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NM_000179.3(MSH6):c.3974A>G (p.Lys1325Arg) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 22, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001358663.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3974A>G (p.Lys1325Arg)]

NM_000179.3(MSH6):c.3974A>G (p.Lys1325Arg)

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.3974A>G (p.Lys1325Arg)
HGVS:
  • NC_000002.12:g.47806624A>G
  • NG_007111.1:g.28478A>G
  • NG_008397.1:g.104052T>C
  • NM_000179.3:c.3974A>GMANE SELECT
  • NM_001281492.2:c.3584A>G
  • NM_001281493.2:c.3068A>G
  • NM_001281494.2:c.3068A>G
  • NP_000170.1:p.Lys1325Arg
  • NP_000170.1:p.Lys1325Arg
  • NP_001268421.1:p.Lys1195Arg
  • NP_001268422.1:p.Lys1023Arg
  • NP_001268423.1:p.Lys1023Arg
  • LRG_219t1:c.3974A>G
  • LRG_219:g.28478A>G
  • LRG_219p1:p.Lys1325Arg
  • NC_000002.11:g.48033763A>G
  • NM_000179.2:c.3974A>G
Protein change:
K1023R
Links:
dbSNP: rs876658189
NCBI 1000 Genomes Browser:
rs876658189
Molecular consequence:
  • NM_000179.3:c.3974A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281492.2:c.3584A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281493.2:c.3068A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281494.2:c.3068A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000695899Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Mar 22, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695899.2

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

Description

Variant summary: MSH6 c.3974A>G (p.Lys1325Arg) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 247380 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3974A>G in individuals affected with Hereditary Nonpolyposis Colorectal Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Five other ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Oct 8, 2024