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NM_000535.7(PMS2):c.1399G>A (p.Val467Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Oct 25, 2020
Accession:
VCV000142447.10
Variation ID:
142447
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1399G>A (p.Val467Ile)

Allele ID
152161
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5987366 (GRCh38) GRCh38 UCSC
7: 6026997 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.26741G>A
LRG_161t1:c.1399G>A
NC_000007.14:g.5987366C>T
... more HGVS
Protein change
V467I, V332I, V415I, V361I, V364I, V156I, V276I, V280I
Other names
-
Canonical SPDI
NC_000007.14:5987365:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00007
Trans-Omics for Precision Medicine (TOPMed) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00006
Links
ClinGen: CA009624
dbSNP: rs373611083
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 25, 2020 RCV000457616.7
Uncertain significance 1 criteria provided, single submitter Mar 24, 2017 RCV000485817.3
Uncertain significance 2 criteria provided, single submitter May 28, 2020 RCV000656947.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 23, 2020 RCV000131574.5
Lynch-like syndrome
Uncertain significance 1 no assertion criteria provided Jul 1, 2019 RCV001249988.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PMS2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3083 3148

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 23, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186580.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The p.V467I variant (also known as c.1399G>A), located in coding exon 11 of the PMS2 gene, results from a G to A substitution at nucleotide … (more)
Uncertain significance
(Mar 24, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000601817.1
Submitted: (Aug 01, 2017)
Evidence details
Likely benign
(Nov 25, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903129.1
Submitted: (Nov 06, 2018)
Evidence details
Uncertain significance
(Oct 25, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000551955.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces valine with isoleucine at codon 467 of the PMS2 protein (p.Val467Ile). The valine residue is weakly conserved and there is a … (more)
Uncertain significance
(May 28, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565403.5
Submitted: (Sep 24, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Uncertain significance
(Jul 01, 2019)
no assertion criteria provided
Method: clinical testing
Lynch-like syndrome
Allele origin: somatic
Constitutional Genetics Lab,Leon Berard Cancer Center
Accession: SCV001424002.1
Submitted: (Jul 20, 2020)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001551003.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The PMS2 p.Val332Ile variant was not identified in the literature nor was it identified in COGR, MutDB, LOVD 3.0, Insight Colon Cancer Gene Variant Database … (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

Text-mined citations for rs373611083...

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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 30, 2021