NM_000179.3(MSH6):c.3482CTG[1] (p.Ala1162del) AND Hereditary nonpolyposis colorectal neoplasms

Clinical significance:Uncertain significance (Last evaluated: Oct 30, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000542403.2

Allele description [Variation Report for NM_000179.3(MSH6):c.3482CTG[1] (p.Ala1162del)]

NM_000179.3(MSH6):c.3482CTG[1] (p.Ala1162del)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3482CTG[1] (p.Ala1162del)
HGVS:
  • NC_000002.12:g.47804953CTG[1]
  • NG_007111.1:g.26807CTG[1]
  • NG_008397.1:g.105718CAG[1]
  • NM_000179.3:c.3482CTG[1]MANE SELECT
  • NM_001281492.2:c.3092CTG[1]
  • NM_001281493.2:c.2576CTG[1]
  • NM_001281494.2:c.2576CTG[1]
  • NP_000170.1:p.Ala1162del
  • NP_001268421.1:p.Ala1032del
  • NP_001268422.1:p.Ala860del
  • NP_001268423.1:p.Ala860del
  • LRG_219:g.26807CTG[1]
  • NC_000002.11:g.48032092CTG[1]
  • NM_000179.2:c.3485_3487delCTG
  • p.A1162del
Protein change:
A1032del
Links:
dbSNP: rs63751427
NCBI 1000 Genomes Browser:
rs63751427
Molecular consequence:
  • NM_000179.3:c.3482CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001281492.2:c.3092CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001281493.2:c.2576CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001281494.2:c.2576CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MedGen: C0009405; Orphanet: 443090

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000624874Invitaecriteria provided, single submitter
Uncertain significance
(Oct 30, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.

Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, Gulden C, Kupfer SS, Swisher EM, Bennett RL, Novetsky AP, Jarvik GP, Olopade OI, Goodfellow PJ, King MC, Tait JF, Walsh T.

J Mol Diagn. 2012 Jul;14(4):357-66. doi: 10.1016/j.jmoldx.2012.03.002. Epub 2012 May 30.

PubMed [citation]
PMID:
22658618
PMCID:
PMC3391416

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000624874.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant, c.3485_3487delCTG, results in the deletion of 1 amino acid of the MSH6 protein (p.Ala1162del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals with suspected Lynch syndrome (PMID: 22658618, 28514183). ClinVar contains an entry for this variant (Variation ID: 140774). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: May 28, 2021

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