NM_000535.7(PMS2):c.652G>A (p.Gly218Ser) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Jan 27, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001290677.1

Allele description [Variation Report for NM_000535.7(PMS2):c.652G>A (p.Gly218Ser)]

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

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.652G>A (p.Gly218Ser)
HGVS:
  • NC_000007.14:g.5999161C>T
  • NG_008466.1:g.14946G>A
  • NM_000535.7:c.652G>AMANE SELECT
  • NM_001322003.2:c.247G>A
  • NM_001322004.2:c.247G>A
  • NM_001322005.2:c.247G>A
  • NM_001322006.2:c.652G>A
  • NM_001322007.2:c.334G>A
  • NM_001322008.2:c.334G>A
  • NM_001322009.2:c.247G>A
  • NM_001322010.2:c.247G>A
  • NM_001322011.2:c.-282G>A
  • NM_001322012.2:c.-282G>A
  • NM_001322013.2:c.133-1738G>A
  • NM_001322014.2:c.652G>A
  • NM_001322015.2:c.343G>A
  • NP_000526.2:p.Gly218Ser
  • NP_001308932.1:p.Gly83Ser
  • NP_001308933.1:p.Gly83Ser
  • NP_001308934.1:p.Gly83Ser
  • NP_001308935.1:p.Gly218Ser
  • NP_001308936.1:p.Gly112Ser
  • NP_001308937.1:p.Gly112Ser
  • NP_001308938.1:p.Gly83Ser
  • NP_001308939.1:p.Gly83Ser
  • NP_001308943.1:p.Gly218Ser
  • NP_001308944.1:p.Gly115Ser
  • LRG_161t1:c.652G>A
  • LRG_161:g.14946G>A
  • NC_000007.13:g.6038792C>T
  • NM_000535.5:c.652G>A
  • NM_000535.6:c.652G>A
  • NR_136154.1:n.739G>A
Protein change:
G112S
Links:
dbSNP: rs878854055
NCBI 1000 Genomes Browser:
rs878854055
Molecular consequence:
  • NM_001322011.2:c.-282G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-282G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.133-1738G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.652G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.652G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.334G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.334G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.652G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.343G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.739G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001478809Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Jan 27, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001478809.1

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

Description

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 effect of the variant on protein function. The variant was absent in 251490 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.652G>A in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as likely benign (1x) or VUS (2x). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Nov 27, 2021

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