NM_000179.2(MSH6):c.3037_3041delAAGAA (p.Lys1013Valfs) AND Lynch syndrome

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 11, 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:: RCV000200490.1

Allele description

NM_000179.2(MSH6):c.3037_3041delAAGAA (p.Lys1013Valfs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.2(MSH6):c.3037_3041delAAGAA (p.Lys1013Valfs)

HGVS:

NC_000002.12:g.47801020_47801024delAAGAA
NG_007111.1:g.22874_22878delAAGAA
NM_000179.2:c.3037_3041delAAGAA
NP_000170.1:p.Lys1013Valfs
LRG_219t1:c.3037_3041delAAGAA
LRG_219:g.22874_22878delAAGAA
LRG_219p1:p.Lys1013Valfs
NC_000002.11:g.48028159_48028163delAAGAA
p.K1013VFS*3

Links:

dbSNP: rs587782712

NCBI 1000 Genomes Browser:

rs587782712

Molecular consequence:

NM_000179.2:c.3037_3041delAAGAA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Lynch syndrome (HNPCC)
Synonyms:: Hereditary nonpolyposis colon cancer
Identifiers:: MedGen: C1333990; OMIM: PS120435

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000255261	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 11, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000255261

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 11, 2015)

germline

clinical testing

Citation Link

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

Details of each submission

From Invitae, SCV000255261.1

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

Description

This sequence change deletes 5 nucleotides from exon 4 of the MSH6 mRNA (c.3037_3041delAAGAA), causing a frameshift at codon 1013. This creates a premature translational stop signal (p.Lys1013Valfs*3) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, truncating variants in MSH6 are known to be pathogenic (PMID: 24362816, 18269114). 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: Mar 25, 2017

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