MITOCHONDRIAL Leber's hereditary optic neuropathy 26448634;20301353;27159682;26683077;23805034;23665487;22553750 False 3 100;0;0 5.54 False ENSG00000198886 ENSG00000198886 HGNC:7459 MT-ND6 gene MT-ND6 Expert Review Green;London North GLH;UKGTN Optic neuropathy Ophthalmology MITOCHONDRIAL Leber hereditary optic neuropathy;Nystagmus;severe infantile-onset complex I deficiency 26448634;24884847;24417559;24398099 False 3 100;0;0 5.54 False ENSG00000198695 ENSG00000198695 HGNC:7462 NBAS gene NBAS Expert list;Expert Review Green Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Short stature, optic nerve atrophy, and Pelger-Huet anomaly, 614800 20577004;26286438;31015584;31761904 False 3 100;0;0 5.54 False ENSG00000151779 ENSG00000151779 HGNC:15625 NDUFA12 gene NDUFA12 Expert Review Green;NHS GMS;PanelApp;South West GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Mitochondrial complex I deficiency, nuclear type 23, OMIM:618244 21617257;33715266;35141356 False 3 67;0;33 5.54 False ENSG00000184752 ENSG00000184752 HGNC:23987 NR2F1 gene NR2F1 Expert Review Green;London North GLH;Radboud University Medical Center, Nijmegen Optic neuropathy Ophthalmology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Bosch-Boonstra-Schaaf optic atrophy syndrome, OMIM:615722 False 3 100;0;0 5.54 False ENSG00000175745 ENSG00000175745 HGNC:7975 OPA1 gene OPA1 Emory Genetics Laboratory;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Optic atrophy 1, OMIM:165500;Optic atrophy plus syndrome, OMIM:125250;Mitochondrial DNA depletion syndrome 14 (encephalocardiomyopathic type), OMIM:616896;Behr syndrome, OMIM:210000 15531309;16158427;17306754;18065439;18158317;19029523;20417570;20157015;21636302;25012220;25146916;35652445 False 3 100;0;0 5.54 False ENSG00000198836 ENSG00000198836 HGNC:8140 OPA3 gene OPA3 Emory Genetics Laboratory;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;London North GLH;Radboud University Medical Center, Nijmegen Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Autosomal Dominant Optic Atrophy;optic atrophy and cataracts;Optic atrophy 3 with cataract 25159689;26190011 False 3 100;0;0 5.54 False ENSG00000125741 ENSG00000125741 HGNC:8142 PDXK gene PDXK Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Neuropathy, hereditary motor and sensory, type VIC, with optic atrophy, OMIM:618511 31187503;32522499 False 3 100;0;0 5.54 False ENSG00000160209 ENSG00000160209 HGNC:8819 RTN4IP1 gene RTN4IP1 Expert Review Green;Literature;London North GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal early-onset recessive optic neuropathy 26593267 False 3 100;0;0 5.54 False ENSG00000130347 ENSG00000130347 HGNC:18647 SLC25A46 gene SLC25A46 Expert Review Green;Literature;London North GLH Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Optic atrophy, MONDO:0003608;Neuropathy, hereditary motor and sensory, type VIB, MIM# 616505;Pontocerebellar hypoplasia, type 1E, MIM# 619303, MONDO:0030260 26168012;27430653;28369803;28376086;28558379;28934388;30178502;33816684 False 3 100;0;0 5.54 False ENSG00000164209 ENSG00000164209 HGNC:25198 SLC44A1 gene SLC44A1 Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, OMIM:618868;Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, MONDO:0030028 31855247 False 3 100;0;0 5.54 False ENSG00000070214 ENSG00000070214 HGNC:18798 SLC52A2 gene SLC52A2 Expert Review Green;London North GLH;Other Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Brown-Vialetto-Van Laere syndrome 2, MIM# 614707, MONDO:0013867;Optic atrophy, MONDO:0003608 22740598;22864630;23243084;24253200;30343981;30377535;31868069;35608644;36186484 False 3 100;0;0 5.54 False ENSG00000185803 ENSG00000185803 HGNC:30224 SPG7 gene SPG7 Expert;Expert Review Green;London North GLH;NHS GMS Optic neuropathy Ophthalmology BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Spastic paraplegia 7, autosomal recessive, OMIM:607259;hereditary spastic paraplegia 7, MONDO:0011803 9635427;23065789;22964162;25034272;32548275;33841295 False 3 100;0;0 5.54 False ENSG00000197912 ENSG00000197912 HGNC:11237 SSBP1 gene SSBP1 Expert list;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Optic atrophy 13 with retinal and foveal abnormalities OMIM:165510 31298765;31550240;31550237;30412255;31479473;31479473 False 3 100;0;0 5.54 False ENSG00000106028 ENSG00000106028 HGNC:11317 TFG gene TFG Expert Review Green;Literature;NHS GMS Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 57, autosomal recessive, OMIM:615658 23479643;27492651;29971521;30467354 False 3 100;0;0 5.54 False ENSG00000114354 ENSG00000114354 HGNC:11758 TMEM126A gene TMEM126A Emory Genetics Laboratory;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;London North GLH;Radboud University Medical Center, Nijmegen Optic neuropathy Ophthalmology BIALLELIC, autosomal or pseudoautosomal Optic Atrophy, Recessive;Optic atrophy 7, 612989 19327736;20405026;22815638;30961538;31119195 False 3 100;0;0 5.54 False ENSG00000171202 ENSG00000171202 HGNC:25382 UCHL1 gene UCHL1 Expert list;Expert Review Green;NHS GMS Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Spastic paraplegia 79B, autosomal recessive, OMIM:615491;early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209;Spastic paraplegia 79A, autosomal dominant, OMIM:620221 29735986;23359680;28007905;35986737 False 3 100;0;0 5.54 False ENSG00000154277 ENSG00000154277 HGNC:12513 WFS1 gene WFS1 Expert;Expert Review Green;London North GLH Optic neuropathy Ophthalmology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Wolfram syndrome 1, OMIM:222300 33693650 False 3 100;0;0 5.54 False ENSG00000109501 ENSG00000109501 HGNC:12762