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NM_000251.3(MSH2):c.2635-1G>T

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Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000091023.4
Variation ID:
91023
Description:
single nucleotide variant
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NM_000251.3(MSH2):c.2635-1G>T

Allele ID
96498
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47482778 (GRCh38) GRCh38 UCSC
2: 47709917 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_218:g.84655G>T
LRG_218t1:c.2635-1G>T
NC_000002.11:g.47709917G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47482777:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA020850
dbSNP: rs267608020
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 RCV000076525.3
Likely pathogenic 1 criteria provided, single submitter Oct 9, 2019 RCV000629741.3
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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: SCV000107556.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical acceptor splice site
Likely pathogenic
(Oct 09, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000750697.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in the last intron (intron 15) of the MSH2 gene. While this is not anticipated to result … (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
Characterization of a rare variant (c.2635-2A>G) of the MSH2 gene in a family with Lynch syndrome. Cariola F The International journal of biological markers 2018 PMID: 29690800
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
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
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098
http://www.insight-database.org/classifications/?gene=MSH2&variant=c.2635-1G%3ET - - - -

Text-mined citations for rs267608020...

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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