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NM_000535.7(PMS2):c.2446-170_*3del AND Endometrial carcinoma

Germline classification:
Pathogenic (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:
RCV001355610.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2446-170_*3del]

NM_000535.7(PMS2):c.2446-170_*3del

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.2446-170_*3del
HGVS:
  • NC_000007.14:g.5973397_5973713del
  • NG_008466.1:g.40395_40711del
  • NM_000535.7:c.2446-170_*3delMANE SELECT
  • NM_001322003.2:c.2041-170_*3del
  • NM_001322004.2:c.2041-170_*3del
  • NM_001322005.2:c.2041-170_*3del
  • NM_001322006.2:c.2290-170_*3del
  • NM_001322007.2:c.2128-170_*3del
  • NM_001322008.2:c.2128-170_*3del
  • NM_001322009.2:c.2074-170_*3del
  • NM_001322010.2:c.1885-170_*3del
  • NM_001322011.2:c.1513-170_*3del
  • NM_001322012.2:c.1513-170_*3del
  • NM_001322013.2:c.1873-170_*3del
  • NM_001322014.2:c.2479-170_*3del
  • NM_001322015.2:c.2137-170_*3del
  • LRG_161:g.40395_40711del
  • NC_000007.13:g.6013028_6013344del
Links:
dbSNP: rs2128656455
NCBI 1000 Genomes Browser:
rs2128656455
Molecular consequence:
  • NM_000535.7:c.2446-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.2041-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.2041-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.2041-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.2290-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.2128-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.2128-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.2074-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.1885-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.1513-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.1513-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.1873-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.2479-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.2137-170_*3del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Endometrial carcinoma
Synonyms:
Endometrial carcinoma, somatic
Identifiers:
MONDO: MONDO:0002447; MedGen: C0476089; OMIM: 608089; Human Phenotype Ontology: HP:0012114

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550542Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

Help

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), SCV001550542.1

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

Description

The PMS2 c.2276-?_2589+?del variant (chr:7 g.6013030_6017388del GRCh37) results in a deletion of exons 14-15, although the precise breakpoints of this deletion were not determined, nor were the effects of this variant on the resulting mRNA or protein product determined. The PMS2 c.2276-?_2589+?del variant was identified in 5(3 homozygous) of 146 proband chromosomes (frequency: 0.05) from individuals or families with constitutional mismatch repair deficiency or Lynch syndrome (Bakry 2014,Bodo 2015, Vaughn 2011). The variant was also identified in ClinVar (classified as pathogenic by Invitae). The variant was not identified in dbSNP database. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). This alteration is predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the PMS2 gene are an established mechanism of disease in PMS2 associated cancers and is the type of variant expected to cause the disorder. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

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

Last Updated: Jun 23, 2024