NM_000251.2(MSH2):c.2075G>A (p.Gly692Glu) AND Carcinoma of colon

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001353568.1

Allele description [Variation Report for NM_000251.2(MSH2):c.2075G>A (p.Gly692Glu)]

NM_000251.2(MSH2):c.2075G>A (p.Gly692Glu)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.2(MSH2):c.2075G>A (p.Gly692Glu)
HGVS:
  • NC_000002.12:g.47476436G>A
  • NG_007110.2:g.78313G>A
  • NM_000251.2:c.2075G>A
  • NM_001258281.1:c.1877G>A
  • NP_000242.1:p.Gly692Glu
  • NP_001245210.1:p.Gly626Glu
  • LRG_218t1:c.2075G>A
  • LRG_218:g.78313G>A
  • LRG_218p1:p.Gly692Glu
  • NC_000002.11:g.47703575G>A
Protein change:
G626E
Links:
dbSNP: rs63751432
NCBI 1000 Genomes Browser:
rs63751432
Molecular consequence:
  • NM_000251.2:c.2075G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258281.1:c.1877G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colorectal cancer, somatic; Colon cancer, somatic; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000592531Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000592531.2

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

Description

The MSH2 p.Gly692Glu variant was not identified in the literature nor was it identified in the dbSNP, NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, HGMD, COSMIC, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database, “Zhejiang Colon Cancer Database”, the ClinVar database and GeneInsight VariantWire database. The variant was only identified in MutDB and UMD (1X as a likely pathogenic variant). The p.Gly692 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the p.Gly692 variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance.

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

Last Updated: Oct 8, 2021

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