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NM_000251.3(MSH2):c.2210+1G>A

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Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000090921.7
Variation ID:
90921
Description:
single nucleotide variant
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NM_000251.3(MSH2):c.2210+1G>A

Allele ID
96396
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47476572 (GRCh38) GRCh38 UCSC
2: 47703711 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_218:g.78449G>A
LRG_218t1:c.2210+1G>A
NC_000002.11:g.47703711G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47476571:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA020243
dbSNP: rs267608002
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 RCV000076423.4
Pathogenic 1 criteria provided, single submitter Jun 21, 2017 RCV000490900.2
Likely pathogenic 1 criteria provided, single submitter Oct 22, 2019 RCV000524382.4
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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
4521 4606

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: SCV000107451.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical donor splice site
Pathogenic
(Jun 21, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000580436.4
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The c.2210+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 13 of the MSH2 gene. This alteration has … (more)
Likely pathogenic
(Oct 22, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000548155.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change affects a donor splice site in intron 13 of the MSH2 gene. It is expected to disrupt RNA splicing and likely results … (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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Systematic study on genetic and epimutational profile of a cohort of Amsterdam criteria-defined Lynch Syndrome in Singapore. Liu Y PloS one 2014 PMID: 24710284
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
Clinical features and mismatch repair genes analyses of Chinese suspected hereditary non-polyposis colorectal cancer: a cost-effective screening strategy proposal. Yan HL Cancer science 2008 PMID: 18307539
Two germline alterations in mismatch repair genes found in a HNPCC patient with poor family history. Kámory E Pathology oncology research : POR 2006 PMID: 17189986
Germline MSH2 and MLH1 mutational spectrum including large rearrangements in HNPCC families from Poland (update study). Kurzawski G Clinical genetics 2006 PMID: 16451135
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
Germline MSH2 and MLH1 mutational spectrum in HNPCC families from Poland and the Baltic States. Kurzawski G Journal of medical genetics 2002 PMID: 12362047
http://www.insight-database.org/classifications/?gene=MSH2&variant=c.2210+1G%3EA - - - -

Text-mined citations for rs267608002...

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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 Nov 27, 2021