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NM_000535.7(PMS2):c.1144+1G>T AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 21, 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:
RCV001053111.6

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+1G>T]

NM_000535.7(PMS2):c.1144+1G>T

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.1144+1G>T
HGVS:
  • NC_000007.14:g.5989799C>A
  • NG_008466.1:g.24308G>T
  • NM_000535.7:c.1144+1G>TMANE SELECT
  • NM_001322003.2:c.739+1G>T
  • NM_001322004.2:c.739+1G>T
  • NM_001322005.2:c.739+1G>T
  • NM_001322006.2:c.988+2174G>T
  • NM_001322007.2:c.826+1G>T
  • NM_001322008.2:c.826+1G>T
  • NM_001322009.2:c.739+1G>T
  • NM_001322010.2:c.583+2174G>T
  • NM_001322011.2:c.211+1G>T
  • NM_001322012.2:c.211+1G>T
  • NM_001322013.2:c.571+1G>T
  • NM_001322014.2:c.1144+1G>T
  • NM_001322015.2:c.835+1G>T
  • NM_001406866.1:c.1330+1G>T
  • NM_001406868.1:c.1168+1G>T
  • NM_001406869.1:c.1036+1G>T
  • NM_001406870.1:c.988+2174G>T
  • NM_001406871.1:c.1144+1G>T
  • NM_001406872.1:c.1144+1G>T
  • NM_001406873.1:c.946+1G>T
  • NM_001406874.1:c.976+1G>T
  • NM_001406875.1:c.835+1G>T
  • NM_001406876.1:c.826+1G>T
  • NM_001406877.1:c.835+1G>T
  • NM_001406878.1:c.835+1G>T
  • NM_001406879.1:c.835+1G>T
  • NM_001406880.1:c.835+1G>T
  • NM_001406881.1:c.835+1G>T
  • NM_001406882.1:c.835+1G>T
  • NM_001406883.1:c.826+1G>T
  • NM_001406884.1:c.820+2174G>T
  • NM_001406885.1:c.808+1G>T
  • NM_001406886.1:c.778+1G>T
  • NM_001406887.1:c.739+1G>T
  • NM_001406888.1:c.739+1G>T
  • NM_001406889.1:c.739+1G>T
  • NM_001406890.1:c.739+1G>T
  • NM_001406891.1:c.739+1G>T
  • NM_001406892.1:c.739+1G>T
  • NM_001406893.1:c.739+1G>T
  • NM_001406894.1:c.739+1G>T
  • NM_001406895.1:c.739+1G>T
  • NM_001406896.1:c.739+1G>T
  • NM_001406897.1:c.739+1G>T
  • NM_001406898.1:c.739+1G>T
  • NM_001406899.1:c.739+1G>T
  • NM_001406900.1:c.679+2174G>T
  • NM_001406901.1:c.670+2174G>T
  • NM_001406902.1:c.670+2174G>T
  • NM_001406903.1:c.826+1G>T
  • NM_001406904.1:c.631+1G>T
  • NM_001406905.1:c.631+1G>T
  • NM_001406906.1:c.583+2174G>T
  • NM_001406907.1:c.583+2174G>T
  • NM_001406908.1:c.739+1G>T
  • NM_001406909.1:c.571+1G>T
  • NM_001406910.1:c.739+1G>T
  • NM_001406911.1:c.373+1G>T
  • NM_001406912.1:c.804-6808G>T
  • LRG_161t1:c.1144+1G>T
  • LRG_161:g.24308G>T
  • NC_000007.13:g.6029430C>A
  • NM_000535.5:c.1144+1G>T
Links:
dbSNP: rs373885654
NCBI 1000 Genomes Browser:
rs373885654
Molecular consequence:
  • NM_001322006.2:c.988+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.583+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406870.1:c.988+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406884.1:c.820+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406900.1:c.679+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406901.1:c.670+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406902.1:c.670+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406906.1:c.583+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406907.1:c.583+2174G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406912.1:c.804-6808G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.1144+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.826+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.826+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.211+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.211+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.571+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.1144+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.1330+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.1168+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.1036+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.1144+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.1144+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.946+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.976+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.826+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.835+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.826+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406885.1:c.808+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.778+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.826+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.631+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.631+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.571+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.739+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.373+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV001217355Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 21, 2023) 		germlineclinical testing

PubMed (6)
[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

Heterozygous mutations in PMS2 cause hereditary nonpolyposis colorectal carcinoma (Lynch syndrome).

Hendriks YM, Jagmohan-Changur S, van der Klift HM, Morreau H, van Puijenbroek M, Tops C, van Os T, Wagner A, Ausems MG, Gomez E, Breuning MH, Bröcker-Vriends AH, Vasen HF, Wijnen JT.

Gastroenterology. 2006 Feb;130(2):312-22.

PubMed [citation]
PMID:
16472587

The clinical phenotype of Lynch syndrome due to germ-line PMS2 mutations.

Senter L, Clendenning M, Sotamaa K, Hampel H, Green J, Potter JD, Lindblom A, Lagerstedt K, Thibodeau SN, Lindor NM, Young J, Winship I, Dowty JG, White DM, Hopper JL, Baglietto L, Jenkins MA, de la Chapelle A.

Gastroenterology. 2008 Aug;135(2):419-28. doi: 10.1053/j.gastro.2008.04.026. Epub 2008 May 2.

PubMed [citation]
PMID:
18602922
PMCID:
PMC2759321
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001217355.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects a donor splice site in intron 10 of the PMS2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 849200). Studies have shown that disruption of this splice site results in skipping of exon 10, but is expected to preserve the integrity of the reading-frame (Invitae). Other variant(s) that result in the loss of exon 10 have been determined to be pathogenic (PMID: 16472587, 18602922, 22577899, 23837913, 26318770). This suggests that this variant may also be clinically significant and likely to be disease-causing. 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