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NM_000535.7(PMS2):c.1798A>G (p.Met600Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jun 11, 2021)
Last evaluated:
May 26, 2020
Accession:
VCV000548758.9
Variation ID:
548758
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1798A>G (p.Met600Val)

Allele ID
539268
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5986967 (GRCh38) GRCh38 UCSC
7: 6026598 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.27140A>G
LRG_161t1:c.1798A>G
NC_000007.13:g.6026598T>C
... more HGVS
Protein change
M600V, M465V, M413V, M548V, M497V, M289V, M409V, M494V
Other names
-
Canonical SPDI
NC_000007.14:5986966:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
dbSNP: rs1304634005
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 Jul 6, 2017 RCV000662640.1
Uncertain significance 1 criteria provided, single submitter May 1, 2019 RCV001030721.1
Uncertain significance 1 criteria provided, single submitter Apr 9, 2019 RCV001061729.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 26, 2020 RCV000772030.3
Uncertain significance 1 no assertion criteria provided - RCV001358228.1
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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
3086 3151

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 06, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal cancer type 4
Allele origin: unknown
Counsyl
Accession: SCV000785326.2
Submitted: (Jun 20, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(May 26, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000904998.2
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This missense variant replaces methionine with valine at codon 600 of the PMS2 protein. Computational prediction suggests that this variant may not impact protein structure … (more)
Uncertain significance
(Apr 09, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colon cancer
Allele origin: germline
Invitae
Accession: SCV001226482.1
Submitted: (Feb 06, 2020)
Evidence details
Comment:
This sequence change replaces methionine with valine at codon 600 of the PMS2 protein (p.Met600Val). The methionine residue is weakly conserved and there is a … (more)
Uncertain significance
(May 01, 2019)
criteria provided, single submitter
Method: research
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Cancer Genomics Group,Japanese Foundation For Cancer Research
Accession: SCV001193689.2
Submitted: (Jun 25, 2020)
Evidence details
Likely benign
(May 22, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV001173766.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Other strong data supporting benign classification
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
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: SCV001553902.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The PMS2 p.Met600Val variant was identified in 1 of 1144 proband chromosomes (frequency: 0.0009) from individuals or families with atherosclerosis (Johnston 2012,). The variant was … (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
Prevalence of disease-causing genes in Japanese patients with <i>BRCA1/2</i>-wildtype hereditary breast and ovarian cancer syndrome. Kaneyasu T NPJ breast cancer 2020 PMID: 32566746
Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Johnston JJ American journal of human genetics 2012 PMID: 22703879

Text-mined citations for rs1304634005...

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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