NM_000251.2(MSH2):c.211G>C (p.Gly71Arg) AND Carcinoma of colon

Clinical significance:Likely pathogenic

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:
RCV001353465.1

Allele description [Variation Report for NM_000251.2(MSH2):c.211G>C (p.Gly71Arg)]

NM_000251.2(MSH2):c.211G>C (p.Gly71Arg)

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.211G>C (p.Gly71Arg)
HGVS:
  • NC_000002.12:g.47403402G>C
  • NG_007110.2:g.5279G>C
  • NM_000251.2:c.211G>C
  • NM_001258281.1:c.13G>C
  • NP_000242.1:p.Gly71Arg
  • NP_001245210.1:p.Gly5Arg
  • LRG_218t1:c.211G>C
  • LRG_218:g.5279G>C
  • LRG_218p1:p.Gly71Arg
  • NC_000002.11:g.47630541G>C
  • NM_000251.1:c.211G>C
  • p.G71R
Protein change:
G5R
Links:
dbSNP: rs587782659
NCBI 1000 Genomes Browser:
rs587782659
Molecular consequence:
  • NM_000251.2:c.211G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258281.1:c.13G>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

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
SCV000592455Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely pathogenicunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not 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), SCV000592455.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

The p.Gly71Arg variant has not been reported in the literature nor previously identified by our laboratory. The variant occurs in the last base of exon 1. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 4 out of 5 different programs. This residue is conserved in mammals but not in lower organisms, and computational analyses (SIFT, AlignGVGD) do not suggest a high likelihood of impact to the protein. However, the information from these software analyses is not predictive enough to rule out pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time, although we would lean towards a more pathogenic role for this variant. This variant is classified as Predicted Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Jun 14, 2021

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