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NM_000535.7(PMS2):c.164-1G>A AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 31, 2023
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:
RCV001378577.4

Allele description [Variation Report for NM_000535.7(PMS2):c.164-1G>A]

NM_000535.7(PMS2):c.164-1G>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.164-1G>A
HGVS:
  • NC_000007.14:g.6004059C>T
  • NG_008466.1:g.10048G>A
  • NM_000535.7:c.164-1G>AMANE SELECT
  • NM_001322003.2:c.-242-1G>A
  • NM_001322004.2:c.-242-1G>A
  • NM_001322005.2:c.-242-1G>A
  • NM_001322006.2:c.164-1G>A
  • NM_001322007.2:c.-52-1G>A
  • NM_001322008.2:c.-52-1G>A
  • NM_001322009.2:c.-242-1G>A
  • NM_001322010.2:c.-242-1G>A
  • NM_001322011.2:c.-721-1G>A
  • NM_001322012.2:c.-721-1G>A
  • NM_001322013.2:c.-242-1G>A
  • NM_001322014.2:c.164-1G>A
  • NM_001322015.2:c.-321-1G>A
  • NM_001406866.1:c.350-1G>A
  • NM_001406868.1:c.164-1G>A
  • NM_001406869.1:c.164-1G>A
  • NM_001406870.1:c.164-1G>A
  • NM_001406871.1:c.164-1G>A
  • NM_001406872.1:c.164-1G>A
  • NM_001406873.1:c.164-1G>A
  • NM_001406874.1:c.164-1G>A
  • NM_001406875.1:c.-321-1G>A
  • NM_001406876.1:c.-52-1G>A
  • NM_001406877.1:c.-321-1G>A
  • NM_001406878.1:c.-321-1G>A
  • NM_001406879.1:c.-321-1G>A
  • NM_001406880.1:c.-268-1G>A
  • NM_001406881.1:c.-218-1G>A
  • NM_001406882.1:c.-321-1G>A
  • NM_001406883.1:c.-52-1G>A
  • NM_001406884.1:c.164-1G>A
  • NM_001406885.1:c.164-1G>A
  • NM_001406886.1:c.164-1G>A
  • NM_001406887.1:c.-242-1G>A
  • NM_001406888.1:c.-189-1G>A
  • NM_001406889.1:c.-189-1G>A
  • NM_001406890.1:c.-232-1G>A
  • NM_001406891.1:c.-242-1G>A
  • NM_001406892.1:c.-189-1G>A
  • NM_001406893.1:c.-242-1G>A
  • NM_001406894.1:c.-189-1G>A
  • NM_001406895.1:c.-189-1G>A
  • NM_001406896.1:c.-52-1423G>A
  • NM_001406897.1:c.-242-1G>A
  • NM_001406898.1:c.-242-1G>A
  • NM_001406899.1:c.-189-1G>A
  • NM_001406900.1:c.-218-1G>A
  • NM_001406901.1:c.-52-1G>A
  • NM_001406902.1:c.-52-1G>A
  • NM_001406903.1:c.-52-1G>A
  • NM_001406904.1:c.-189-1G>A
  • NM_001406905.1:c.-242-1G>A
  • NM_001406906.1:c.-242-1G>A
  • NM_001406907.1:c.-189-1G>A
  • NM_001406908.1:c.-242-1G>A
  • NM_001406909.1:c.-189-1G>A
  • NM_001406910.1:c.-242-1G>A
  • NM_001406911.1:c.-242-1G>A
  • NM_001406912.1:c.164-1G>A
  • LRG_161t1:c.164-1G>A
  • LRG_161:g.10048G>A
  • NC_000007.13:g.6043690C>T
  • NM_000535.5:c.164-1G>A
  • NM_000535.6:c.164-1G>A
Links:
dbSNP: rs763308607
NCBI 1000 Genomes Browser:
rs763308607
Molecular consequence:
  • NM_001406896.1:c.-52-1423G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.-721-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.-721-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406866.1:c.350-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406868.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406869.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406870.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406871.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406872.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406873.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406874.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406875.1:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406876.1:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406877.1:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406878.1:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406879.1:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406880.1:c.-268-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406881.1:c.-218-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406882.1:c.-321-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406883.1:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406884.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406885.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406886.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406887.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406888.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406889.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406890.1:c.-232-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406891.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406892.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406893.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406894.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406895.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406897.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406898.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406899.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406900.1:c.-218-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406901.1:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406902.1:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406903.1:c.-52-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406904.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406905.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406906.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406907.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406908.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406909.1:c.-189-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406910.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406911.1:c.-242-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406912.1:c.164-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001576178Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Aug 31, 2023) 		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 Invitae, SCV001576178.4

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

Description

This variant is present in population databases (rs763308607, gnomAD 0.0009%). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 484252). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. This sequence change affects an acceptor splice site in intron 2 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).

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

Last Updated: Feb 20, 2024