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NM_000535.7(PMS2):c.652G>A (p.Gly218Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Nov 10, 2021)
Last evaluated:
Sep 10, 2021
Accession:
VCV000455732.8
Variation ID:
455732
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.652G>A (p.Gly218Ser)

Allele ID
456860
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5999161 (GRCh38) GRCh38 UCSC
7: 6038792 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.14946G>A
LRG_161t1:c.652G>A
NC_000007.13:g.6038792C>T
... more HGVS
Protein change
G218S, G112S, G83S, G115S
Other names
-
Canonical SPDI
NC_000007.14:5999160:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA366743913
dbSNP: rs878854055
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 Aug 30, 2018 RCV000547672.3
Uncertain significance 1 criteria provided, single submitter Jan 27, 2021 RCV001290677.1
Uncertain significance 1 criteria provided, single submitter Sep 10, 2021 RCV001775843.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 8, 2020 RCV001025376.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
(Aug 30, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colon cancer
Allele origin: germline
Invitae
Accession: SCV000625673.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glycine with serine at codon 218 of the PMS2 protein (p.Gly218Ser). The glycine residue is weakly conserved and there is a … (more)
Likely benign
(Apr 04, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV001187553.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other strong data supporting benign classification
Uncertain significance
(Jan 27, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001478809.1
Submitted: (Feb 09, 2021)
Evidence details
Comment:
Variant summary: PMS2 c.652G>A (p.Gly218Ser) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Uncertain significance
(Sep 08, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001341887.2
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This missense variant replaces glycine with serine at codon 218 of the PMS2 protein. Computational prediction is inconclusive regarding the impact of this variant on … (more)
Uncertain significance
(Sep 10, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV002013931.1
Submitted: (Nov 10, 2021)
Evidence details
Comment:
Not observed at significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has … (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 rs878854055...

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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 12, 2021