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NM_000251.3(MSH2):c.1927G>A (p.Glu643Lys) AND MSH2-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 11, 2023
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:
RCV004532666.1

Allele description [Variation Report for NM_000251.3(MSH2):c.1927G>A (p.Glu643Lys)]

NM_000251.3(MSH2):c.1927G>A (p.Glu643Lys)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.1927G>A (p.Glu643Lys)
Other names:
p.E643K:GAA>AAA
HGVS:
  • NC_000002.12:g.47475192G>A
  • NG_007110.2:g.77069G>A
  • NM_000251.3:c.1927G>AMANE SELECT
  • NM_001258281.1:c.1729G>A
  • NP_000242.1:p.Glu643Lys
  • NP_000242.1:p.Glu643Lys
  • NP_001245210.1:p.Glu577Lys
  • LRG_218t1:c.1927G>A
  • LRG_218:g.77069G>A
  • LRG_218p1:p.Glu643Lys
  • NC_000002.11:g.47702331G>A
  • NM_000251.1:c.1927G>A
  • NM_000251.2:c.1927G>A
  • p.E643K
Protein change:
E577K
Links:
dbSNP: rs374840361
NCBI 1000 Genomes Browser:
rs374840361
Molecular consequence:
  • NM_000251.3:c.1927G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258281.1:c.1729G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
MSH2-related disorder
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004120695PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 11, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 PreventionGenetics, part of Exact Sciences, SCV004120695.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The MSH2 c.1927G>A variant is predicted to result in the amino acid substitution p.Glu643Lys. This variant was reported in an individual with ovarian cancer and an individual with pancreatic adenocarcinoma (Table 2, Pal et al. 2012. PubMed ID: 23047549; Table A2, Shindo et al. 2017. PubMed ID: 28767289). This variant is reported in 4 of ~251,000 alleles in gnomAD (http://gnomad.broadinstitute.org/variant/2-47702331-G-A; Table S1, Amendola et al. 2015. PubMed ID: 25637381) and has conflicting interpretations of likely benign and uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/161299/643). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024