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NM_000251.2(MSH2):c.2006-2A>G

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Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
3 (Most recent: May 19, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000090847.6
Variation ID:
90847
Description:
single nucleotide variant
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NM_000251.2(MSH2):c.2006-2A>G

Allele ID
96322
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47476365 (GRCh38) GRCh38 UCSC
2: 47703504 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.47703504A>G
NC_000002.12:g.47476365A>G
NG_007110.2:g.78242A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47476364:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA019751
dbSNP: rs267607991
Varsome
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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 RCV000076349.5
Pathogenic 1 criteria provided, single submitter Feb 28, 2019 RCV000774579.2
Pathogenic 1 criteria provided, single submitter May 5, 2021 RCV001420710.1
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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

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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: SCV000107375.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical donor splice site
Pathogenic
(Feb 28, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000908323.2
Submitted: (May 19, 2020)
Evidence details
Pathogenic
(May 05, 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: SCV000917706.2
Submitted: (May 19, 2021)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: MSH2 c.2006-2A>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

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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

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Title Author Journal Year Link
Report on de-novo mutation in the MSH2 gene as a rare event in hereditary nonpolyposis colorectal cancer. Morak M European journal of gastroenterology & hepatology 2008 PMID: 19047842
Novel germline and somatic mutations of the MSH2 gene in hereditary non-polyposis colorectal cancer. Ding DC Clinical genetics 2007 PMID: 17250671
Cancer risk in 348 French MSH2 or MLH1 gene carriers. Parc Y Journal of medical genetics 2003 PMID: 12624141
http://www.insight-database.org/classifications/?gene=MSH2&variant=c.2006-2A%3EG - - - -

Text-mined citations for rs267607991...

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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 08, 2021