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NM_000535.7(PMS2):c.65C>A (p.Ser22Ter) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 26, 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:
RCV001383035.6

Allele description

NM_000535.7(PMS2):c.65C>A (p.Ser22Ter)

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.65C>A (p.Ser22Ter)
HGVS:
  • NC_000007.14:g.6005990G>T
  • NG_008466.1:g.8117C>A
  • NG_050738.1:g.1740G>T
  • NM_000535.7:c.65C>AMANE SELECT
  • NM_001322003.2:c.-341C>A
  • NM_001322004.2:c.-242-1932C>A
  • NM_001322005.2:c.-341C>A
  • NM_001322006.2:c.65C>A
  • NM_001322007.2:c.-151C>A
  • NM_001322008.2:c.-52-1932C>A
  • NM_001322009.2:c.-341C>A
  • NM_001322010.2:c.-242-1932C>A
  • NM_001322011.2:c.-820C>A
  • NM_001322012.2:c.-820C>A
  • NM_001322013.2:c.-341C>A
  • NM_001322014.2:c.65C>A
  • NM_001322015.2:c.-420C>A
  • NP_000526.2:p.Ser22Ter
  • NP_001308935.1:p.Ser22Ter
  • NP_001308943.1:p.Ser22Ter
  • LRG_161t1:c.65C>A
  • LRG_161:g.8117C>A
  • NC_000007.13:g.6045621G>T
  • NM_000535.5:c.65C>A
  • NR_136154.1:n.152C>A
Protein change:
S22*
Links:
dbSNP: rs767028531
NCBI 1000 Genomes Browser:
rs767028531
Molecular consequence:
  • NM_001322003.2:c.-341C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-341C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.-151C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-341C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-820C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-820C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-341C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-420C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-242-1932C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.-52-1932C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.-242-1932C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NR_136154.1:n.152C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.65C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322006.2:c.65C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322014.2:c.65C>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001582044Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 26, 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

A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

Li J, Dai H, Feng Y, Tang J, Chen S, Tian X, Gorman E, Schmitt ES, Hansen TA, Wang J, Plon SE, Zhang VW, Wong LJ.

J Mol Diagn. 2015 Sep;17(5):545-53. doi: 10.1016/j.jmoldx.2015.04.001.

PubMed [citation]
PMID:
26320870

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, SCV001582044.4

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

Description

This premature translational stop signal has been observed in individual(s) with clinical features of PMS2-related conditions (PMID: 26320870). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 826502). This variant is present in population databases (rs767028531, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Ser22*) in the PMS2 gene. It is expected to result in an absent or disrupted protein product. 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: May 7, 2024