NM_000179.3(MSH6):c.4081_4082del (p.Ter1361AspextTer?) AND Lynch syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 22, 2015
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:: RCV000196781.8

Allele description

NM_000179.3(MSH6):c.4081_4082del (p.Ter1361AspextTer?)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.4081_4082del (p.Ter1361AspextTer?)

HGVS:

NC_000002.12:g.47806856TA[1]
NG_007111.1:g.28710TA[1]
NG_008397.1:g.103817TA[1]
NM_000179.2:c.4081_4082delTA
NM_000179.3:c.4081_4082delMANE SELECT
NM_001281492.2:c.3691_3692del
NM_001281493.2:c.3175_3176del
NM_001281494.2:c.3175_3176del
NP_000170.1:p.Ter1361AspextTer?
NP_001268421.1:p.Ter1231AspextTer?
NP_001268422.1:p.Ter1059AspextTer?
NP_001268423.1:p.Ter1059AspextTer?
LRG_219t1:c.4081_4082del
LRG_219:g.28710TA[1]
NC_000002.11:g.48033995TA[1]
NC_000002.11:g.48033995_48033996del
NM_000179.2:c.4079_4080delTA
NM_000179.2:c.4081_4082del
NM_000179.2:c.4081_4082delTA

Links:

dbSNP: rs863224830

NCBI 1000 Genomes Browser:

rs863224830

Molecular consequence:

NM_000179.3:c.4081_4082del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3691_3692del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.3175_3176del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.3175_3176del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000179.3:c.4081_4082del - stop lost - [Sequence Ontology: SO:0001578]
NM_001281492.2:c.3691_3692del - stop lost - [Sequence Ontology: SO:0001578]
NM_001281493.2:c.3175_3176del - stop lost - [Sequence Ontology: SO:0001578]
NM_001281494.2:c.3175_3176del - stop lost - [Sequence Ontology: SO:0001578]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000255265	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 22, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000255265

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 22, 2015)

germline

clinical testing

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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000255265.2

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

Description

This sequence change deletes 2 nucleotide from exon 10 of the MSH6 mRNA (c.4079_4080delTA). This deletion disrupts the translational stop signal of the MSH6 mRNA and it is expected to extend the length of the MSH6 protein by 2 additional amino acid residues (p.*1361Aspext*2). The effect of this extension on protein function is uncertain. This variant has not been published in the literature and is not present in population databases. In summary, this is a novel stop-loss variant with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

#	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: Sep 16, 2024

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