NM_000535.7(PMS2):c.1798A>G (p.Met600Val) AND Malignant tumor of breast

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001358228.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1798A>G (p.Met600Val)]

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

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.1798A>G (p.Met600Val)
HGVS:
  • NC_000007.14:g.5986967T>C
  • NG_008466.1:g.27140A>G
  • NM_000535.7:c.1798A>GMANE SELECT
  • NM_001322003.2:c.1393A>G
  • NM_001322004.2:c.1393A>G
  • NM_001322005.2:c.1393A>G
  • NM_001322006.2:c.1642A>G
  • NM_001322007.2:c.1480A>G
  • NM_001322008.2:c.1480A>G
  • NM_001322009.2:c.1393A>G
  • NM_001322010.2:c.1237A>G
  • NM_001322011.2:c.865A>G
  • NM_001322012.2:c.865A>G
  • NM_001322013.2:c.1225A>G
  • NM_001322014.2:c.1798A>G
  • NM_001322015.2:c.1489A>G
  • NP_000526.2:p.Met600Val
  • NP_001308932.1:p.Met465Val
  • NP_001308933.1:p.Met465Val
  • NP_001308934.1:p.Met465Val
  • NP_001308935.1:p.Met548Val
  • NP_001308936.1:p.Met494Val
  • NP_001308937.1:p.Met494Val
  • NP_001308938.1:p.Met465Val
  • NP_001308939.1:p.Met413Val
  • NP_001308940.1:p.Met289Val
  • NP_001308941.1:p.Met289Val
  • NP_001308942.1:p.Met409Val
  • NP_001308943.1:p.Met600Val
  • NP_001308944.1:p.Met497Val
  • LRG_161t1:c.1798A>G
  • LRG_161:g.27140A>G
  • NC_000007.13:g.6026598T>C
  • NM_000535.5:c.1798A>G
  • NM_000535.6:c.1798A>G
  • NR_136154.1:n.1885A>G
Protein change:
M289V
Links:
dbSNP: rs1304634005
NCBI 1000 Genomes Browser:
rs1304634005
Molecular consequence:
  • NM_000535.7:c.1798A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1393A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1393A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1393A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1642A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1480A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1480A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1393A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1237A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.865A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.865A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1225A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.1798A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1489A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.1885A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001553902Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot 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), SCV001553902.1

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

Description

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 identified in dbSNP (rs1304634005) as “NA” and ClinVar (classified as uncertain significance by Color and Counsyl). The variant was identified in control databases in 2 of 251,454 chromosomes at a frequency of 0.000008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 1 of 10,078 chromosomes (freq: 0.0001) and East Asian in 1 of 18,394 chromosomes (freq: 0.00005), while it was not observed in the African, Latino, Finnish, European, Other or South Asian populations. The p.Met600 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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 providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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