NM_000251.3(MSH2):c.157G>A (p.Ala53Thr) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 2, 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:
RCV000772332.3

Allele description [Variation Report for NM_000251.3(MSH2):c.157G>A (p.Ala53Thr)]

NM_000251.3(MSH2):c.157G>A (p.Ala53Thr)

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.157G>A (p.Ala53Thr)
HGVS:
  • NC_000002.12:g.47403348G>A
  • NG_007110.2:g.5225G>A
  • NM_000251.3:c.157G>AMANE SELECT
  • NM_001258281.1:c.-30-12G>A
  • NP_000242.1:p.Ala53Thr
  • NP_000242.1:p.Ala53Thr
  • LRG_218t1:c.157G>A
  • LRG_218:g.5225G>A
  • LRG_218p1:p.Ala53Thr
  • NC_000002.11:g.47630487G>A
  • NM_000251.2:c.157G>A
Protein change:
A53T
Links:
dbSNP: rs755931648
NCBI 1000 Genomes Browser:
rs755931648
Molecular consequence:
  • NM_001258281.1:c.-30-12G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.3:c.157G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000905491Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Comprehensive screening for mutations associated with colorectal cancer in unselected cases reveals penetrant and nonpenetrant mutations.

Kraus C, Rau TT, Lux P, Erlenbach-Wünsch K, Löhr S, Krumbiegel M, Thiel CT, Stöhr R, Agaimy A, Croner RS, Stürzl M, Hohenberger W, Hartmann A, Reis A.

Int J Cancer. 2015 Mar 15;136(6):E559-68. doi: 10.1002/ijc.29149. Epub 2014 Aug 30.

PubMed [citation]
PMID:
25142776

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 Color Diagnostics, LLC DBA Color Health, SCV000905491.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This missense variant replaces alanine with threonine at codon 53 of the MSH2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individuals presenting with two Lynch-syndrome associated cancers and therefore fulfilled one of the revised Bethesda criteria (PMID: 25142776). Tumors from this individual showed microsatellite stability and normal MSH2 expression (PMID: 25142776). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024