NM_015836.4(WARS2):c.716G>A (p.Arg239Gln) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 13, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001935609.5

Allele description

NM_015836.4(WARS2):c.716G>A (p.Arg239Gln)

Gene:

WARS2:tryptophanyl tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p12

Genomic location:

Preferred name:

NM_015836.4(WARS2):c.716G>A (p.Arg239Gln)

HGVS:

NC_000001.11:g.119033278C>T
NG_050658.1:g.112511G>A
NM_001378226.1:c.647G>A
NM_001378227.1:c.647G>A
NM_001378228.1:c.545G>A
NM_001378229.1:c.458G>A
NM_001378230.1:c.434G>A
NM_001378231.1:c.*51G>A
NM_015836.4:c.716G>AMANE SELECT
NM_201263.2:c.*82G>A
NP_001365155.1:p.Arg216Gln
NP_001365156.1:p.Arg216Gln
NP_001365157.1:p.Arg182Gln
NP_001365158.1:p.Arg153Gln
NP_001365159.1:p.Arg145Gln
NP_056651.1:p.Arg239Gln
NC_000001.10:g.119575901C>T

Protein change:

R145Q

Links:

dbSNP: rs751913292

NCBI 1000 Genomes Browser:

rs751913292

Molecular consequence:

NM_001378231.1:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_201263.2:c.*82G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001378226.1:c.647G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378227.1:c.647G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378228.1:c.545G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378229.1:c.458G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378230.1:c.434G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015836.4:c.716G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002197389	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 13, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002197389

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 13, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002197389.3

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

Description

This variant has not been reported in the literature in individuals affected with WARS2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant is present in population databases (rs751913292, gnomAD 0.005%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 239 of the WARS2 protein (p.Arg239Gln).

#	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

Last Updated: Feb 28, 2024

ClinVar

Relating variation to medicine