NM_000251.3(MSH2):c.696_697del (p.Ser233fs) AND Hereditary nonpolyposis colorectal neoplasms

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 22, 2019
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:: RCV001223404.7

Allele description

NM_000251.3(MSH2):c.696_697del (p.Ser233fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.696_697del (p.Ser233fs)

HGVS:

NC_000002.12:g.47412464_47412465del
NG_007110.2:g.14341_14342del
NM_000251.3:c.696_697delMANE SELECT
NM_001258281.1:c.498_499del
NP_000242.1:p.Ser233fs
NP_000242.1:p.Ser233fs
NP_001245210.1:p.Ser167fs
LRG_218t1:c.696_697del
LRG_218:g.14341_14342del
LRG_218p1:p.Ser233fs
NC_000002.11:g.47639601_47639602del
NC_000002.11:g.47639603_47639604del
NM_000251.1:c.696_697del
NM_000251.1:c.696_697delTT
NM_000251.2:c.696_697del

Protein change:

S167fs

Links:

dbSNP: rs63750426

NCBI 1000 Genomes Browser:

rs63750426

Molecular consequence:

NM_000251.3:c.696_697del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.498_499del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

Recent activity

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MULTISPECIES: hypothetical protein [Burkholderiaceae]
MULTISPECIES: hypothetical protein [Burkholderiaceae]
gi|2159891250|ref|WP_230973087.1|

Protein
MULTISPECIES: helix-turn-helix domain-containing protein [Burkholderiaceae]
MULTISPECIES: helix-turn-helix domain-containing protein [Burkholderiaceae]
gi|1770519068|ref|WP_152415019.1|

Protein
cytochrome oxidase subunit 1, partial (mitochondrion) [Raphicerus campestris]
cytochrome oxidase subunit 1, partial (mitochondrion) [Raphicerus campestris]
gi|1033208134|gb|ANH56753.1|

Protein
Microcephaly 18, primary, autosomal dominant
Microcephaly 18, primary, autosomal dominant

MedGen
Neurodevelopmental disorder with seizures, microcephaly, and brain abnormalities
Neurodevelopmental disorder with seizures, microcephaly, and brain abnormalities

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001395553	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 22, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11151427, 15849733, 24362816, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001395553

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 22, 2019)

germline

clinical testing

PubMed (4)
[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

Clinical consequences of molecular diagnosis in families with mismatch repair gene germline mutations.

Pistorius SR, Kruppa C, Haas S, Plaschke J, Kruger S, Bulitta CJ, Nagel M, Saeger HD, Schackert HK.

Int J Colorectal Dis. 2000 Nov;15(5-6):255-63.

PubMed [citation]

PMID:: 11151427

Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer.

Mangold E, Pagenstecher C, Friedl W, Mathiak M, Buettner R, Engel C, Loeffler M, Holinski-Feder E, Müller-Koch Y, Keller G, Schackert HK, Krüger S, Goecke T, Moeslein G, Kloor M, Gebert J, Kunstmann E, Schulmann K, Rüschoff J, Propping P.

Int J Cancer. 2005 Sep 20;116(5):692-702.

PubMed [citation]

PMID:: 15849733

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001395553.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ser233Hisfs*22) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. This variant has been observed in an individual affected with Lynch syndrome (PMID: 11151427). ClinVar contains an entry for this variant (Variation ID: 11151427). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 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: Jun 23, 2024

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Relating variation to medicine