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NM_000535.7(PMS2):c.1425_1428del (p.Ser476fs) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 17, 2018
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:
RCV000693888.6

Allele description [Variation Report for NM_000535.7(PMS2):c.1425_1428del (p.Ser476fs)]

NM_000535.7(PMS2):c.1425_1428del (p.Ser476fs)

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.1425_1428del (p.Ser476fs)
HGVS:
  • NC_000007.13:g.6026968_6026971del
  • NC_000007.14:g.5987340_5987343del
  • NG_008466.1:g.26767_26770del
  • NM_000535.7:c.1425_1428delMANE SELECT
  • NM_001322003.2:c.1020_1023del
  • NM_001322004.2:c.1020_1023del
  • NM_001322005.2:c.1020_1023del
  • NM_001322006.2:c.1269_1272del
  • NM_001322007.2:c.1107_1110del
  • NM_001322008.2:c.1107_1110del
  • NM_001322009.2:c.1020_1023del
  • NM_001322010.2:c.864_867del
  • NM_001322011.2:c.492_495del
  • NM_001322012.2:c.492_495del
  • NM_001322013.2:c.852_855del
  • NM_001322014.2:c.1425_1428del
  • NM_001322015.2:c.1116_1119del
  • NP_000526.2:p.Ser476fs
  • NP_001308932.1:p.Ser341fs
  • NP_001308933.1:p.Ser341fs
  • NP_001308934.1:p.Ser341fs
  • NP_001308935.1:p.Ser424fs
  • NP_001308936.1:p.Ser370fs
  • NP_001308937.1:p.Ser370fs
  • NP_001308938.1:p.Ser341fs
  • NP_001308939.1:p.Ser289fs
  • NP_001308940.1:p.Ser165fs
  • NP_001308941.1:p.Ser165fs
  • NP_001308942.1:p.Ser285fs
  • NP_001308943.1:p.Ser476fs
  • NP_001308944.1:p.Ser373fs
  • LRG_161t1:c.1425_1428del
  • LRG_161:g.26767_26770del
  • NC_000007.13:g.6026968_6026971del
  • NC_000007.13:g.6026968_6026971delACTC
  • NC_000007.13:g.6026971_6026974del
  • NM_000535.5:c.1425_1428delGAGT
  • NR_136154.1:n.1512_1515del
Protein change:
S165fs
Links:
dbSNP: rs1554297764
NCBI 1000 Genomes Browser:
rs1554297764
Molecular consequence:
  • NM_000535.7:c.1425_1428del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322003.2:c.1020_1023del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322004.2:c.1020_1023del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322005.2:c.1020_1023del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322006.2:c.1269_1272del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322007.2:c.1107_1110del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322008.2:c.1107_1110del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322009.2:c.1020_1023del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322010.2:c.864_867del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322011.2:c.492_495del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322012.2:c.492_495del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322013.2:c.852_855del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322014.2:c.1425_1428del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322015.2:c.1116_1119del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_136154.1:n.1512_1515del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000822310Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 17, 2018) 		germlineclinical testing

PubMed (3)
[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

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

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.

Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, et al.

Nat Genet. 2014 Feb;46(2):107-115. doi: 10.1038/ng.2854. Epub 2013 Dec 22.

PubMed [citation]
PMID:
24362816
PMCID:
PMC4294709
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000822310.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Ser476Profs*118) in the PMS2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PMS2-related disease. ClinVar contains an entry for this variant (Variation ID: 484330). Loss-of-function variants in PMS2 are known to be pathogenic (PMID: 21376568, 24362816). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024