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NM_001005242.3(PKP2):c.1379-1972G>A AND not specified

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 15, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000603241.6

Allele description [Variation Report for NM_001005242.3(PKP2):c.1379-1972G>A]

NM_001005242.3(PKP2):c.1379-1972G>A

Gene:
PKP2:plakophilin 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p11.21
Genomic location:
Preferred name:
NM_001005242.3(PKP2):c.1379-1972G>A
HGVS:
  • NC_000012.12:g.32843177C>T
  • NG_009000.1:g.58670G>A
  • NM_001005242.3:c.1379-1972G>AMANE SELECT
  • NM_004572.4:c.1510+5G>A
  • LRG_398t1:c.1510+5G>A
  • LRG_398:g.58670G>A
  • NC_000012.11:g.32996111C>T
  • NM_004572.3:c.1510+5G>A
Links:
dbSNP: rs779392697
NCBI 1000 Genomes Browser:
rs779392697
Molecular consequence:
  • NM_001005242.3:c.1379-1972G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004572.4:c.1510+5G>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000710873Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Uncertain significance
(Dec 29, 2017)
germlineclinical testing

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

SCV001370650Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Nov 15, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Electronic health record phenotype in subjects with genetic variants associated with arrhythmogenic right ventricular cardiomyopathy: a study of 30,716 subjects with exome sequencing.

Haggerty CM, James CA, Calkins H, Tichnell C, Leader JB, Hartzel DN, Nevius CD, Pendergrass SA, Person TN, Schwartz M, Ritchie MD, Carey DJ, Ledbetter DH, Williams MS, Dewey FE, Lopez A, Penn J, Overton JD, Reid JG, Lebo M, Mason-Suares H, Austin-Tse C, et al.

Genet Med. 2017 Nov;19(11):1245-1252. doi: 10.1038/gim.2017.40. Epub 2017 May 4.

PubMed [citation]
PMID:
28471438
PMCID:
PMC5671380
See all PubMed Citations (3)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000710873.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.1510+5G>A variant in PKP2 has not been reported in the literature, but was identified in 3/27754 of Latino and 3/91752 of European chromosomes by the Geno me Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs77939 2697). This variant has also been reported in ClinVar (Variation ID:239953). Thi s variant is located in the 5' splice region. Computational tools suggest some i mpact to splicing. However, this information is not predictive enough to determi ne pathogenicity. In summary, the clinical significance of the c.1510+5G>A varia nt is uncertain. ACMG/AMP Criteria applied: PP3.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001370650.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: PKP2 c.1510+5G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes the canonical 5' splicing donor site. Two predict the variant weakens the canonical 5' splice donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.1e-05 in 181044 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1510+5G>A has been reported in the literature in a study of individuals enrolled in MyCode Community Health Initiative of Geisinger Health System (GHS), an IRB-approved research biorepository and precision medicine project (Haggerty_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Cardiomyopathy. At-least two co-occurrences with other pathogenic variant(s) have been reported at our laboratory (HCM-MYBPC3 c.1505G>A, p.Arg502Gln; ARVD-PKP2 c.2509delA, p.Ser837fs), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

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

Last Updated: Sep 29, 2024