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NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jan 17, 2020
Accession:
VCV000496033.3
Variation ID:
496033
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter)

Allele ID
487320
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5986856 (GRCh38) GRCh38 UCSC
7: 6026487 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.14:g.5986856G>A
NG_008466.1:g.27251C>T
NM_000535.7:c.1909C>T MANE Select NP_000526.2:p.Gln637Ter nonsense
... more HGVS
Protein change
Q637*, Q446*, Q450*, Q531*, Q585*, Q326*, Q502*, Q534*
Other names
-
Canonical SPDI
NC_000007.14:5986855:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA366739308
dbSNP: rs1554297125
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 criteria provided, single submitter Apr 13, 2016 RCV000590029.1
Likely pathogenic 1 criteria provided, single submitter Jan 12, 2018 RCV000759915.1
Pathogenic 1 criteria provided, single submitter Jan 17, 2020 RCV001219508.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PMS2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3086 3151

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Apr 13, 2016)
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: SCV000697311.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: Variant affects a non-conserved nucleotide and results in a nonsense mutation predicted to cause a loss of normal protein function due to production … (more)
Likely pathogenic
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000889612.1
Submitted: (Aug 31, 2018)
Evidence details
Pathogenic
(Jan 17, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV001391451.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Gln637*) in the PMS2 gene. It is expected to result in an absent or disrupted protein … (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
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
Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations: case series, review and follow-up guidelines. Herkert JC European journal of cancer (Oxford, England : 1990) 2011 PMID: 21376568

Text-mined citations for rs1554297125...

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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