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NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) AND Carcinoma of colon

Germline classification:
Benign (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:
RCV001353505.9

Allele description [Variation Report for NM_000179.3(MSH6):c.116G>A (p.Gly39Glu)]

NM_000179.3(MSH6):c.116G>A (p.Gly39Glu)

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.116G>A (p.Gly39Glu)
HGVS:
  • NC_000002.12:g.47783349G>A
  • NG_007111.1:g.5203G>A
  • NM_000179.3:c.116G>AMANE SELECT
  • NM_001281492.2:c.116G>A
  • NM_001281493.2:c.-621G>A
  • NP_000170.1:p.Gly39Glu
  • NP_001268421.1:p.Gly39Glu
  • LRG_219t1:c.116G>A
  • LRG_219:g.5203G>A
  • LRG_219p1:p.Gly39Glu
  • NC_000002.11:g.48010488G>A
  • NM_000179.2:c.116G>A
  • P52701:p.Gly39Glu
  • c.116G>A
  • p.G39E
Protein change:
G39E
Links:
UniProtKB: P52701#VAR_004490; dbSNP: rs1042821
NCBI 1000 Genomes Browser:
rs1042821
Molecular consequence:
  • NM_001281493.2:c.-621G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000179.3:c.116G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281492.2:c.116G>A - missense variant - [Sequence Ontology: SO:0001583]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000592563Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Benignunknownclinical 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), SCV000592563.2

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

Description

The p.Gly39Glu variant has been previously reported in the literature and is recorded in dbSNP as a polymorphism with an average heterozygosity of 0.307+/-0.243 (dbSNP#: rs1042821); this appreciable frequency in different populations of origin increases the likelihood this is a benign variant. In addition, this variant has been identified by our laboratory in at least one individual with a second pathogenic vairiant, increasing the likelihood this variant is benign. In summary, based on the above information, this variant is classified as benign.

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

Last Updated: Jun 9, 2024