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NM_000251.3(MSH2):c.39C>G (p.Ser13Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 26, 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:
RCV003303146.2

Allele description [Variation Report for NM_000251.3(MSH2):c.39C>G (p.Ser13Arg)]

NM_000251.3(MSH2):c.39C>G (p.Ser13Arg)

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.39C>G (p.Ser13Arg)
HGVS:
  • NC_000002.12:g.47403230C>G
  • NG_007110.2:g.5107C>G
  • NM_000251.1:c.39C>G
  • NM_000251.3:c.39C>GMANE SELECT
  • NM_001258281.1:c.-31+55C>G
  • NP_000242.1:p.Ser13Arg
  • NP_000242.1:p.Ser13Arg
  • LRG_218t1:c.39C>G
  • LRG_218:g.5107C>G
  • LRG_218p1:p.Ser13Arg
  • NC_000002.11:g.47630369C>G
  • NM_000251.2:c.39C>G
  • NM_000251.3:c.39C>G
Protein change:
S13R
Links:
dbSNP: rs1060502015
NCBI 1000 Genomes Browser:
rs1060502015
Molecular consequence:
  • NM_001258281.1:c.-31+55C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.3:c.39C>G - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003996629Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 26, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk.

Jia X, Burugula BB, Chen V, Lemons RM, Jayakody S, Maksutova M, Kitzman JO.

Am J Hum Genet. 2021 Jan 7;108(1):163-175. doi: 10.1016/j.ajhg.2020.12.003. Epub 2020 Dec 23.

PubMed [citation]
PMID:
33357406
PMCID:
PMC7820803

Details of each submission

From Ambry Genetics, SCV003996629.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Oct 8, 2024