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NM_000179.3(MSH6):c.999del (p.Lys334fs) AND Lynch syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 31, 2016
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:
RCV000456722.1

Allele description

NM_000179.3(MSH6):c.999del (p.Lys334fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.999del (p.Lys334fs)
HGVS:
  • NC_000002.12:g.47798982del
  • NG_007111.1:g.20836del
  • NM_000179.3:c.999delMANE SELECT
  • NM_001281492.2:c.609del
  • NM_001281493.2:c.93del
  • NM_001281494.2:c.93del
  • NP_000170.1:p.Lys334fs
  • NP_001268421.1:p.Lys204fs
  • NP_001268422.1:p.Lys32fs
  • NP_001268423.1:p.Lys32fs
  • LRG_219:g.20836del
  • NC_000002.11:g.48026121del
  • NM_000179.2:c.999delC
Protein change:
K204fs
Links:
dbSNP: rs1060502932
NCBI 1000 Genomes Browser:
rs1060502932
Molecular consequence:
  • NM_000179.3:c.999del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.609del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.93del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.93del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000551242Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 31, 2016) 		germlineclinical testing

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

Help

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, SCV000551242.2

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

Description

This sequence change deletes 1 nucleotide from exon 4 of the MSH6 mRNA (c.999delC), causing a frameshift at codon 334. This creates a premature translational stop signal (p.Lys334Argfs*4) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, loss-of-function variants in MSH6 are known to be pathogenic (PMID: 24362816, 18269114). 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: Apr 23, 2022