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NM_000535.7(PMS2):c.537+1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 26, 2021
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:
RCV002345713.2

Allele description [Variation Report for NM_000535.7(PMS2):c.537+1G>A]

NM_000535.7(PMS2):c.537+1G>A

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.537+1G>A
HGVS:
  • NC_000007.14:g.6002452C>T
  • NG_008466.1:g.11655G>A
  • NM_000535.7:c.537+1G>AMANE SELECT
  • NM_001322003.2:c.132+1G>A
  • NM_001322004.2:c.132+1G>A
  • NM_001322005.2:c.132+1G>A
  • NM_001322006.2:c.537+1G>A
  • NM_001322007.2:c.219+1G>A
  • NM_001322008.2:c.219+1G>A
  • NM_001322009.2:c.132+1G>A
  • NM_001322010.2:c.132+1G>A
  • NM_001322011.2:c.-348+1G>A
  • NM_001322012.2:c.-348+1G>A
  • NM_001322013.2:c.132+1G>A
  • NM_001322014.2:c.537+1G>A
  • NM_001322015.2:c.228+1G>A
  • NM_001406866.1:c.723+1G>A
  • NM_001406868.1:c.561+1G>A
  • NM_001406869.1:c.537+1G>A
  • NM_001406870.1:c.537+1G>A
  • NM_001406871.1:c.537+1G>A
  • NM_001406872.1:c.537+1G>A
  • NM_001406873.1:c.537+1G>A
  • NM_001406874.1:c.537+1G>A
  • NM_001406875.1:c.228+1G>A
  • NM_001406876.1:c.219+1G>A
  • NM_001406877.1:c.228+1G>A
  • NM_001406878.1:c.228+1G>A
  • NM_001406879.1:c.228+1G>A
  • NM_001406880.1:c.228+1G>A
  • NM_001406881.1:c.228+1G>A
  • NM_001406882.1:c.228+1G>A
  • NM_001406883.1:c.219+1G>A
  • NM_001406884.1:c.537+1G>A
  • NM_001406885.1:c.250+1520G>A
  • NM_001406886.1:c.537+1G>A
  • NM_001406887.1:c.132+1G>A
  • NM_001406888.1:c.132+1G>A
  • NM_001406889.1:c.132+1G>A
  • NM_001406890.1:c.132+1G>A
  • NM_001406891.1:c.132+1G>A
  • NM_001406892.1:c.132+1G>A
  • NM_001406893.1:c.132+1G>A
  • NM_001406894.1:c.132+1G>A
  • NM_001406895.1:c.132+1G>A
  • NM_001406896.1:c.132+1G>A
  • NM_001406897.1:c.132+1G>A
  • NM_001406898.1:c.132+1G>A
  • NM_001406899.1:c.132+1G>A
  • NM_001406900.1:c.228+1G>A
  • NM_001406901.1:c.219+1G>A
  • NM_001406902.1:c.219+1G>A
  • NM_001406903.1:c.219+1G>A
  • NM_001406904.1:c.132+1G>A
  • NM_001406905.1:c.132+1G>A
  • NM_001406906.1:c.132+1G>A
  • NM_001406907.1:c.132+1G>A
  • NM_001406908.1:c.132+1G>A
  • NM_001406909.1:c.132+1G>A
  • NM_001406910.1:c.132+1G>A
  • NM_001406911.1:c.132+1G>A
  • NM_001406912.1:c.537+1G>A
  • LRG_161t1:c.537+1G>A
  • LRG_161:g.11655G>A
  • NC_000007.13:g.6042083C>T
  • NM_000535.5:c.537+1G>A
  • NM_000535.6:c.537+1G>A
Links:
dbSNP: rs863224450
NCBI 1000 Genomes Browser:
rs863224450
Molecular consequence:
  • NM_001406885.1:c.250+1520G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322006.2:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322010.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.-348+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.-348+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.723+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.561+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406870.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406884.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406900.1:c.228+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406901.1:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406902.1:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.219+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406906.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406907.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.132+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406912.1:c.537+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002645128Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 26, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Characterisation of heterozygous PMS2 variants in French patients with Lynch syndrome.

Wang Q, Leclerc J, Bougeard G, Olschwang S, Vasseur S, Cassinari K, Boidin D, Lefol C, Naïbo P, Frébourg T, Buisine MP, Baert-Desurmont S; French Consortium of Oncogenetic laboratories for colorectal cancers, Unicancer Cancer Genetic Group (GGC)..

J Med Genet. 2020 Jul;57(7):487-499. doi: 10.1136/jmedgenet-2019-106256. Epub 2020 Jan 28.

PubMed [citation]
PMID:
31992580

Details of each submission

From Ambry Genetics, SCV002645128.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.537+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 5 of the PMS2 gene. This nucleotide position is highly conserved in available vertebrate species. This variant is reported in an individual diagnosed with MSI-H colorectal cancer at age 55 (Wang Q et al. J Med Genet, 2020 07;57:487-499). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

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

Last Updated: Oct 13, 2024