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NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000135940.8
Variation ID:
135940
Description:
2bp indel
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NM_000535.7(PMS2):c.1688_1689delinsAG (p.Arg563Gln)

Allele ID
139652
Variant type
Indel
Variant length
2 bp
Cytogenetic location
7p22.1
Genomic location
7: 5987076-5987077 (GRCh38) GRCh38 UCSC
7: 6026707-6026708 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.6026707_6026708delinsCT
NC_000007.14:g.5987076_5987077delinsCT
NM_000535.7:c.1688_1689delinsAG MANE Select NP_000526.2:p.Arg563Gln missense
... more HGVS
Protein change
R372Q, R511Q, R376Q, R457Q, R252Q, R428Q, R563Q, R460Q
Other names
-
Canonical SPDI
NC_000007.14:5987075:TC:CT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA010042
dbSNP: rs587780725
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 Jan 15, 2018 RCV000587523.4
Likely benign 1 criteria provided, single submitter Dec 3, 2020 RCV001080776.2
Likely benign 1 criteria provided, single submitter Oct 15, 2020 RCV001263509.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 7, 2020 RCV000132456.6
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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
3060 3125

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 15, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806184.1
Submitted: (Jan 29, 2018)
Evidence details
Likely benign
(Jul 14, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000902632.1
Submitted: (Nov 06, 2018)
Evidence details
Likely benign
(Oct 15, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697307.2
Submitted: (Nov 10, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: PMS2 c.1688_1689delinsAG (p.Arg563Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign … (more)
Uncertain significance
(Jul 07, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187550.6
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The c.1688_1689delGAinsAG variant (also known as p.R563Q), located in coding exon 11 of the PMS2 gene, results from an in-frame deletion of GA and insertion … (more)
Likely benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000166380.11
Submitted: (Jan 07, 2021)
Evidence details

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
Clinical genetic testing outcome with multi-gene panel in Asian patients with multiple primary cancers. Chan GHJ Oncotarget 2018 PMID: 30093976

Text-mined citations for rs587780725...

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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 Jun 23, 2021