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NM_000535.7(PMS2):c.1129CTG[1] (p.Leu378del) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 23, 2022
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:
RCV001345418.7

Allele description [Variation Report for NM_000535.7(PMS2):c.1129CTG[1] (p.Leu378del)]

NM_000535.7(PMS2):c.1129CTG[1] (p.Leu378del)

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.1129CTG[1] (p.Leu378del)
HGVS:
  • NC_000007.14:g.5989810CAG[1]
  • NG_008466.1:g.24292CTG[1]
  • NM_000535.7:c.1129CTG[1]MANE SELECT
  • NM_001322003.2:c.724CTG[1]
  • NM_001322004.2:c.724CTG[1]
  • NM_001322005.2:c.724CTG[1]
  • NM_001322006.2:c.988+2161_988+2163del
  • NM_001322007.2:c.811CTG[1]
  • NM_001322008.2:c.811CTG[1]
  • NM_001322009.2:c.724CTG[1]
  • NM_001322010.2:c.583+2161_583+2163del
  • NM_001322011.2:c.196CTG[1]
  • NM_001322012.2:c.196CTG[1]
  • NM_001322013.2:c.556CTG[1]
  • NM_001322014.2:c.1129CTG[1]
  • NM_001322015.2:c.820CTG[1]
  • NP_000526.2:p.Leu378del
  • NP_001308932.1:p.Leu243del
  • NP_001308933.1:p.Leu243del
  • NP_001308934.1:p.Leu243del
  • NP_001308936.1:p.Leu272del
  • NP_001308937.1:p.Leu272del
  • NP_001308938.1:p.Leu243del
  • NP_001308940.1:p.Leu67del
  • NP_001308941.1:p.Leu67del
  • NP_001308942.1:p.Leu187del
  • NP_001308943.1:p.Leu378del
  • NP_001308944.1:p.Leu275del
  • LRG_161t1:c.1132_1134del
  • LRG_161:g.24292CTG[1]
  • NC_000007.13:g.6029441CAG[1]
  • NC_000007.13:g.6029441_6029443del
  • NM_000535.5:c.1132_1134delCTG
  • NR_136154.1:n.1216CTG[1]
Protein change:
L187del
Links:
dbSNP: rs1783510412
NCBI 1000 Genomes Browser:
rs1783510412
Molecular consequence:
  • NM_000535.7:c.1129CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322003.2:c.724CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322004.2:c.724CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322005.2:c.724CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322007.2:c.811CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322008.2:c.811CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322009.2:c.724CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322011.2:c.196CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322012.2:c.196CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322013.2:c.556CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322014.2:c.1129CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322015.2:c.820CTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322006.2:c.988+2161_988+2163del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.583+2161_583+2163del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_136154.1:n.1216CTG[1] - 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
SCV001539531Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 23, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001539531.4

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with PMS2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.1132_1134del, results in the deletion of 1 amino acid(s) of the PMS2 protein (p.Leu378del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Sep 29, 2024