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NM_000179.3(MSH6):c.3498del (p.Arg1166fs) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 4, 2023
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:
RCV003759297.2

Allele description [Variation Report for NM_000179.3(MSH6):c.3498del (p.Arg1166fs)]

NM_000179.3(MSH6):c.3498del (p.Arg1166fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3498del (p.Arg1166fs)
HGVS:
  • NC_000002.12:g.47804969del
  • NG_007111.1:g.26823del
  • NG_008397.1:g.105708del
  • NM_000179.3:c.3498delMANE SELECT
  • NM_001281492.2:c.3108del
  • NM_001281493.2:c.2592del
  • NM_001281494.2:c.2592del
  • NM_001406795.1:c.3594del
  • NM_001406796.1:c.3498del
  • NM_001406797.1:c.3201del
  • NM_001406798.1:c.3324del
  • NM_001406799.1:c.2973del
  • NM_001406800.1:c.3498del
  • NM_001406801.1:c.3201del
  • NM_001406802.1:c.3594del
  • NM_001406803.1:c.2634del
  • NM_001406804.1:c.3420del
  • NM_001406805.1:c.3201del
  • NM_001406806.1:c.2973del
  • NM_001406807.1:c.2973del
  • NM_001406808.1:c.3498del
  • NM_001406809.1:c.3498del
  • NM_001406811.1:c.2592del
  • NM_001406812.1:c.2592del
  • NM_001406813.1:c.3504del
  • NM_001406814.1:c.2592del
  • NM_001406815.1:c.2592del
  • NM_001406816.1:c.2592del
  • NM_001406817.1:c.1932del
  • NM_001406818.1:c.3201del
  • NM_001406819.1:c.3201del
  • NM_001406820.1:c.3201del
  • NM_001406821.1:c.3201del
  • NM_001406822.1:c.3201del
  • NM_001406823.1:c.2592del
  • NM_001406824.1:c.3201del
  • NM_001406825.1:c.3201del
  • NM_001406826.1:c.3330del
  • NM_001406827.1:c.3201del
  • NM_001406828.1:c.3201del
  • NM_001406829.1:c.2592del
  • NM_001406830.1:c.3201del
  • NM_001406831.1:c.279del
  • NM_001406832.1:c.345del
  • NM_001407362.1:c.1443del
  • NP_000170.1:p.Arg1166Serfs
  • NP_000170.1:p.Arg1166fs
  • NP_001268421.1:p.Arg1036fs
  • NP_001268422.1:p.Arg864fs
  • NP_001268423.1:p.Arg864fs
  • NP_001393724.1:p.Arg1198fs
  • NP_001393725.1:p.Arg1166fs
  • NP_001393726.1:p.Arg1067fs
  • NP_001393727.1:p.Arg1108fs
  • NP_001393728.1:p.Arg991fs
  • NP_001393729.1:p.Arg1166fs
  • NP_001393730.1:p.Arg1067fs
  • NP_001393731.1:p.Arg1198fs
  • NP_001393732.1:p.Arg878fs
  • NP_001393733.1:p.Arg1140fs
  • NP_001393734.1:p.Arg1067fs
  • NP_001393735.1:p.Arg991fs
  • NP_001393736.1:p.Arg991fs
  • NP_001393737.1:p.Arg1166fs
  • NP_001393738.1:p.Arg1166fs
  • NP_001393740.1:p.Arg864fs
  • NP_001393741.1:p.Arg864fs
  • NP_001393742.1:p.Arg1168fs
  • NP_001393743.1:p.Arg864fs
  • NP_001393744.1:p.Arg864fs
  • NP_001393745.1:p.Arg864fs
  • NP_001393746.1:p.Arg644fs
  • NP_001393747.1:p.Arg1067fs
  • NP_001393748.1:p.Arg1067fs
  • NP_001393749.1:p.Arg1067fs
  • NP_001393750.1:p.Arg1067fs
  • NP_001393751.1:p.Arg1067fs
  • NP_001393752.1:p.Arg864fs
  • NP_001393753.1:p.Arg1067fs
  • NP_001393754.1:p.Arg1067fs
  • NP_001393755.1:p.Arg1110fs
  • NP_001393756.1:p.Arg1067fs
  • NP_001393757.1:p.Arg1067fs
  • NP_001393758.1:p.Arg864fs
  • NP_001393759.1:p.Arg1067fs
  • NP_001393760.1:p.Arg93fs
  • NP_001393761.1:p.Arg115fs
  • NP_001394291.1:p.Arg481fs
  • LRG_219t1:c.3498del
  • LRG_219:g.26823del
  • LRG_219p1:p.Arg1166Serfs
  • NC_000002.11:g.48032107del
  • NC_000002.11:g.48032108del
  • NM_000179.2:c.3498delG
  • NR_176256.1:n.2428del
  • NR_176257.1:n.3759del
  • NR_176258.1:n.3688del
  • NR_176259.1:n.3587del
  • NR_176260.1:n.1532delG
Protein change:
R1036fs
Molecular consequence:
  • NM_000179.3:c.3498del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.3108del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406795.1:c.3594del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406796.1:c.3498del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406797.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406798.1:c.3324del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406799.1:c.2973del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406800.1:c.3498del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406801.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406802.1:c.3594del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406803.1:c.2634del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406804.1:c.3420del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406805.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406806.1:c.2973del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406807.1:c.2973del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406808.1:c.3498del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406809.1:c.3498del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406811.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406812.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406813.1:c.3504del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406814.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406815.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406816.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406817.1:c.1932del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406818.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406819.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406820.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406821.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406822.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406823.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406824.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406825.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406826.1:c.3330del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406827.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406828.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406829.1:c.2592del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406830.1:c.3201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406831.1:c.279del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406832.1:c.345del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407362.1:c.1443del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_176256.1:n.2428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176257.1:n.3759del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176258.1:n.3688del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176259.1:n.3587del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MeSH: D003123; MedGen: C0009405

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004464079Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 4, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Germline MSH6 mutations are more prevalent in endometrial cancer patient cohorts than hereditary non polyposis colorectal cancer cohorts.

Devlin LA, Graham CA, Price JH, Morrison PJ.

Ulster Med J. 2008 Jan;77(1):25-30.

PubMed [citation]
PMID:
18269114
PMCID:
PMC2397009

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.

Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, et al.

Nat Genet. 2014 Feb;46(2):107-115. doi: 10.1038/ng.2854. Epub 2013 Dec 22.

PubMed [citation]
PMID:
24362816
PMCID:
PMC4294709
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004464079.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with MSH6-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg1166Serfs*18) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816).

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

Last Updated: Sep 29, 2024