NM_000179.3(MSH6):c.3878_3881dup (p.Pro1295fs) AND Hereditary nonpolyposis colorectal neoplasms

Clinical significance:Pathogenic (Last evaluated: Feb 1, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000695362.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3878_3881dup (p.Pro1295fs)]

NM_000179.3(MSH6):c.3878_3881dup (p.Pro1295fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3878_3881dup (p.Pro1295fs)
HGVS:
  • NC_000002.12:g.47806528_47806531dup
  • NG_007111.1:g.28382_28385dup
  • NG_008397.1:g.104146_104149dup
  • NM_000179.3:c.3878_3881dupMANE SELECT
  • NM_001281492.2:c.3488_3491dup
  • NM_001281493.2:c.2972_2975dup
  • NM_001281494.2:c.2972_2975dup
  • NP_000170.1:p.Pro1295fs
  • NP_001268421.1:p.Pro1165fs
  • NP_001268422.1:p.Pro993fs
  • NP_001268423.1:p.Pro993fs
  • LRG_219:g.28382_28385dup
  • NC_000002.11:g.48033667_48033670dup
  • NM_000179.2:c.3878_3881dupCTTG
Protein change:
P1165fs
Links:
dbSNP: rs1553333500
NCBI 1000 Genomes Browser:
rs1553333500
Molecular consequence:
  • NM_000179.3:c.3878_3881dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.3488_3491dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.2972_2975dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.2972_2975dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MedGen: C0009405; Orphanet: 443090

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000823857Invitaecriteria provided, single submitter
Pathogenic
(Feb 1, 2018)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000823857.1

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

Description

This sequence change creates a premature translational stop signal (p.Pro1295Leufs*3) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MSH6-related disease. ClinVar contains an entry for this variant (Variation ID: 418332). Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 25, 2021

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