MSeqDR Mitochondrial disease browser phenotype pathogenic gene and muatation portal

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Examples Gene: MT-ND1, POLG, Region: M:1-1000 Variant: m.8993T>G, 1:g.10042757T>C rs3888511 MSCV_0000006, ClinVar: RCV000000015, Disease: Leigh syndrome, Phenotype: Retinopathy

MSeqDR Mitochondrial Disease Portal

*:HP: HPO terms, UMDF: 1= Disease, ND: NAMDC terms.
Most Studied CPEO, Complex I Deficiency, COXPD1, Leigh, LHON, MELAS, MERRF, Myopathy, SANDO

Disease Browser
Parent Node: Mitochondrial Diseases (D028361)
Parent Node: Optic Atrophies, Hereditary (D015418)
..Starting node ..Optic Atrophy, Hereditary, Leber (D029242)
Child Nodes:
........Marsden syndrome (C536024)
Sister Nodes:
..Berk-Tabatznik syndrome (C535432)
..Friedreich Ataxia, So-Called, with Optic Atrophy and Sensorineural Deafness (C564999)
..Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy (C535642)
..Hagemoser Weinstein Bresnick syndrome (C537626)
..Konigsmark Knox Hussels syndrome (C537214)
..Metaphyseal Dysplasia, Anetoderma, and Optic Atrophy (C565395)
..Necrotizing Encephalomyelopathy, Subacute, of Leigh, Adult (C563530) L: 00433;
..Optic atrophy 1 and deafness (C537124)
..Optic Atrophy 4 (C565343)
..Optic atrophy 5 (C537126)
..Optic atrophy 6 (C537127)
..Optic Atrophy 7 (C567833)
..Optic atrophy and cataract, autosomal dominant (C537128)
..Optic atrophy polyneuropathy deafness (C537129)
..Optic Atrophy Spastic Paraplegia Syndrome (C564084)
..Optic Atrophy with Demyelinating Disease of CNS (C563496) L: 00656;
..Optic Atrophy with Negative Electroretinograms (C563494)
..Optic Atrophy, Autosomal Dominant (D029241) L: 00073;
..Optic Atrophy, Deafness, Ophthalmoplegia, and Myopathy (C565117)
..Optic Atrophy, Hereditary, Leber (D029242) 1 L: 00072; 00492;
..Senior Loken Syndrome (C537580)
..Senior-Loken Syndrome 3 (C564637)
..Senior-Loken Syndrome 5 (C563763)
..Senior-Loken Syndrome 6 (C565708)
..Spastic Paraplegia, Optic Atrophy, And Dementia (C566679)
..Spastic Paraplegia, Optic Atrophy, Microcephaly, And Xy Sex Reversal (C566409)
..Wolfram Syndrome (D014929) 1
..Wolfram Syndrome, Mitochondrial Form (C564012) L: 00156;
Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM,ClinVar, CTD

Term ID:

8283

Name:

Optic Atrophy, Hereditary, Leber

Definition:

A maternally linked genetic disorder that presents in mid-life as acute or subacute central vision loss leading to central scotoma and blindness. The disease has been associated with missense mutations in the mtDNA, in genes for Complex I, III, and IV polypeptides, that can act autonomously or in association with each other to cause the disease. (from Online Mendelian Inheritance in Man, http://www.ncbi.nlm.nih.gov/Omim/, MIM#535000 (April 17, 2001))

Alternative IDs:

OMIM:308905|OMIM:535000

ParentIDs:

MESH:D015418|MESH:D028361

TreeNumbers:

C10.292.700.225.500.400 |C10.574.500.662.400 |C11.270.564.400 |C11.640.451.451.400 |C16.320.290.564.400 |C16.320.400.630.400 |C18.452.660.670

Synonyms:

Slim Mappings:

Eye disease|Genetic disease (inborn)|Metabolic disease|Nervous system disease

Reference:

MedGen: D029242
MeSH: D029242
OMIM: 53500;
MSeqDR : 00072; 00492;
Genes:

Phenotypes

Disease Causing ClinVar Variants

Variation_Name	GeneID	GeneSymbol	ClinicalSignificance	dbSNP	RCVaccession	TestedInGTR	PhenotypeIDs	Chromosome	Start	Stop	HGVS_g	OtherIDs	Disease_ClinVar
m.8686T>C	4508	MT-ATP6	not provided	-1	RCV000709918; RCV000709918; RCV000709918;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN043634; MedGen:C1328349,OMIM:551500, Orphanet:ORPHA644	M	8686	8686	m.8686T>C	-
m.9101T>C	4508	MT-ATP6	Pathogenic	199476134	RCV000010277;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	9101	9101	m.9101T>C	OMIM Allelic Variant:516060.0003	C0917796 535000 Leber's optic atrophy;
m.7444G>A	-1	MT-CO1;MT-TS1	Pathogenic	199474822	RCV000010300; RCV000010301; RCV000010299;	Y	MedGen:C1838854,OMIM:580000, Orphanet:ORPHA168609; MedGen:C3151897,OMIM:500008; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	7444	7444	m.7444G>A	OMIM Allelic Variant:516030.0001,OMIM Allelic Variant:590080.0006	C1838854 580000 Aminoglycoside-induced deafness;
m.9438G>A	4514	MT-CO3	Pathogenic	267606611	RCV000010286;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	9438	9438	m.9438G>A	OMIM Allelic Variant:516050.0001	C0917796 535000 Leber's optic atrophy;
m.9804G>A	4514	MT-CO3	Conflicting interpretations of pathogenicity	200613617	RCV000010287; RCV000756352;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	9804	9804	m.9804G>A	OMIM Allelic Variant:516050.0002	C0917796 535000 Leber's optic atrophy;
m.14831G>A	4519	MT-CYB	Pathogenic	199795644	RCV000055706;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14831	14831	m.14831G>A	-	C0917796 535000 Leber's optic atrophy;
m.15257G>A	4519	MT-CYB	Conflicting interpretations of pathogenicity	41518645	RCV000010312;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	15257	15257	m.15257G>A	OMIM Allelic Variant:516020.0001	C0917796 535000 Leber's optic atrophy;
m.15437G>A	4519	MT-CYB	Uncertain significance	878853058	RCV000764855; RCV000764855; RCV000224435;	N	MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	15437	15437	m.15437G>A	-	CN517202 not provided;
m.15812G>A	4519	MT-CYB	Pathogenic	200336777	RCV000010313;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	15812	15812	m.15812G>A	OMIM Allelic Variant:516020.0002	C0917796 535000 Leber's optic atrophy;
m.3376G>A	4535	MT-ND1	Pathogenic	397515612	RCV000056167;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	3376	3376	m.3376G>A	-	C0917796 535000 Leber's optic atrophy;
m.3394T>C	4535	MT-ND1	Pathogenic	41460449	RCV000010375; RCV000507319;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	3394	3394	m.3394T>C	OMIM Allelic Variant:516000.0004	C0917796 535000 Leber's optic atrophy;
m.3460G>A	4535	MT-ND1	Pathogenic	199476118	RCV000010370; RCV000143998; RCV000735416; RCV000757484;	Y	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; na; MedGen:CN517202	M	3460	3460	m.3460G>A	OMIM Allelic Variant:516000.0001	C0917796 535000 Leber's optic atrophy;
m.3635G>A	4535	MT-ND1	Pathogenic	397515507	RCV000055707;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	3635	3635	m.3635G>A	-	C0917796 535000 Leber's optic atrophy;
m.3697G>A	4535	MT-ND1	Pathogenic	199476122	RCV000010385; RCV000010386; RCV000056168;	N	MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	3697	3697	m.3697G>A	OMIM Allelic Variant:516000.0012	C0162671 540000 Juvenile myopathy, encephalopathy, lactic acidosis AND stroke;
m.3700G>A	4535	MT-ND1	Pathogenic	397515508	RCV000415448; RCV000055708; RCV000415448; RCV000415448;	N	Human Phenotype Ontology:HP:0000512,MedGen:C0476397; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; Human Phenotype Ontology:HP:0001138,MedGen:C3887709; Human Phenotype Ontology:HP:0000572,MedGen:C3665	M	3700	3700	m.3700G>A	-	C1849688 Abnormal electroretinogram;
m.3733G>A	4535	MT-ND1	Pathogenic	199476125	RCV000010389;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	3733	3733	m.3733G>A	OMIM Allelic Variant:516000.0015	C0917796 535000 Leber's optic atrophy;
m.4025C>T	4535	MT-ND1	Pathogenic	397515509	RCV000055709;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4025	4025	m.4025C>T	-	C0917796 535000 Leber's optic atrophy;
m.4136A>G	4535	MT-ND1	Pathogenic	199476121	RCV000010378;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4136	4136	m.4136A>G	OMIM Allelic Variant:516000.0006	C0917796 535000 Leber's optic atrophy;
m.4160T>C	4535	MT-ND1	Pathogenic	199476119	RCV000010372;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4160	4160	m.4160T>C	OMIM Allelic Variant:516000.0002	C0917796 535000 Leber's optic atrophy;
m.4171C>A	4535	MT-ND1	Pathogenic	28616230	RCV000010384;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4171	4171	m.4171C>A	OMIM Allelic Variant:516000.0010	C0917796 535000 Leber's optic atrophy;
m.4216T>C	4535	MT-ND1	Conflicting interpretations of pathogenicity	1599988	RCV000010373; RCV000709875;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	4216	4216	m.4216T>C	OMIM Allelic Variant:516000.0003	C0917796 535000 Leber's optic atrophy;
m.4640C>A	4536	MT-ND2	Pathogenic	387906426	RCV000010366;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4640	4640	m.4640C>A	OMIM Allelic Variant:516001.0003	C0917796 535000 Leber's optic atrophy;
m.4917A>G	4536	MT-ND2	Uncertain significance	28357980	RCV000010364;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	4917	4917	m.4917A>G	OMIM Allelic Variant:516001.0001	C0917796 535000 Leber's optic atrophy;
m.5244G>A	4536	MT-ND2	Pathogenic	199476115	RCV000010365;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	5244	5244	m.5244G>A	OMIM Allelic Variant:516001.0002	C0917796 535000 Leber's optic atrophy;
m.10237T>C	4537	MT-ND3	Pathogenic	1556423787	RCV000055695;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	10237	10237	m.10237T>C	-	C0917796 535000 Leber's optic atrophy;
m.11253T>C	4538	MT-ND4	Pathogenic	200145866	RCV000055696;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	11253	11253	m.11253T>C	-	C0917796 535000 Leber's optic atrophy;
m.11360A>G	4538	MT-ND4	Uncertain significance	878928689	RCV000764854; RCV000626558;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; Human Phenotype Ontology:HP:0001250,MedGen:C0036572	M	11360	11360	m.11360A>G	-	C0036572 Seizures;
m.11696G>A	4538	MT-ND4	Pathogenic	200873900	RCV000010356; RCV000055697;	N	MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	11696	11696	m.11696G>A	OMIM Allelic Variant:516003.0003	C1839040 500001 Leber hereditary optic neuropathy with dystonia;
m.11778G>A	4538	MT-ND4	Pathogenic	199476112	RCV000010354; RCV000224219;	Y	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	11778	11778	m.11778G>A	OMIM Allelic Variant:516003.0001	C0917796 535000 Leber's optic atrophy;
m.10663T>C	4539	MT-ND4L	Pathogenic	1556423844	RCV000010353;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	10663	10663	m.10663T>C	OMIM Allelic Variant:516004.0002	C0917796 535000 Leber's optic atrophy;
m.12338T>C	4540	MT-ND5	Pathogenic	201863060	RCV000022893;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	12338	12338	m.12338T>C	OMIM Allelic Variant:516005.0011	C0917796 535000 Leber's optic atrophy;
m.12811T>C	4540	MT-ND5	Uncertain significance	199974018	RCV000055698; RCV000507393;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:CN517202	M	12811	12811	m.12811T>C	-	C0917796 535000 Leber's optic atrophy;
m.12848C>T	4540	MT-ND5	Pathogenic	267606899	RCV000010350;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	12848	12848	m.12848C>T	OMIM Allelic Variant:516005.0009	C0917796 535000 Leber's optic atrophy;
m.13045A>C	4540	MT-ND5	Pathogenic	267606895	RCV000010340; RCV000010341; RCV000010342;	N	MedGen:C0162671,OMIM:540000, Orphanet:ORPHA550,SNOMED CT:39925003; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C1838951	M	13045	13045	m.13045A>C	OMIM Allelic Variant:516005.0005	C0162671 540000 Juvenile myopathy, encephalopathy, lactic acidosis AND stroke;
m.13637A>G	4540	MT-ND5	Pathogenic	200855215	RCV000055699;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	13637	13637	m.13637A>G	-	C0917796 535000 Leber's optic atrophy;
m.13708G>A	4540	MT-ND5	Conflicting interpretations of pathogenicity	28359178	RCV000010336;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	13708	13708	m.13708G>A	OMIM Allelic Variant:516005.0001	C0917796 535000 Leber's optic atrophy;
m.13730G>A	4540	MT-ND5	Pathogenic	387906425	RCV000010337;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	13730	13730	m.13730G>A	OMIM Allelic Variant:516005.0002	C0917796 535000 Leber's optic atrophy;
m.14279G>A	4541	MT-ND6	Pathogenic	869025187	RCV000055705;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14279	14279	m.14279G>A	-	C0917796 535000 Leber's optic atrophy;
m.14325T>C	4541	MT-ND6	Pathogenic	397515505	RCV000055700;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14325	14325	m.14325T>C	-	C0917796 535000 Leber's optic atrophy;
m.14459G>A	4541	MT-ND6	Pathogenic	199476105	RCV000010326; RCV000010327; RCV000144019; RCV000010328;	N	MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; MedGen:C1838951	M	14459	14459	m.14459G>A	OMIM Allelic Variant:516006.0002	C1839040 500001 Leber hereditary optic neuropathy with dystonia;
m.14482C>A	4541	MT-ND6	Pathogenic	199476108	RCV000010332;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14482	14482	m.14482C>A	OMIM Allelic Variant:516006.0006	C0917796 535000 Leber's optic atrophy;
m.14482C>G	4541	MT-ND6	Pathogenic	199476108	RCV000055701;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14482	14482	m.14482C>G	-	C0917796 535000 Leber's optic atrophy;
m.14484T>C	4541	MT-ND6	Pathogenic	199476104	RCV000010325; RCV000144018; RCV000223709;	Y	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003; MedGen:C0023264,OMIM:256000, Orphanet:ORPHA506,SNOMED CT:29570005; MedGen:CN517202	M	14484	14484	m.14484T>C	OMIM Allelic Variant:516006.0001	C0917796 535000 Leber's optic atrophy;
m.14495A>G	4541	MT-ND6	Pathogenic	199476106	RCV000010330;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14495	14495	m.14495A>G	OMIM Allelic Variant:516006.0004	C0917796 535000 Leber's optic atrophy;
m.14498T>C	4541	MT-ND6	Pathogenic	869025186	RCV000055702;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14498	14498	m.14498T>C	-	C0917796 535000 Leber's optic atrophy;
m.14568C>T	4541	MT-ND6	Pathogenic	397515506	RCV000055703;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14568	14568	m.14568C>T	-	C0917796 535000 Leber's optic atrophy;
m.14596A>T	4541	MT-ND6	Pathogenic	387906424	RCV000010329; RCV000055704;	N	MedGen:C1839040,OMIM:500001; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	M	14596	14596	m.14596A>T	OMIM Allelic Variant:516006.0003	C1839040 500001 Leber hereditary optic neuropathy with dystonia;
m.3275C>T	4567	MT-TL1	Uncertain significance	1057516057	RCV000408928; RCV000408950; RCV000408938; RCV000408938; RCV000408938; RCV000408925; RCV000408938; RCV000408950;	N	MedGen:C0424605; MedGen:C0424605; MedGen:C0016059; Human Phenotype Ontology:HP:0001397,MedGen:C2711227; Human Phenotype Ontology:HP:0012115,MedGen:C0019158; Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003;	M	3275	3275	m.3275C>T	-	C0424605 Developmental delay;
NM_001166159.1(NDUFS2):c.268G>A (p.Ala90Thr)	4720	NDUFS2	Pathogenic	1553249704	RCV000625868;	N	Human Phenotype Ontology:HP:0001112,MedGen:C0917796,OMIM:535000, Orphanet:ORPHA104,SNOMED CT:58610003	1	161176262	161176262		-	C0917796 535000 Leber's optic atrophy;

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