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NM_000535.7(PMS2):c.1906G>A (p.Ala636Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Nov 30, 2020)
Last evaluated:
Jan 19, 2019
Accession:
VCV000231053.5
Variation ID:
231053
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1906G>A (p.Ala636Thr)

Allele ID
233496
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5986859 (GRCh38) GRCh38 UCSC
7: 6026490 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.27248G>A
LRG_161t1:c.1906G>A
NC_000007.13:g.6026490C>T
... more HGVS
Protein change
A636T, A449T, A530T, A445T, A325T, A501T, A584T, A533T
Other names
-
Canonical SPDI
NC_000007.14:5986858:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA10578660
dbSNP: rs876658863
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 Dec 13, 2016 RCV000473624.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 19, 2019 RCV000221721.4
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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
3086 3151

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 13, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000552060.2
Submitted: (Mar 14, 2017)
Evidence details
Comment:
This sequence change replaces alanine with threonine at codon 636 of the PMS2 protein (p.Ala636Thr). The alanine residue is weakly conserved and there is a … (more)
Uncertain significance
(Jan 19, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000904862.2
Submitted: (May 19, 2020)
Evidence details
Likely benign
(Mar 11, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000274788.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other strong data supporting benign classification

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs876658863...

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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