NM_000179.3(MSH6):c.476C>T (p.Ala159Val) AND Hereditary nonpolyposis colorectal neoplasms

Clinical significance:Uncertain significance (Last evaluated: Aug 30, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000179.3(MSH6):c.476C>T (p.Ala159Val)]

NM_000179.3(MSH6):c.476C>T (p.Ala159Val)

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.476C>T (p.Ala159Val)
  • NC_000002.12:g.47795912C>T
  • NG_007111.1:g.17766C>T
  • NM_000179.2:c.476C>T
  • NM_000179.3:c.476C>TMANE SELECT
  • NM_001281492.2:c.238-2699C>T
  • NM_001281493.2:c.-279-2699C>T
  • NM_001281494.2:c.-427C>T
  • NP_000170.1:p.Ala159Val
  • NP_000170.1:p.Ala159Val
  • LRG_219t1:c.476C>T
  • LRG_219:g.17766C>T
  • LRG_219p1:p.Ala159Val
  • NC_000002.11:g.48023051C>T
Protein change:
dbSNP: rs587778528
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001281494.2:c.-427C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001281492.2:c.238-2699C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281493.2:c.-279-2699C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000179.2:c.476C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000179.3:c.476C>T - missense variant - [Sequence Ontology: SO:0001583]


Hereditary nonpolyposis colorectal neoplasms
MedGen: C0009405; Orphanet: 443090

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000551076Invitaecriteria provided, single submitter
Uncertain significance
(Aug 30, 2020)
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



CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein.

Terui H, Akagi K, Kawame H, Yura K.

J Biomed Sci. 2013 Apr 28;20:25. doi: 10.1186/1423-0127-20-25.

PubMed [citation]

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]

Details of each submission

From Invitae, SCV000551076.5

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


This sequence change replaces alanine with valine at codon 159 of the MSH6 protein (p.Ala159Val). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and valine. This variant is present in population databases (rs587778528, ExAC 0.005%). This variant has not been reported in the literature in individuals with MSH6-related disease. ClinVar contains an entry for this variant (Variation ID: 134848). General algorithms developed to predict the effect of missense changes on protein structure and function (SIFT: Tolerated; PolyPhen-2: Benign; Align-GVGD: Class C0) and an algorithm developed specifically for the MSH6 gene (PMID: 23621914), suggest that this missense change is likely to be tolerated. The valine amino acid residue is also found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. However, these predictions have not been confirmed by published functional studies and its clinical significance is uncertain. In summary, this variant is a rare missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 30, 2021

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