NM_000251.3(MSH2):c.2150_2153del (p.Ser717fs) AND Lynch syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 14, 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:: RCV000234418.2

Allele description [Variation Report for NM_000251.3(MSH2):c.2150_2153del (p.Ser717fs)]

NM_000251.3(MSH2):c.2150_2153del (p.Ser717fs)

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2150_2153del (p.Ser717fs)

HGVS:

NC_000002.11:g.47703648_47703651del
NC_000002.12:g.47476511_47476514del
NG_007110.2:g.78388_78391del
NM_000251.3:c.2150_2153delMANE SELECT
NM_001258281.1:c.1952_1955del
NP_000242.1:p.Ser717fs
NP_001245210.1:p.Ser651fs
LRG_218:g.78388_78391del
NC_000002.11:g.47703648_47703651del
NC_000002.11:g.47703648_47703651delCAGT
NC_000002.11:g.47703650_47703653del
NM_000251.2:c.2150_2153delGTCA

Protein change:

S651fs

Links:

dbSNP: rs878853809

NCBI 1000 Genomes Browser:

rs878853809

Molecular consequence:

NM_000251.3:c.2150_2153del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.1952_1955del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000284139	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 14, 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

SCV000284139

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 14, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000284139.2

#	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 4 nucleotides from exon 13 of the MSH2 mRNA (c.2150_2153delGTCA), causing a frameshift at codon 717. This creates a premature translational stop signal (p.Ser717Asnfs*2) 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 MSH2 are known to be pathogenic (PMID: 15849733, 24362816). 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: Sep 29, 2024

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