NM_000179.3(MSH6):c.2079del (p.Lys693fs) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 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:: RCV000687847.5

Allele description [Variation Report for NM_000179.3(MSH6):c.2079del (p.Lys693fs)]

NM_000179.3(MSH6):c.2079del (p.Lys693fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.2079del (p.Lys693fs)

HGVS:

NC_000002.12:g.47800062del
NG_007111.1:g.21916del
NM_000179.2:c.2079del
NM_000179.3:c.2079delMANE SELECT
NM_001281492.2:c.1689del
NM_001281493.2:c.1173del
NM_001281494.2:c.1173del
NP_000170.1:p.Lys693fs
NP_001268421.1:p.Lys563fs
NP_001268422.1:p.Lys391fs
NP_001268423.1:p.Lys391fs
LRG_219t1:c.2079del
LRG_219:g.21916del
NC_000002.11:g.48027196del
NC_000002.11:g.48027201del
NM_000179.2:c.2079delA
NM_000179.3:c.2079delAMANE SELECT

Protein change:

K391fs

Links:

dbSNP: rs267608083

NCBI 1000 Genomes Browser:

rs267608083

Molecular consequence:

NM_000179.3:c.2079del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.1689del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.1173del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.1173del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

Recent activity

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Ndel1 nudE neurodevelopment protein 1-like 1 [Rattus norvegicus]
Ndel1 nudE neurodevelopment protein 1-like 1 [Rattus norvegicus]
Gene ID:170845

Gene
170845[uid] AND (alive[prop]) (1)
Gene
Erigeron epiroticus (0)
Nucleotide
PREDICTED: Mus musculus predicted gene, 30515 (Gm30515), transcript variant X7, ...
PREDICTED: Mus musculus predicted gene, 30515 (Gm30515), transcript variant X7, ncRNA
gi|1039742512|ref|XR_001780583.1|

Nucleotide
Homo sapiens bone morphogenetic protein 4 (BMP4), transcript variant 5, mRNA
Homo sapiens bone morphogenetic protein 4 (BMP4), transcript variant 5, mRNA
gi|1122781518|ref|NM_001347913.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000815436	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18269114, 24362816, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000815436

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 9, 2023)

germline

clinical testing

PubMed (3)
[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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000815436.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 567689). 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.Lys693Asnfs*43) 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).

#	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: Oct 8, 2024

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