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NM_000535.7(PMS2):c.2438G>A (p.Arg813Gln) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 6, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000483291.1

Allele description

NM_000535.7(PMS2):c.2438G>A (p.Arg813Gln)

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.2438G>A (p.Arg813Gln)
HGVS:
  • NC_000007.14:g.5977595C>T
  • NG_008466.1:g.36512G>A
  • NM_000535.7:c.2438G>A
  • NM_001322003.2:c.2033G>A
  • NM_001322004.2:c.2033G>A
  • NM_001322005.2:c.2033G>A
  • NM_001322006.2:c.2282G>A
  • NM_001322007.1:c.2120G>A
  • NM_001322008.2:c.2120G>A
  • NM_001322009.2:c.2066G>A
  • NM_001322010.2:c.1877G>A
  • NM_001322011.2:c.1505G>A
  • NM_001322012.2:c.1505G>A
  • NM_001322013.2:c.1865G>A
  • NM_001322014.2:c.2471G>A
  • NM_001322015.2:c.2129G>A
  • NP_000526.2:p.Arg813Gln
  • NP_001308932.1:p.Arg678Gln
  • NP_001308933.1:p.Arg678Gln
  • NP_001308934.1:p.Arg678Gln
  • NP_001308935.1:p.Arg761Gln
  • NP_001308936.1:p.Arg707Gln
  • NP_001308937.1:p.Arg707Gln
  • NP_001308938.1:p.Arg689Gln
  • NP_001308939.1:p.Arg626Gln
  • NP_001308940.1:p.Arg502Gln
  • NP_001308941.1:p.Arg502Gln
  • NP_001308942.1:p.Arg622Gln
  • NP_001308943.1:p.Arg824Gln
  • NP_001308944.1:p.Arg710Gln
  • LRG_161t1:c.2438G>A
  • LRG_161:g.36512G>A
  • NC_000007.13:g.6017226C>T
  • NM_000535.5:c.2438G>A
  • NR_136154.1:n.2482G>A
Protein change:
R502Q
Links:
dbSNP: rs587782665
NCBI 1000 Genomes Browser:
rs587782665
Molecular consequence:
  • NM_000535.7:c.2438G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.2033G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.2033G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.2033G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.2282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.1:c.2120G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.2120G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.2066G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1877G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.1505G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.1505G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1865G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.2471G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.2129G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2482G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000566118GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Feb 6, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000566118.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is denoted PMS2 c.2438G>A at the cDNA level, p.Arg813Gln (R813Q) at the protein level, and results in the change of an Arginine to a Glutamine (CGG>CAG). This variant has not, to our knowledge, been published in the literature as either a pathogenic germline variant or a benign polymorphism. However, it has been reported as a somatic variant in a colorectal cancer specimen (Kim 2015). PMS2 Arg813Gln was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Arginine and Glutamine differ in some properties, this is considered a semi-conservative amino acid substitution. PMS2 Arg813Gln occurs at a position that is conserved across species and is within the endonuclease domain (Fukui 2011). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available information, it is unclear whether PMS2 Arg813Gln is pathogenic or benign. We consider it to be a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 2, 2019