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NM_000535.7(PMS2):c.632G>A (p.Arg211Gln) AND Malignant tumor of breast

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001356210.3

Allele description [Variation Report for NM_000535.7(PMS2):c.632G>A (p.Arg211Gln)]

NM_000535.7(PMS2):c.632G>A (p.Arg211Gln)

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.632G>A (p.Arg211Gln)
Other names:
p.R211Q:CGA>CAA
HGVS:
  • NC_000007.14:g.5999181C>T
  • NG_008466.1:g.14926G>A
  • NM_000535.7:c.632G>AMANE SELECT
  • NM_001322003.2:c.227G>A
  • NM_001322004.2:c.227G>A
  • NM_001322005.2:c.227G>A
  • NM_001322006.2:c.632G>A
  • NM_001322007.2:c.314G>A
  • NM_001322008.2:c.314G>A
  • NM_001322009.2:c.227G>A
  • NM_001322010.2:c.227G>A
  • NM_001322011.2:c.-302G>A
  • NM_001322012.2:c.-302G>A
  • NM_001322013.2:c.133-1758G>A
  • NM_001322014.2:c.632G>A
  • NM_001322015.2:c.323G>A
  • NP_000526.2:p.Arg211Gln
  • NP_001308932.1:p.Arg76Gln
  • NP_001308933.1:p.Arg76Gln
  • NP_001308934.1:p.Arg76Gln
  • NP_001308935.1:p.Arg211Gln
  • NP_001308936.1:p.Arg105Gln
  • NP_001308937.1:p.Arg105Gln
  • NP_001308938.1:p.Arg76Gln
  • NP_001308939.1:p.Arg76Gln
  • NP_001308943.1:p.Arg211Gln
  • NP_001308944.1:p.Arg108Gln
  • LRG_161t1:c.632G>A
  • LRG_161:g.14926G>A
  • NC_000007.13:g.6038812C>T
  • NM_000535.5:c.632G>A
  • NM_000535.6:c.632G>A
  • NR_136154.1:n.719G>A
  • p.R211Q
Protein change:
R105Q
Links:
dbSNP: rs587781934
NCBI 1000 Genomes Browser:
rs587781934
Molecular consequence:
  • NM_001322011.2:c.-302G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-302G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.133-1758G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.314G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.314G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.632G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.323G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.719G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001551317Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001551317.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The PMS2 p.Arg211Gln variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, Zhejiang University Database, or the Mismatch Repair Genes Variant Database. The variant was identified in dbSNP (ID: rs587781934) as “With Uncertain significance allele”, in ClinVar (classified as uncertain significance by Ambry Genetics, GeneDx, Invitae, Counsyl, Color Genomics), Clinvitae, and the Insight Hereditary Tumors Database (effect unknown). The variant was identified in control databases in 12 of 277218 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). The variant was identified in the following populations: African in 1 of 24024 chromosomes (freq: 0.00004), European in 11 of 126724 chromosomes (freq: 0.0001), while the variant was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Arg211 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024