NM_000179.3(MSH6):c.476C>T (p.Ala159Val) AND not provided

Clinical significance:Uncertain significance (Last evaluated: May 3, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000586380.1

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

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

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.476C>T (p.Ala159Val)
HGVS:
  • 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:
A159V
Links:
dbSNP: rs587778528
NCBI 1000 Genomes Browser:
rs587778528
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]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000695915Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(May 3, 2016)
germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

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

Citations

PubMed

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]
PMID:
23621914
PMCID:
PMC3651391

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695915.1

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

Description

Variant summary: The c.476C>T variant affects a conserved nucleotide, resulting in amino acid change from Ala to Val. 2/4 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index). This variant is found in 4/120712 control chromosomes at a frequency of 0.0000331, which does not exceed maximal expected frequency of a pathogenic allele (0.0001421). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical laboratories; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.

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

Last Updated: Oct 30, 2021

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