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 disease Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1 NARP syndrome Condition: not provided Leber optic atrophy	Reviewed By Expert Panel	CA120596	rs_199476133	12 SubmittersRCV000010275 RCV000010276 RCV000495030 RCV000754647 RCV000854390 RCV001268873 RCV002247300
NC_012920.1(MT-ATP6):m.9176T>C	SNV Germline	ChrMT:9176	Pathogenic	Leigh syndrome Striatonigral degeneration, infantile, mitochondrial Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1 Condition: not provided Leber optic atrophy Maternally-inherited spastic paraplegia Mitochondrial disease Leigh syndrome, mitochondrial NARP syndrome MT-ATP6-related disorder Primary mitochondrial disorders	Reviewed By Expert Panel	CA120597	rs_199476135	16 SubmittersRCV000010279 RCV000010278 RCV000754652 RCV001027501 RCV001542707 RCV002251425 RCV002260585 RCV004554599 RCV004766998 RCV005867740 RCV006555302
NC_012920.1(MT-ATP6):m.9185T>C	SNV Germline	ChrMT:9185	Pathogenic	Leigh syndrome Charcot-Marie-Tooth disease Mitochondrial disease Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1 Leber optic atrophy Condition: not provided Mitochondrial DNA-Associated Leigh Syndrome and NARP Charcot-Marie-Tooth disease, type IA NARP syndrome Primary mitochondrial disorders	Reviewed By Expert Panel	CA340928	rs_199476138	18 SubmittersRCV000010282 RCV000240612 RCV000495689 RCV000754648 RCV001542709 RCV001267926 RCV002267606 RCV003224857 RCV004760325 RCV006555303
NC_012920.1(MT-ATP6):m.9176T>G	SNV Germline	ChrMT:9176	Likely pathogenic	Leigh syndrome Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1 Leber optic atrophy Condition: not provided Mitochondrial disease	Reviewed By Expert Panel	CA340929	rs_199476135	6 SubmittersRCV000010285 RCV000754649 RCV001542708 RCV001543462 RCV002221473
NC_012920.1(MT-CYB):m.15150G>A	SNV Germline	ChrMT:15150	Likely pathogenic	Exercise intolerance Mitochondrial myopathy with reversible cytochrome C oxidase deficiency Leber optic atrophy Mitochondrial disease	Reviewed By Expert Panel	CA120619	rs_207460000	4 SubmittersRCV000010319 RCV000855232 RCV002247305 RCV004791207
NC_012920.1(MT-ND6):m.14484T>C	SNV Germline	ChrMT:14484	Pathogenic	Leber optic atrophy Leigh syndrome Condition: not provided Mitochondrial disease Retinal dystrophy Optic atrophy Leber optic atrophy and dystonia Primary mitochondrial disorders	Reviewed By Expert Panel	CA340932	rs_199476104	16 SubmittersRCV000010325 RCV000144018 RCV000223709 RCV003162238 RCV004814873 RCV004814874 RCV005867741 RCV006555306
NC_012920.1(MT-ND6):m.14495A>G	SNV Germline	ChrMT:14495	Likely pathogenic	Leber optic atrophy Mitochondrial disease	Reviewed By Expert Panel	CA340933	rs_199476106	3 SubmittersRCV000010330 RCV002260588
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 SubmittersRCV000010332 RCV002260590
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 MELAS syndrome	Reviewed By Expert Panel	CA120627	rs_199476109	6 SubmittersRCV000010334 RCV000010333 RCV000144020 RCV002247307 RCV003162239 RCV005252673
NC_012920.1(MT-ND5):m.12706T>C (p.Phe124Leu)	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 SubmittersRCV000010338 RCV000144015 RCV002247308 RCV002260591
NC_012920.1(MT-ND5):m.13042G>A	SNV Germline	ChrMT:13042	Likely pathogenic	MELAS syndrome MERRF syndrome Leigh syndrome due to mitochondrial complex I deficiency Leber optic atrophy Mitochondrial disease Primary mitochondrial disorders	Reviewed By Expert Panel	CA120633	rs_267606898	6 SubmittersRCV000010347 RCV000010348 RCV000010349 RCV000854885 RCV002260592 RCV006555310
NC_012920.1(MT-ND4L):m.10663T>C	SNV Germline	ChrMT:10663	Likely pathogenic	Leber optic atrophy Mitochondrial disease	Reviewed By Expert Panel	CA340938	rs_1556423844	5 SubmittersRCV000010353 RCV003153302
NC_012920.1(MT-ND4):m.11778G>A	SNV Germline	ChrMT:11778	Pathogenic	Leber optic atrophy Condition: not provided Mitochondrial disease not specified Leber optic atrophy, susceptibility to Retinal dystrophy Leber optic atrophy and dystonia Optic atrophy Primary mitochondrial disorders	Reviewed By Expert Panel	CA340939	rs_199476112	23 SubmittersRCV000010354 RCV000224219 RCV002260593 RCV002285007 RCV002288481 RCV004814875 RCV005252674 RCV004814876 RCV006555311
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 Leber optic atrophy and dystonia	Reviewed By Expert Panel	CA120636	rs_28384199	5 SubmittersRCV000010357 RCV000144013 RCV000854746 RCV002260594 RCV005252675
NC_012920.1(MT-ND3):m.10197G>A	SNV Germline	ChrMT:10197	Pathogenic	Leber optic atrophy and dystonia Mitochondrial complex I deficiency, mitochondrial type 1 Leigh syndrome Condition: not provided Mitochondrial DNA-Associated Leigh Syndrome and NARP not specified Mitochondrial disease See cases Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy Primary mitochondrial disorders	Reviewed By Expert Panel	CA120640	rs_267606891	12 SubmittersRCV000010363 RCV000010362 RCV000144011 RCV000507278 RCV002247309 RCV002285008 RCV002291213 RCV004017234 RCV004767000 RCV006555313
NC_012920.1(MT-ND1):m.3460G>A	SNV Germline	ChrMT:3460	Pathogenic	Leber optic atrophy Leigh syndrome Condition: not provided MITOCHONDRIAL COMPLEX I DEFICIENCY, MITOCHONDRIAL TYPE 3 Mitochondrial disease Optic atrophy Leber optic atrophy and dystonia Primary mitochondrial disorders	Reviewed By Expert Panel	CA120646	rs_199476118	12 SubmittersRCV000010370 RCV000143998 RCV000757484 RCV000735416 RCV003319165 RCV004814877 RCV005867742 RCV006555314
NC_012920.1(MT-ND1):m.3697G>A	SNV Germline	ChrMT:3697	Likely pathogenic	Leber optic atrophy and dystonia MELAS syndrome Leber optic atrophy Mitochondrial disease 7 conditions	Reviewed By Expert Panel	CA120647	rs_199476122	6 SubmittersRCV000010386 RCV000010385 RCV000056168 RCV002221474 RCV003298030
NC_012920.1(MT-ND6):m.14482C>G	SNV Germline	ChrMT:14482	Likely pathogenic	Leber optic atrophy Mitochondrial disease	Reviewed By Expert Panel	CA344824	rs_199476108	2 SubmittersRCV000055701 RCV003162433
NC_012920.1(MT-ND6):m.14568C>T	SNV Germline	ChrMT:14568	Likely pathogenic	Leber optic atrophy Mitochondrial disease	Reviewed By Expert Panel	CA344825	rs_397515506	3 SubmittersRCV000055703 RCV002260604
NC_012920.1(MT-ND1):m.3635G>A	SNV Germline	ChrMT:3635	Likely pathogenic	Leber optic atrophy Mitochondrial disease Leber optic atrophy and dystonia Primary mitochondrial disorders	Reviewed By Expert Panel	CA344827	rs_397515507	7 SubmittersRCV000055707 RCV002291214 RCV005867840 RCV006555390
NC_012920.1(MT-ATP6):m.8969G>A	SNV Germline	ChrMT:8969	Likely pathogenic	Myopathy, lactic acidosis, and sideroblastic anemia 3 MELAS syndrome Leber optic atrophy Mitochondrial disease Condition: not provided MT-ATP6-related disorder Primary mitochondrial disorders	Reviewed By Expert Panel	CA199769	rs_794726857	7 SubmittersRCV000171545 RCV000854381 RCV002247579 RCV002260628 RCV005434668 RCV005867990 RCV006555537
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 MT-ATP6-related disorder NARP syndrome Primary mitochondrial disorders	Reviewed By Expert Panel	CA414801955	rs_1603222000	11 SubmittersRCV000851177 RCV000854406 RCV001196557 RCV002249546 RCV002260672 RCV002466594 RCV005870934 RCV004768714 RCV006556754
NC_012920.1(MT-ND5):m.13094T>C	SNV Germline	ChrMT:13094	Pathogenic	MELAS syndrome Mitochondrial disease Leber optic atrophy Leigh syndrome, mitochondrial Primary mitochondrial disorders	Reviewed By Expert Panel	CA414816540	rs_1603224029	6 SubmittersRCV000854891 RCV002291219 RCV002249552 RCV005638538 RCV006556762
NC_012920.1(MT-ND5):m.12923G>A	SNV Germline	ChrMT:12923	Likely pathogenic	Leigh syndrome MELAS syndrome Leber optic atrophy	Criteria Provided Single Submitter	CA414815506	rs_1603223971	1 SubmittersRCV003150916 RCV003150917 RCV003150918

SNV
Germline

ChrMT:8993

Pathogenic

Leigh syndrome
Ataxia and polyneuropathy, adult-onset
Mitochondrial disease
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
NARP syndrome
Condition: not provided
Leber optic atrophy

Reviewed By Expert Panel

CA120596

rs_199476133

12 SubmittersRCV000010275 RCV000010276 RCV000495030 RCV000754647 RCV000854390 RCV001268873 RCV002247300

NC_012920.1(MT-ATP6):m.9176T>C

SNV
Germline

ChrMT:9176

Pathogenic

Leigh syndrome
Striatonigral degeneration, infantile, mitochondrial
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Condition: not provided
Leber optic atrophy
Maternally-inherited spastic paraplegia
Mitochondrial disease
Leigh syndrome, mitochondrial
NARP syndrome
MT-ATP6-related disorder
Primary mitochondrial disorders

Reviewed By Expert Panel

CA120597

rs_199476135

16 SubmittersRCV000010279 RCV000010278 RCV000754652 RCV001027501 RCV001542707 RCV002251425 RCV002260585 RCV004554599 RCV004766998 RCV005867740 RCV006555302

NC_012920.1(MT-ATP6):m.9185T>C

SNV
Germline

ChrMT:9185

Pathogenic

Leigh syndrome
Charcot-Marie-Tooth disease
Mitochondrial disease
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Leber optic atrophy
Condition: not provided
Mitochondrial DNA-Associated Leigh Syndrome and NARP
Charcot-Marie-Tooth disease, type IA
NARP syndrome
Primary mitochondrial disorders

Reviewed By Expert Panel

CA340928

rs_199476138

18 SubmittersRCV000010282 RCV000240612 RCV000495689 RCV000754648 RCV001542709 RCV001267926 RCV002267606 RCV003224857 RCV004760325 RCV006555303

NC_012920.1(MT-ATP6):m.9176T>G

SNV
Germline

ChrMT:9176

Likely pathogenic

Leigh syndrome
Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1
Leber optic atrophy
Condition: not provided
Mitochondrial disease

Reviewed By Expert Panel

CA340929

rs_199476135

6 SubmittersRCV000010285 RCV000754649 RCV001542708 RCV001543462 RCV002221473

NC_012920.1(MT-CYB):m.15150G>A

SNV
Germline

ChrMT:15150

Likely pathogenic

Exercise intolerance
Mitochondrial myopathy with reversible cytochrome C oxidase deficiency
Leber optic atrophy
Mitochondrial disease

Reviewed By Expert Panel

CA120619

rs_207460000

4 SubmittersRCV000010319 RCV000855232 RCV002247305 RCV004791207

NC_012920.1(MT-ND6):m.14484T>C

SNV
Germline

ChrMT:14484

Pathogenic

Leber optic atrophy
Leigh syndrome
Condition: not provided
Mitochondrial disease
Retinal dystrophy
Optic atrophy
Leber optic atrophy and dystonia
Primary mitochondrial disorders

Reviewed By Expert Panel

CA340932

rs_199476104

16 SubmittersRCV000010325 RCV000144018 RCV000223709 RCV003162238 RCV004814873 RCV004814874 RCV005867741 RCV006555306

NC_012920.1(MT-ND6):m.14495A>G

SNV
Germline

ChrMT:14495

Likely pathogenic

Leber optic atrophy
Mitochondrial disease

Reviewed By Expert Panel

CA340933

rs_199476106

3 SubmittersRCV000010330 RCV002260588

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 SubmittersRCV000010332 RCV002260590

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
MELAS syndrome

Reviewed By Expert Panel

CA120627

rs_199476109

6 SubmittersRCV000010334 RCV000010333 RCV000144020 RCV002247307 RCV003162239 RCV005252673

NC_012920.1(MT-ND5):m.12706T>C (p.Phe124Leu)

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 SubmittersRCV000010338 RCV000144015 RCV002247308 RCV002260591

NC_012920.1(MT-ND5):m.13042G>A

SNV
Germline

ChrMT:13042

Likely pathogenic

MELAS syndrome
MERRF syndrome
Leigh syndrome due to mitochondrial complex I deficiency
Leber optic atrophy
Mitochondrial disease
Primary mitochondrial disorders

Reviewed By Expert Panel

CA120633

rs_267606898

6 SubmittersRCV000010347 RCV000010348 RCV000010349 RCV000854885 RCV002260592 RCV006555310

NC_012920.1(MT-ND4L):m.10663T>C

SNV
Germline

ChrMT:10663

Likely pathogenic

Leber optic atrophy
Mitochondrial disease

Reviewed By Expert Panel

CA340938

rs_1556423844

5 SubmittersRCV000010353 RCV003153302

NC_012920.1(MT-ND4):m.11778G>A

SNV
Germline

ChrMT:11778

Pathogenic

Leber optic atrophy
Condition: not provided
Mitochondrial disease
not specified
Leber optic atrophy, susceptibility to
Retinal dystrophy
Leber optic atrophy and dystonia
Optic atrophy
Primary mitochondrial disorders

Reviewed By Expert Panel

CA340939

rs_199476112

23 SubmittersRCV000010354 RCV000224219 RCV002260593 RCV002285007 RCV002288481 RCV004814875 RCV005252674 RCV004814876 RCV006555311

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
Leber optic atrophy and dystonia

Reviewed By Expert Panel

CA120636

rs_28384199

5 SubmittersRCV000010357 RCV000144013 RCV000854746 RCV002260594 RCV005252675

NC_012920.1(MT-ND3):m.10197G>A

SNV
Germline

ChrMT:10197

Pathogenic

Leber optic atrophy and dystonia
Mitochondrial complex I deficiency, mitochondrial type 1
Leigh syndrome
Condition: not provided
Mitochondrial DNA-Associated Leigh Syndrome and NARP
not specified
Mitochondrial disease
See cases
Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy
Primary mitochondrial disorders

Reviewed By Expert Panel

CA120640

rs_267606891

12 SubmittersRCV000010363 RCV000010362 RCV000144011 RCV000507278 RCV002247309 RCV002285008 RCV002291213 RCV004017234 RCV004767000 RCV006555313

NC_012920.1(MT-ND1):m.3460G>A

SNV
Germline

ChrMT:3460

Pathogenic

Leber optic atrophy
Leigh syndrome
Condition: not provided
MITOCHONDRIAL COMPLEX I DEFICIENCY, MITOCHONDRIAL TYPE 3
Mitochondrial disease
Optic atrophy
Leber optic atrophy and dystonia
Primary mitochondrial disorders

Reviewed By Expert Panel

CA120646

rs_199476118

12 SubmittersRCV000010370 RCV000143998 RCV000757484 RCV000735416 RCV003319165 RCV004814877 RCV005867742 RCV006555314

NC_012920.1(MT-ND1):m.3697G>A

SNV
Germline

ChrMT:3697

Likely pathogenic

Leber optic atrophy and dystonia
MELAS syndrome
Leber optic atrophy
Mitochondrial disease
7 conditions

Reviewed By Expert Panel

CA120647

rs_199476122

6 SubmittersRCV000010386 RCV000010385 RCV000056168 RCV002221474 RCV003298030

NC_012920.1(MT-ND6):m.14482C>G

SNV
Germline

ChrMT:14482

Likely pathogenic

Leber optic atrophy
Mitochondrial disease

Reviewed By Expert Panel

CA344824

rs_199476108

2 SubmittersRCV000055701 RCV003162433

NC_012920.1(MT-ND6):m.14568C>T

SNV
Germline

ChrMT:14568

Likely pathogenic

Leber optic atrophy
Mitochondrial disease

Reviewed By Expert Panel

CA344825

rs_397515506

3 SubmittersRCV000055703 RCV002260604

NC_012920.1(MT-ND1):m.3635G>A

SNV
Germline

ChrMT:3635

Likely pathogenic

Leber optic atrophy
Mitochondrial disease
Leber optic atrophy and dystonia
Primary mitochondrial disorders

Reviewed By Expert Panel

CA344827

rs_397515507

7 SubmittersRCV000055707 RCV002291214 RCV005867840 RCV006555390

NC_012920.1(MT-ATP6):m.8969G>A

SNV
Germline

ChrMT:8969

Likely pathogenic

Myopathy, lactic acidosis, and sideroblastic anemia 3
MELAS syndrome
Leber optic atrophy
Mitochondrial disease
Condition: not provided
MT-ATP6-related disorder
Primary mitochondrial disorders

Reviewed By Expert Panel

CA199769

rs_794726857

7 SubmittersRCV000171545 RCV000854381 RCV002247579 RCV002260628 RCV005434668 RCV005867990 RCV006555537

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
MT-ATP6-related disorder
NARP syndrome
Primary mitochondrial disorders

Reviewed By Expert Panel

CA414801955

rs_1603222000

11 SubmittersRCV000851177 RCV000854406 RCV001196557 RCV002249546 RCV002260672 RCV002466594 RCV005870934 RCV004768714 RCV006556754

NC_012920.1(MT-ND5):m.13094T>C

SNV
Germline

ChrMT:13094

Pathogenic

MELAS syndrome
Mitochondrial disease
Leber optic atrophy
Leigh syndrome, mitochondrial
Primary mitochondrial disorders

Reviewed By Expert Panel

CA414816540

rs_1603224029