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.1662-2A>G

Help
Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
3 (Most recent: Jun 17, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000090728.6
Variation ID:
90728
Description:
single nucleotide variant
Help

NM_000251.3(MSH2):c.1662-2A>G

Allele ID
96203
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47470963 (GRCh38) GRCh38 UCSC
2: 47698102 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.47698102A>G
NC_000002.12:g.47470963A>G
NG_007110.2:g.72840A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47470962:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs267607971
ClinGen: CA018902
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 RCV000076225.5
Pathogenic 1 criteria provided, single submitter Feb 4, 2020 RCV000560516.3
Pathogenic 1 criteria provided, single submitter May 24, 2021 RCV001526860.1
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
4498 4583

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: SCV000107249.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical donor splice site
Pathogenic
(Feb 04, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000625295.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change affects an acceptor splice site in intron 10 of the MSH2 gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(May 24, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colon cancer
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919688.2
Submitted: (Jun 17, 2021)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: MSH2 c.1662-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (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
A survey of the clinicopathological and molecular characteristics of patients with suspected Lynch syndrome in Latin America. Rossi BM BMC cancer 2017 PMID: 28874130
Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Thompson BA Nature genetics 2014 PMID: 24362816
Functional examination of MLH1, MSH2, and MSH6 intronic mutations identified in Danish colorectal cancer patients. Petersen SM BMC medical genetics 2013 PMID: 24090359
Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome. Bonadona V JAMA 2011 PMID: 21642682
Major contribution from recurrent alterations and MSH6 mutations in the Danish Lynch syndrome population. Nilbert M Familial cancer 2009 PMID: 18566915
Clinical and genetic characteristics of Chinese hereditary nonpolyposis colorectal cancer families. Wang XL World journal of gastroenterology 2006 PMID: 16810763
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
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
http://www.insight-database.org/classifications/?gene=MSH2&variant=c.1662-2A%3EG - - - -

Text-mined citations for rs267607971...

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 Oct 24, 2021