Total 39 pathogenic variants reported for Leber optic atrophy 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NC_012920.1(MT-ATP6):m.8993T>C SNV
Germline		 ChrMT:8993 Pathogenic Leigh syndrome
Ataxia and polyneuropathy, adult-onset
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
NARP syndrome
Mitochondrial disease
Condition: not provided
Leber optic atrophy		 Reviewed By Expert Panel
 CA120596 rs_199476133

9 SubmittersRCV000010275RCV000010276RCV000754647RCV000854390RCV000495030RCV001268873RCV002247300
NC_012920.1(MT-ATP6):m.9176T>C SNV
Germline		 ChrMT:9176 Pathogenic Striatonigral degeneration, infantile, mitochondrial
Leigh syndrome
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Condition: not provided
Leber optic atrophy
Maternally-inherited spastic paraplegia
Mitochondrial disease
LEIGH SYNDROME, MITOCHONDRIAL		 Reviewed By Expert Panel
 CA120597 rs_199476135

11 SubmittersRCV000010278RCV000010279RCV000754652RCV001027501RCV001542707RCV002251425RCV002260585RCV004554599
NC_012920.1(MT-ATP6):m.9185T>C SNV
Germline		 ChrMT:9185 Pathogenic Leigh syndrome
Charcot-Marie-Tooth disease
Mitochondrial disease
Condition: not provided
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Charcot-Marie-Tooth disease, type IA
Leber optic atrophy
Mitochondrial DNA-Associated Leigh Syndrome and NARP		 Reviewed By Expert Panel
 CA340928 rs_199476138

12 SubmittersRCV000010282RCV000240612RCV000495689RCV001267926RCV000754648RCV003224857RCV001542709RCV002267606
NC_012920.1(MT-ATP6):m.9176T>G SNV
Germline		 ChrMT:9176 Likely pathogenic Leigh syndrome
Leber optic atrophy
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Mitochondrial disease
Condition: not provided		 Reviewed By Expert Panel
 CA340929 rs_199476135

6 SubmittersRCV000010285RCV001542708RCV000754649RCV002221473RCV001543462
NC_012920.1(MT-CO3):m.9804G>A SNV
Germline		 ChrMT:9804 Conflicting classifications of pathogenicity Leber optic atrophy
Condition: not provided
Leigh syndrome
See cases
not specified		 Criteria Provided
Conflicting Classifications
 CA340930 rs_200613617

7 SubmittersRCV000010287RCV000756352RCV000854582RCV001196020RCV004017233
m.15150G>A SNV
Germline		 ChrMT:15150 Pathogenic Exercise intolerance
Mitochondrial myopathy with reversible cytochrome C oxidase deficiency
Leber optic atrophy		 Criteria Provided
Multiple Submitters
No Conflicts
 CA120619 rs_207460000

3 SubmittersRCV000010319RCV000855232RCV002247305
NC_012920.1(MT-ND6):m.14484T>C SNV
Germline		 ChrMT:14484 Pathogenic Leber optic atrophy
Leigh syndrome
Condition: not provided
Mitochondrial disease		 Reviewed By Expert Panel
 CA340932 rs_199476104

11 SubmittersRCV000010325RCV000144018RCV000223709RCV003162238
NC_012920.1(MT-ND6):m.14459G>A SNV
Germline		 ChrMT:14459 Pathogenic Leber optic atrophy
Leber optic atrophy and dystonia
Leigh syndrome due to mitochondrial complex I deficiency
Leigh syndrome
Mitochondrial disease		 Reviewed By Expert Panel
 CA120625 rs_199476105

7 SubmittersRCV000010327RCV000010326RCV000010328RCV000144019RCV001796715
m.14596A>T SNV
Germline		 ChrMT:14596 Pathogenic Leber optic atrophy and dystonia
Leber optic atrophy		 No Assertion Criteria Provided
 CA120626 rs_387906424

2 SubmittersRCV000010329RCV000055704
m.14495A>G SNV
Germline		 ChrMT:14495 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA340933 rs_199476106

3 SubmittersRCV000010330RCV002260588
NC_012920.1(MT-ND6):m.14482C>A SNV
Germline		 ChrMT:14482 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA340934 rs_199476108

3 SubmittersRCV000010332RCV002260590
NC_012920.1(MT-ND6):m.14487T>C SNV
Germline		 ChrMT:14487 Pathogenic Striatal necrosis, bilateral, with dystonia
Leigh syndrome due to mitochondrial complex I deficiency
Leigh syndrome
Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA120627 rs_199476109

5 SubmittersRCV000010334RCV000010333RCV000144020RCV002247307RCV003162239
m.13730G>A SNV
Germline		 ChrMT:13730 Pathogenic Leber optic atrophy No Assertion Criteria Provided
 CA340936 rs_387906425

2 SubmittersRCV000010337
NC_012920.1(MT-ND5):m.12706T>C SNV
Germline		 ChrMT:12706 Likely pathogenic Leigh syndrome due to mitochondrial complex I deficiency
Leigh syndrome
Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA120628 rs_267606893

5 SubmittersRCV000010338RCV000144015RCV002247308RCV002260591
m.13045A>C SNV
Germline		 ChrMT:13045 Pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Leber optic atrophy
Leigh syndrome due to mitochondrial complex I deficiency		 No Assertion Criteria Provided
 CA120629 rs_267606895

1 SubmittersRCV000010340RCV000010341RCV000010342
NC_012920.1(MT-ND5):m.13042G>A SNV
Germline		 ChrMT:13042 Likely pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
MERRF syndrome
Leigh syndrome due to mitochondrial complex I deficiency
Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA120633 rs_267606898

5 SubmittersRCV000010347RCV000010348RCV000010349RCV000854885RCV002260592
m.12848C>T SNV
Germline		 ChrMT:12848 Pathogenic Leber optic atrophy No Assertion Criteria Provided
 CA340937 rs_267606899

2 SubmittersRCV000010350
m.10663T>C SNV
Germline		 ChrMT:10663 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA340938 rs_1556423844

5 SubmittersRCV000010353RCV003153302
NC_012920.1(MT-ND4):m.11778G>A SNV
Germline		 ChrMT:11778 Pathogenic Leber optic atrophy
Condition: not provided
Leber optic atrophy, susceptibility to
Mitochondrial disease
not specified		 Reviewed By Expert Panel
 CA340939 rs_199476112

19 SubmittersRCV000010354RCV000224219RCV002288481RCV002260593RCV002285007
NC_012920.1(MT-ND4):m.11777C>A SNV
Germline		 ChrMT:11777 Likely pathogenic Mitochondrial complex I deficiency
Leigh syndrome
Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA120636 rs_28384199

4 SubmittersRCV000010357RCV000144013RCV000854746RCV002260594
NC_012920.1(MT-ND3):m.10197G>A SNV
Germline		 ChrMT:10197 Pathogenic Mitochondrial complex 1 deficiency, mitochondrial type 1
Leber optic atrophy and dystonia
Leigh syndrome
Condition: not provided
See cases
Mitochondrial DNA-Associated Leigh Syndrome and NARP
not specified
Mitochondrial disease		 Reviewed By Expert Panel
 CA120640 rs_267606891

9 SubmittersRCV000010362RCV000010363RCV000144011RCV000507278RCV004017234RCV002247309RCV002285008RCV002291213
NC_012920.1(MT-ND1):m.3460G>A SNV
Germline		 ChrMT:3460 Pathogenic Leber optic atrophy
Leigh syndrome
MITOCHONDRIAL COMPLEX I DEFICIENCY, MITOCHONDRIAL TYPE 3
Condition: not provided
Mitochondrial disease		 Reviewed By Expert Panel
 CA120646 rs_199476118

8 SubmittersRCV000010370RCV000143998RCV000735416RCV000757484RCV003319165
m.4160T>C SNV
Germline		 ChrMT:4160 Pathogenic Leber optic atrophy Criteria Provided
Single Submitter
 CA340942 rs_199476119

3 SubmittersRCV000010372
NC_012920.1(MT-ND1):m.3394T>C SNV
Germline		 ChrMT:3394 Conflicting classifications of pathogenicity Leber optic atrophy
Condition: not provided
Leigh syndrome		 Criteria Provided
Conflicting Classifications
 CA340944 rs_41460449

3 SubmittersRCV000010375RCV000507319RCV000853650
m.3697G>A SNV
Germline		 ChrMT:3697 Likely pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Leber optic atrophy and dystonia
Leber optic atrophy
Mitochondrial disease
7 conditions		 Reviewed By Expert Panel
 CA120647 rs_199476122

6 SubmittersRCV000010385RCV000010386RCV000056168RCV002221474RCV003298030
NC_012920.1(MT-ND1):m.3946G>A SNV
Germline		 ChrMT:3946 Pathogenic/Likely pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Leigh syndrome
Leber optic atrophy		 Criteria Provided
Multiple Submitters
No Conflicts
 CA254862 rs_199476123

6 SubmittersRCV000010387RCV000853718RCV001542704
m.14482C>G SNV
Germline		 ChrMT:14482 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA344824 rs_199476108

2 SubmittersRCV000055701RCV003162433
m.14568C>T SNV
Germline		 ChrMT:14568 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA344825 rs_397515506

3 SubmittersRCV000055703RCV002260604
m.3635G>A SNV
Germline		 ChrMT:3635 Likely pathogenic Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA344827 rs_397515507

4 SubmittersRCV000055707RCV002291214
NC_012920.1:m.8969G>A SNV
Germline		 ChrMT:8969 Likely pathogenic Myopathy, lactic acidosis, and sideroblastic anemia 3
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Leber optic atrophy
Mitochondrial disease		 Reviewed By Expert Panel
 CA199769 rs_794726857

4 SubmittersRCV000171545RCV000854381RCV002247579RCV002260628
NC_012920.1:m.9237G>A SNV
Germline		 ChrMT:9237 Pathogenic Epilepsy
Mitochondrial encephalopathy
Developmental delay
Leber optic atrophy		 Criteria Provided
Single Submitter
 CA16040652 rs_1057516064

2 SubmittersRCV000408945RCV002248640
NC_012920.1:m.13051G>A SNV
Germline		 ChrMT:13051 Pathogenic/Likely pathogenic Mitochondrial disease
Leber optic atrophy		 Criteria Provided
Multiple Submitters
No Conflicts
 CA414816093 rs_1131692063

3 SubmittersRCV000495629RCV000854887
NM_001377299.1(NDUFS2):c.268G>A (p.Ala90Thr) SNV
Unknown		 Chr1:161206472 Likely pathogenic Leber optic atrophy Criteria Provided
Single Submitter
 CA343377955 rs_1553249704

1 SubmittersRCV000625868
NC_012920.1(MT-ATP6):m.9035T>C SNV
Germline		 ChrMT:9035 Likely pathogenic Progressive cerebellar ataxia
Leigh syndrome
See cases
Leber optic atrophy
Mitochondrial disease
MT-ATP6-related primary mitochondrial disease		 Reviewed By Expert Panel
 rs_1603222000

7 SubmittersRCV000851177RCV000854406RCV001196557RCV002249546RCV002260672RCV002466594
NC_012920.1(MT-ND5):m.13063G>A SNV
Germline		 ChrMT:13063 Pathogenic/Likely pathogenic Leigh syndrome
Leber optic atrophy		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_1603224017

2 SubmittersRCV000854888RCV002249551
NC_012920.1:m.13094T>C SNV
Germline		 ChrMT:13094 Pathogenic Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Mitochondrial disease
Leber optic atrophy		 Reviewed By Expert Panel
 rs_1603224029

4 SubmittersRCV000854891RCV002291219RCV002249552
NC_012920.1(MT-ATP6):m.8783G>A SNV
Germline		 ChrMT:8783 Pathogenic/Likely pathogenic Leigh syndrome
Leber optic atrophy		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_1603221804

2 SubmittersRCV000854322RCV002249549
NC_012920.1(MT-ND5):m.12923G>A SNV
Germline		 ChrMT:12923 Likely pathogenic Leigh syndrome
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke
Leber optic atrophy		 Criteria Provided
Single Submitter

1 SubmittersRCV003150916RCV003150917RCV003150918