NM_001005242.3(PKP2):c.302G>A (p.Arg101His) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 18, 2021
Review status:: criteria provided, conflicting classifications

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:: RCV000172093.15

Allele description [Variation Report for NM_001005242.3(PKP2):c.302G>A (p.Arg101His)]

NM_001005242.3(PKP2):c.302G>A (p.Arg101His)

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.302G>A (p.Arg101His)

HGVS:

NC_000012.12:g.32878954C>T
NG_009000.1:g.22893G>A
NM_001005242.3:c.302G>AMANE SELECT
NM_004572.4:c.302G>A
NP_001005242.2:p.Arg101His
NP_004563.2:p.Arg101His
NP_004563.2:p.Arg101His
LRG_398t1:c.302G>A
LRG_398:g.22893G>A
LRG_398p1:p.Arg101His
NC_000012.11:g.33031888C>T
NM_004572.3:c.302G>A
c.302G>A

Protein change:

R101H

Links:

dbSNP: rs149542398

NCBI 1000 Genomes Browser:

rs149542398

Molecular consequence:

NM_001005242.3:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004572.4:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens cDNA clone IMAGE:5267863
Homo sapiens cDNA clone IMAGE:5267863
gi|66267555|gb|BC094790.1|

Nucleotide
Homo sapiens cDNA FLJ43635 fis, clone SPLEN2037580
Homo sapiens cDNA FLJ43635 fis, clone SPLEN2037580
gi|34531777|dbj|AK125623.1|

Nucleotide
telomere-associated protein RIF1 isoform X12 [Homo sapiens]
telomere-associated protein RIF1 isoform X12 [Homo sapiens]
gi|2462574748|ref|XP_054198735.1|

Protein
telomere-associated protein RIF1 isoform X5 [Homo sapiens]
telomere-associated protein RIF1 isoform X5 [Homo sapiens]
gi|2462574727|ref|XP_054198725.1|

Protein
PREDICTED: Homo sapiens replication timing regulatory factor 1 (RIF1), transcrip...
PREDICTED: Homo sapiens replication timing regulatory factor 1 (RIF1), transcript variant X35, misc_RNA
gi|2462574749|ref|XR_008486440.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000051041	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	criteria provided, single submitter (Ng et al. (Circ Cardiovasc Genet. 2013))	Uncertain significance (Jun 24, 2013)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV001785746	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Feb 18, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000051041

Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq

criteria provided, single submitter

(Ng et al. (Circ Cardiovasc Genet. 2013))

Uncertain significance
(Jun 24, 2013)

unknown

research

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

SCV001785746

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Feb 18, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	1	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]

PMID:: 23861362
PMCID:: PMC3887521

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000051041.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV001785746.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Reported in association with various clinical phenotypes including DCM, ARVC, HCM, and Brugada syndrome (Fressart et al., 2010; Lopes et al., 2013; Pugh et al., 2014; Allegue et al., 2015); Observed in one individual from a cohort not selected for cardiomyopathy, arrhythmia, or family history of sudden cardiac death that underwent exome sequencing (Ng et al., 2013); In silico analysis supports that this missense variant does not alter protein structure/function; Reported in ClinVar but additional evidence is not available (ClinVar Variant ID# 45076; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 30821013, 27085656, 25351510, 23396983, 23861362, 24503780, 20400443, 26230511)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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