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NM_000179.3(MSH6):c.3801G>A (p.Met1267Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 4, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001184154.5

Allele description [Variation Report for NM_000179.3(MSH6):c.3801G>A (p.Met1267Ile)]

NM_000179.3(MSH6):c.3801G>A (p.Met1267Ile)

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.3801G>A (p.Met1267Ile)
HGVS:
  • NC_000002.12:g.47806358G>A
  • NG_007111.1:g.28212G>A
  • NG_008397.1:g.104318C>T
  • NM_000179.3:c.3801G>AMANE SELECT
  • NM_001281492.2:c.3411G>A
  • NM_001281493.2:c.2895G>A
  • NM_001281494.2:c.2895G>A
  • NP_000170.1:p.Met1267Ile
  • NP_001268421.1:p.Met1137Ile
  • NP_001268422.1:p.Met965Ile
  • NP_001268423.1:p.Met965Ile
  • LRG_219t1:c.3801G>A
  • LRG_219:g.28212G>A
  • NC_000002.11:g.48033497G>A
  • NC_000002.11:g.48033497G>A
  • NM_000179.2:c.3801G>A
Protein change:
M1137I
Links:
dbSNP: rs1670069736
NCBI 1000 Genomes Browser:
rs1670069736
Molecular consequence:
  • NM_000179.3:c.3801G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281492.2:c.3411G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281493.2:c.2895G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281494.2:c.2895G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001350071Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 6, 2019) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002622272Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Feb 4, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV001350071.2

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

Description

This variant causes a G>A nucleotide substitution at the last nucleotide of exon 8 of the MSH6 gene and replaces methionine with isoleucine at codon 1267 of the MSH6 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on the protein function. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing, however, this prediction has not been confirmed in published RNA studies. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

From Ambry Genetics, SCV002622272.2

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

Description

The p.M1267I variant (also known as c.3801G>A), located in coding exon 8 of the MSH6 gene, results from a G to A substitution at nucleotide position 3801. The amino acid change results in methionine to isoleucine at codon 1267, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 8, which makes it likely to have some effect on normal mRNA splicing. This nucleotide position is highly conserved in available vertebrate species. This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024