NM_002437.5(MPV17):c.461G>T (p.Arg154Met) AND Mitochondrial DNA depletion syndrome 6 (hepatocerebral type)

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Aug 13, 2019
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:: RCV000625516.2

Allele description [Variation Report for NM_002437.5(MPV17):c.461G>T (p.Arg154Met)]

NM_002437.5(MPV17):c.461G>T (p.Arg154Met)

Gene:

MPV17:mitochondrial inner membrane protein MPV17 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.3

Genomic location:

Preferred name:

NM_002437.5(MPV17):c.461G>T (p.Arg154Met)

HGVS:

NC_000002.12:g.27311899C>A
NG_008075.1:g.15665G>T
NG_033055.1:g.1364G>T
NM_002437.5:c.461G>TMANE SELECT
NP_002428.1:p.Arg154Met
NC_000002.11:g.27534767C>A
NM_002437.4:c.461G>T

Protein change:

R154M

Links:

dbSNP: rs886044113

NCBI 1000 Genomes Browser:

rs886044113

Molecular consequence:

NM_002437.5:c.461G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Mitochondrial DNA depletion syndrome 6 (hepatocerebral type)
Synonyms:: Navajo neurohepatopathy; Navajo neuropathy; Mitochondrial DNA depletion syndrome type 6
Identifiers:: MONDO: MONDO:0009747; MedGen: C1850406; Orphanet: 255229; OMIM: 256810

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000746012	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 1, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000998886	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 13, 2019)	unknown	curation	PubMed (2) [See all records that cite these PMIDs] 29282788, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000746012

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 1, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000998886

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 13, 2019)

unknown

curation

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

El-Hattab AW, Wang J, Dai H, Almannai M, Staufner C, Alfadhel M, Gambello MJ, Prasun P, Raza S, Lyons HJ, Afqi M, Saleh MAM, Faqeih EA, Alzaidan HI, Alshenqiti A, Flore LA, Hertecant J, Sacharow S, Barbouth DS, Murayama K, Shah AA, Lin HC, et al.

Hum Mutat. 2018 Apr;39(4):461-470. doi: 10.1002/humu.23387. Epub 2018 Jan 13.

PubMed [citation]

PMID:: 29282788

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV000746012.1

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

From SIB Swiss Institute of Bioinformatics, SCV000998886.1

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

Description

This variant is interpreted as a Likely pathogenic for Mitochondrial DNA depletion syndrome 6, autosomal recessive. The following ACMG Tag(s) were applied: PM2, PP3, PM3-strong.

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

Last Updated: Dec 30, 2023

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