Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000251.3(MSH2):c.943-1G>A

Help
Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000091252.4
Variation ID:
91252
Description:
single nucleotide variant
Help

NM_000251.3(MSH2):c.943-1G>A

Allele ID
96727
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47416295 (GRCh38) GRCh38 UCSC
2: 47643434 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.47643434G>A
NC_000002.12:g.47416295G>A
NG_007110.2:g.18172G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47416294:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA022598
dbSNP: rs12476364
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 reviewed by expert panel Jun 21, 2019 RCV000076757.3
Pathogenic 1 criteria provided, single submitter Oct 15, 2019 RCV000532450.4
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MSH2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
4518 4603

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 21, 2019)
reviewed by expert panel
Method: curation
Lynch syndrome
Allele origin: germline
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000107798.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical donor splice site
Pathogenic
(Oct 15, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000625485.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in intron 5 of the MSH2 gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Patients with colorectal cancer associated with Lynch syndrome and MLH1 promoter hypermethylation have similar prognoses. Haraldsdottir S Genetics in medicine : official journal of the American College of Medical Genetics 2016 PMID: 26866578
Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer. Mangold E International journal of cancer 2005 PMID: 15849733
Economic and Practical Factors in Diagnosing HNPCC Using Clinical Criteria, Immunohistochemistry and Microsatellite Instability Analysis. Pigatto F Hereditary cancer in clinical practice 2004 PMID: 20233461
Clinical consequences of molecular diagnosis in families with mismatch repair gene germline mutations. Pistorius SR International journal of colorectal disease 2000 PMID: 11151427
http://www.insight-database.org/classifications/?gene=MSH2&variant=c.943-1G%3EA - - - -

Text-mined citations for rs12476364...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021