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NM_000535.7(PMS2):c.949C>T (p.Gln317Ter)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel
Submissions:
4 (Most recent: Jul 16, 2021)
Last evaluated:
Sep 5, 2013
Accession:
VCV000091383.8
Variation ID:
91383
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.949C>T (p.Gln317Ter)

Allele ID
96858
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5992012 (GRCh38) GRCh38 UCSC
7: 6031643 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.22095C>T
LRG_161t1:c.949C>T
NC_000007.13:g.6031643G>A
... more HGVS
Protein change
Q317*, Q182*, Q211*, Q214*, Q126*, Q6*
Other names
-
Canonical SPDI
NC_000007.14:5992011:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA013352
dbSNP: rs143277125
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 reviewed by expert panel Sep 5, 2013 RCV000076902.2
Pathogenic 1 criteria provided, single submitter Nov 6, 2019 RCV000570620.1
Pathogenic 1 criteria provided, single submitter Apr 29, 2020 RCV000686600.4
Pathogenic 1 criteria provided, single submitter Apr 27, 2021 RCV001536747.2
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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
3065 3130

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 05, 2013)
reviewed by expert panel
Method: research
Lynch Syndrome
Allele origin: germline
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000108399.2
Submitted: (Dec 18, 2013)
Comment:
Classified with v1.9 guidelines: https://docs.google.com/file/d/0B3JL6rP6JzhoN2EydHRVMEI1UGs
Evidence details
Comment:
Coding sequence variation resulting in a stop codon
Pathogenic
(Nov 06, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000670801.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (4)
Comment:
The p.Q317* pathogenic mutation (also known as c.949C>T), located in coding exon 9 of the PMS2 gene, results from a C to T substitution at … (more)
Pathogenic
(Apr 29, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000814125.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Gln317*) in the PMS2 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Apr 27, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001753553.1
Submitted: (Jul 16, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Observed … (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
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
The gastrointestinal phenotype of germline biallelic mismatch repair gene mutations. Durno CA The American journal of gastroenterology 2010 PMID: 20531397
Pediatric duodenal cancer and biallelic mismatch repair gene mutations. Roy S Pediatric blood & cancer 2009 PMID: 19283792
The clinical phenotype of Lynch syndrome due to germ-line PMS2 mutations. Senter L Gastroenterology 2008 PMID: 18602922
http://www.insight-database.org/classifications/index.html?gene=PMS2&variant=c.949C%3ET - - - -

Text-mined citations for rs143277125...

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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 Sep 23, 2021