U.S. flag

An official website of the United States government

NM_000535.7(PMS2):c.2007-2_2007-1delinsCA AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 16, 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:
RCV002560268.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2007-2_2007-1delinsCA]

NM_000535.7(PMS2):c.2007-2_2007-1delinsCA

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.2007-2_2007-1delinsCA
HGVS:
  • NC_000007.14:g.5982992_5982993delinsTG
  • NG_008466.1:g.31114_31115delinsCA
  • NM_000535.7:c.2007-2_2007-1delinsCAMANE SELECT
  • NM_001322003.2:c.1602-2_1602-1delinsCA
  • NM_001322004.2:c.1602-2_1602-1delinsCA
  • NM_001322005.2:c.1602-2_1602-1delinsCA
  • NM_001322006.2:c.1851-2_1851-1delinsCA
  • NM_001322007.2:c.1689-2_1689-1delinsCA
  • NM_001322008.2:c.1689-2_1689-1delinsCA
  • NM_001322009.2:c.1602-2_1602-1delinsCA
  • NM_001322010.2:c.1446-2_1446-1delinsCA
  • NM_001322011.2:c.1074-2_1074-1delinsCA
  • NM_001322012.2:c.1074-2_1074-1delinsCA
  • NM_001322013.2:c.1434-2_1434-1delinsCA
  • NM_001322014.2:c.2007-2_2007-1delinsCA
  • NM_001322015.2:c.1698-2_1698-1delinsCA
  • LRG_161:g.31114_31115delinsCA
  • NC_000007.13:g.6022623_6022624delinsTG
  • NM_000535.6:c.2007-2_2007-1delinsCA
Links:
dbSNP: rs1782473185
NCBI 1000 Genomes Browser:
rs1782473185
Molecular consequence:
  • NM_000535.7:c.2007-2_2007-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.1851-2_1851-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.1689-2_1689-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.1689-2_1689-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.1446-2_1446-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.1074-2_1074-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.1074-2_1074-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.1434-2_1434-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.2007-2_2007-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.1698-2_1698-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MeSH: D003123; MedGen: C0009405

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003250654Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 16, 2021) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations: case series, review and follow-up guidelines.

Herkert JC, Niessen RC, Olderode-Berends MJ, Veenstra-Knol HE, Vos YJ, van der Klift HM, Scheenstra R, Tops CM, Karrenbeld A, Peters FT, Hofstra RM, Kleibeuker JH, Sijmons RH.

Eur J Cancer. 2011 May;47(7):965-82. doi: 10.1016/j.ejca.2011.01.013. Epub 2011 Mar 4. Review.

PubMed [citation]
PMID:
21376568
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003250654.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects a splice site in intron 11 of the PMS2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PMS2 are known to be pathogenic (PMID: 21376568, 24362816). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024