NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 28, 2024
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:: RCV000524183.10

Allele description [Variation Report for NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)]

NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs)

HGVS:

NC_000002.12:g.47806256_47806259del
NG_007111.1:g.28110_28113del
NG_008397.1:g.104419_104422del
NM_000179.3:c.3699_3702delMANE SELECT
NM_001281492.2:c.3309_3312del
NM_001281493.2:c.2793_2796del
NM_001281494.2:c.2793_2796del
NP_000170.1:p.Lys1233fs
NP_001268421.1:p.Lys1103fs
NP_001268422.1:p.Lys931fs
NP_001268423.1:p.Lys931fs
LRG_219:g.28110_28113del
NC_000002.11:g.48033393_48033396del
NC_000002.11:g.48033395_48033398del
NM_000179.2:c.3699_3702delAGAA
NM_000179.3:c.3699_3702del
p.K1233NFS*6
p.Lys1233Asnfs*6
p.Lys1233AsnfsX6

Protein change:

K1103fs

Links:

dbSNP: rs193922343

NCBI 1000 Genomes Browser:

rs193922343

Molecular consequence:

NM_000179.3:c.3699_3702del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3309_3312del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.2793_2796del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.2793_2796del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000551259	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 28, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 18269114, 24362816, 18389388, 21642682, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000551259

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 28, 2024)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000551259.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Lys1233Asnfs*6) 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). This variant is present in population databases (rs267608115, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 18389388, 21642682). This variant is also known as c.3697_3700delAAAG. ClinVar contains an entry for this variant (Variation ID: 36593). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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