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NM_000251.3(MSH2):c.459del (p.Ala154fs) AND Carcinoma of colon

Germline classification:
Pathogenic (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001357715.2

Allele description [Variation Report for NM_000251.3(MSH2):c.459del (p.Ala154fs)]

NM_000251.3(MSH2):c.459del (p.Ala154fs)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.459del (p.Ala154fs)
HGVS:
  • NC_000002.12:g.47410186del
  • NG_007110.2:g.12063del
  • NM_000251.3:c.459delMANE SELECT
  • NM_001258281.1:c.261del
  • NP_000242.1:p.Ala154fs
  • NP_001245210.1:p.Ala88fs
  • LRG_218:g.12063del
  • NC_000002.11:g.47637325del
Protein change:
A154fs
Links:
dbSNP: rs2104023773
NCBI 1000 Genomes Browser:
rs2104023773
Molecular consequence:
  • NM_000251.3:c.459del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258281.1:c.261del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001553266Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

Help

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), SCV001553266.1

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

Description

The MSH2 p.Ala154GlnfsX20 variant was not identified in the literature nor was it identified in the following databases: dbSNP, ClinVar, UMD-LSDB, the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The c.459del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 154 and leads to a premature stop codon 20 codons downstream. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the MSH2 gene are an established mechanism of disease in Lynch Syndrome and is the type of variant expected to cause the disorder. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

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

Last Updated: Jun 23, 2024