NM_000251.3(MSH2):c.1189C>G (p.Gln397Glu) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Nov 24, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000251.3(MSH2):c.1189C>G (p.Gln397Glu)]

NM_000251.3(MSH2):c.1189C>G (p.Gln397Glu)

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.1189C>G (p.Gln397Glu)
Other names:
  • NC_000002.12:g.47429854C>G
  • NG_007110.2:g.31731C>G
  • NM_000251.2:c.1189C>G
  • NM_000251.3:c.1189C>GMANE SELECT
  • NM_001258281.1:c.991C>G
  • NP_000242.1:p.Gln397Glu
  • NP_000242.1:p.Gln397Glu
  • NP_001245210.1:p.Gln331Glu
  • LRG_218t1:c.1189C>G
  • LRG_218:g.31731C>G
  • LRG_218p1:p.Gln397Glu
  • NC_000002.11:g.47656993C>G
  • NM_000251.1:c.1189C>G
Protein change:
dbSNP: rs63750611
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000251.2:c.1189C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000251.3:c.1189C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258281.1:c.991C>G - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001448495Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Nov 24, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001448495.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


Variant summary: MSH2 c.1189C>G (p.Gln397Glu) results in a conservative amino acid change located in the DNA mismatch repair protein MutS, core (IPR007696) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 251454 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in MSH2 causing Lynch Syndrome (4.4e-05 vs 0.00057), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1189C>G in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=4). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Nov 27, 2021

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