NC_012920.1(MT-ND5):m.13513G>A AND Leigh syndrome

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Sep 22, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000144016.10

Allele description [Variation Report for NC_012920.1(MT-ND5):m.13513G>A]

NC_012920.1(MT-ND5):m.13513G>A

Gene:

MT-ND5:mitochondrially encoded NADH dehydrogenase 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Genomic location:

Preferred name:

NC_012920.1(MT-ND5):m.13513G>A

Other names:

MTND5, 13513G-A, ASP393ASN; D393N

HGVS:

NC_012920.1:m.13513G>A
p.Asp393Asn

Protein change:

ASP393ASN

Links:

Genetic Testing Registry (GTR): GTR000500597; OMIM: 516005.0007; dbSNP: rs267606897

NCBI 1000 Genomes Browser:

rs267606897

Observations:

Condition(s)

Name:: Leigh syndrome (NULS)
Synonyms:: Leigh Disease; Subacute necrotizing encephalopathy; Necrotizing encephalopathy infantile subacute of Leigh; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009723; MedGen: C2931891; Orphanet: 506; OMIM: 256000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000188908	GeneReviews	no classification provided	not provided	germline	literature only
SCV000997986	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (Modified ACMG Guidelines (Unpublished))	Pathogenic (Oct 17, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10589546, 9299505 Citation Link,
SCV002574885	Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin See additional submitters CUBI - Core Unit Bioinformatics, Berlin Institute of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002580352	MGZ Medical Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	5	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, literature only

Citations

PubMed

The mitochondrial DNA G13513A transition in ND5 is associated with a LHON/MELAS overlap syndrome and may be a frequent cause of MELAS.

Pulkes T, Eunson L, Patterson V, Siddiqui A, Wood NW, Nelson IP, Morgan-Hughes JA, Hanna MG.

Ann Neurol. 1999 Dec;46(6):916-9. Erratum in: Ann Neurol 2000 Jun;47(6):841.

PubMed [citation]

PMID:: 10589546

Identification of a novel mutation in the mtDNA ND5 gene associated with MELAS.

Santorelli FM, Tanji K, Kulikova R, Shanske S, Vilarinho L, Hays AP, DiMauro S.

Biochem Biophys Res Commun. 1997 Sep 18;238(2):326-8.

PubMed [citation]

PMID:: 9299505

See all PubMed Citations (3)

Details of each submission

From GeneReviews, SCV000188908.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV000997986.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The NC_012920.1:m.13513G>A (YP_003024036.1:p.Asp393Asn) variant in MTND5 gene is interpretated to be a Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PS1, PS3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, SCV002574885.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	Blood	not provided		1	not provided	not provided	not provided

From MGZ Medical Genetics Center, SCV002580352.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		4	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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