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NM_000179.3(MSH6):c.2062_2063del (p.Val688fs) 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:
RCV001353545.2

Allele description [Variation Report for NM_000179.3(MSH6):c.2062_2063del (p.Val688fs)]

NM_000179.3(MSH6):c.2062_2063del (p.Val688fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.2062_2063del (p.Val688fs)
HGVS:
  • NC_000002.11:g.48027184_48027185del
  • NC_000002.12:g.47800043GT[1]
  • NG_007111.1:g.21897GT[1]
  • NM_000179.3:c.2062_2063delMANE SELECT
  • NM_001281492.2:c.1672_1673del
  • NM_001281493.2:c.1156_1157del
  • NM_001281494.2:c.1156_1157del
  • NP_000170.1:p.Val688fs
  • NP_001268421.1:p.Val558fs
  • NP_001268422.1:p.Val386fs
  • NP_001268423.1:p.Val386fs
  • LRG_219:g.21897GT[1]
  • NC_000002.11:g.48027181_48027182del
  • NC_000002.11:g.48027182GT[1]
  • NC_000002.11:g.48027184_48027185del
  • NM_000179.2:c.2062_2063delGT
  • NM_000179.3:c.2062_2063del
  • p.V688LFS*9
Protein change:
V386fs
Links:
dbSNP: rs63750075
NCBI 1000 Genomes Browser:
rs63750075
Molecular consequence:
  • NM_000179.3:c.2062_2063del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.1672_1673del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.1156_1157del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.1156_1157del - 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
SCV000592597Department 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), SCV000592597.2

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

Description

The MSH6 p.Val688LeufsX9 variant was identified in 1 of 1412 proband chromosomes (frequency: 0.001) from individuals or families with Lynch Syndrome (Plaschke 2004). The variant was identified in dbSNP (ID: rs63750075) “With Pathogenic allele”, HGMD, InSiGHT Colon Cancer Database, the ClinVar database (classified as a pathogenic variant by InSIGHT) and UMD (1X as a pathogenic variant). The p.Val688LeufsX9 deletion variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 688 and leads to a premature stop codon 9 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 MSH6 gene are an established mechanism of disease in Lynch syndrome and this 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