chr12-32796108-C-T

Position:

• chr12-32796108-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

The ENST00000340811.9(PKP2):​c.2357+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.0000223 in 1,613,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000020 (0 hom.)
• Consequence: PKP2 ENST00000340811.9 splice_donor
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:23
• Conservation: PhyloP100: 5.10

Genes affected

PKP2 (HGNC:9024): (plakophilin 2) This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This gene may regulate the signaling activity of beta-catenin and is required to maintain transcription of genes that control intracellular calcium cycling including ryanodine receptor 2, ankyrin-B, triadin, and calcium channel, voltage-dependent, L type, alpha 1C. Mutations in this gene are associated with different inherited cardiac conditions including Arrythmogenic Cardiomyopathy, Brugada Syndrome, and Idiopathic Ventricular Fibrillation. A processed pseudogene with high similarity to this gene has been mapped to chromosome 12p13. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP5: Variant 12-32796108-C-T is Pathogenic according to our data. Variant chr12-32796108-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 6757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-32796108-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKP2	NM_001005242.3	c.2357+1G>A		splice_donor_variant		ENST00000340811.9	NP_001005242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKP2	ENST00000340811.9	c.2357+1G>A		splice_donor_variant		1	NM_001005242.3	ENSP00000342800	P1

Frequencies

GnomAD3 genomes AF: 0.0000460 AC: 7 AN: 152130 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000966

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000278 AC: 7 AN: 251434 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135898

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000440

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000199 AC: 29 AN: 1460820 Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12 AN XY: 726752

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000216

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.0000460 AC: 7 AN: 152248 Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3 AN XY: 74426

Gnomad4 AFR AF: 0.0000963

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000436 Hom.: 0

Bravo AF: 0.0000340

ExAC AF: 0.0000247 AC: 3

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:23

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Apr 14, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Aug 18, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2024	PKP2: PVS1, PS4:Moderate -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 27, 2014	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. IVS12+1 G>A (c.2489+1 G>A) in the PKP2 gene Mutations in the PKP2 gene have been reported in at least 11% of patients with autosomal dominant arrhythmogenic right ventricular cardiomyopathy (ARVC). This is a variant that we can have high confidence causes ARVC. It has been reported previously in multiple patients with ARVC, from multiple ethnicities, and also in multiple unrelated individuals tested for ARVC at GeneDx, according to their report. It is a splice-site variant that destroys the canonical splice donor site in intron 12. It is expected to cause abnormal gene splicing, which may lead to protein truncation or absence of protein due to mRNA decay. At least 24 patients with this specific variant have been published in the literature. Gerull et al. (2004) identified it in 1 ARVC proband of Western European descent. Dalal et al. (2006) found it in 3 unrelated patients with ARVC from the Johns Hopkins registry– and den Haan et al. (2009) added 1 more North American patient to this group. Age at first symptom for these patients ranged from 22-51 years. [Reports by Dalal et al. (2009) and Tan et al. (2010) appear to refer to these same patients.] van Tintelen et al. (2006) found the variant in 3 unrelated Dutch Caucasian individuals with ARVC. Of the cohort studied, patients with this variant had the youngest age of onset (ages 17, 17, and 20). Haplotype analysis indicated that it may be a founder mutation. One patient also carried a missense variant in PKP2: p.Glu62Lys. [Bhuiyan et al. (2009) appears to refer to the same patients as the van Tintelen et al. study.] Cox et al. 2011 identified it in 6 index patients (it is unclear how many of these were in the prior paper by van Tintelen et al. 2006 from the same group); two patients also carried a missense variant in DSG2 or JUP. Two 16-year-old males in one of these families suffered sudden cardiac death. Wlodarska et al. 2008 saw it in at least one Polish patient. Fressart et al. (2010) found it in 3 unrelated individuals recruited in France and/or Switzerland. Quarta et al. (2011) saw it in one patient referred to a center in London. Palmisano et al. (2011) studied a young male athlete with aborted cardiac arrest at age 21 and his affected but asymptomatic father, who both carried this variant and also a DSC2 I109M variant. The family’s ancestry may have been from Iran. Nakajima et al. (2012) found the variant in a Japanese patient who also carried the PKP2 variant D812N (in trans, one inherited from each of his unaffected parents). He had his first cardiac syncopal event (VT) at age 11 and was diagnosed at age 20. Baskin et al. (2013) found the variant in 2 ARVC patients tested in Canada. Bao et al. (2013) found it in 4 Chinese patients with ARVC. There is only very weak segregation data available: van Tintelen et al. (2006) saw it segregate in 2 affected family members. Palmisano et al. (2011) saw it segregate in an affected father and son. In total the variant has not been seen in more than 8500 presumably unaffected individuals, including 2000 controls and ~6500 individuals from population datasets. Dalal et al. (2006) did not find it in 200 controls (ancestry not specified); van Tintelen et al. (2006), 150 Caucasian controls; Wlodarska et al. (2008), 100 Caucasian controls; Fressart et al. (2010), 300 Caucasian controls; Cox et al. (2011), 200 Dutch Caucasian controls; Quarta et al. (2011), 300 ethnically-matched controls; Nakajima et al. (2012), 80 Japanese controls; Baskin et al. (2013), 427 controls; Bao et al. (2013), 300 Chinese(?) controls. It is not seen in the NHLBI Exome Sequencing Project (ESP) dataset, which currently includes variant calls on ~4300 Cauca -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 15, 2022	Haplotype analysis suggests this variant may be a Dutch founder mutation (van Tintelen et al., 2006); Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 21822014, 24585727, 23812740, 30391969, 30571190, 30830208, 31447099, 22214898, 21606390, 20400443, 25525159, 21606396, 26332594, 15489853, 20857253, 17010805, 27532257, 16567567, 19358943, 20031617, 20031616, 24125834, 30385303, 30790397, 30847666, 31737537, 32916635, 32931854, 32372669, 31386562, 31402444, 34426522, 33087929) -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	Jul 17, 2017	- -

Arrhythmogenic right ventricular dysplasia 9 Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 21, 2024	This sequence change affects a donor splice site in intron 12 of the PKP2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PKP2 are known to be pathogenic (PMID: 15489853, 17041889, 23911551). This variant is present in population databases (rs111517471, gnomAD 0.008%). Disruption of this splice site has been observed in individuals with arrhythmogenic right ventricular cardiomyopathy (PMID: 15489853, 17010805, 20031616, 20031617, 21822014, 22214898). ClinVar contains an entry for this variant (Variation ID: 6757). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	May 31, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Oct 18, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 08, 2014	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 2004	- -

Arrhythmogenic right ventricular cardiomyopathy Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Jul 27, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 08, 2024	This variant causes a G to A nucleotide substitution at the +1 position of intron 12 splice donor site of the PKP2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. This variant has been reported in over twenty individuals affected with arrhythmogenic right ventricular cardiomyopathy (PMID: 15489853, 17010805, 20031616, 20031617, 21822014, 22214898, 23871674, 28523642, 32916635, 36225810). An RT-PCR of an affected carrier individual has shown that this variant causes either skipping of PKP2 exon 12 or, alternatively, activates a cryptic splice donor site in intron 12 (PMID: 15489853). This variant has been identified in 8/282816 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PKP2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 20, 2016	The c.2489+1G>A variant in PKP2 has been reported in >25 ethnically diverse indi viduals with ARVC and segregated with disease in 4 affected relatives from 4 fam ilies (Gerull 2004, Baskin 2013, Dalal 2009, Dalal 2006, van Tintelen 2006, Cox 2011, Quarta 2011, Fressart 2010, Jordan 1985, Nakajima 2012, Palmisano 2011). T his variant has also been identified by our laboratory in 4 individuals (3 with ARVD/C and 1 with HCM) and segregated with disease in 2 affected relatives from 2 families. The c.2489+1G>A variant has been reported by other clinical laborato ries in ClinVar (Variation ID 6757) and has been identified in 4/126660 European and 2/24030 African chromosomes by the Genome Aggregation Database (gnomAD, htt p://gnomad.broadinstitute.org; dbSNP rs111517471). The c.2489+1G>A variant occur s in the invariant region (+/- 1,2) of the splice consensus sequence and is pred icted to cause altered splicing leading to an abnormal or absent protein. In sum mary, this variant meets criteria to be classified as pathogenic based upon segr egation studies, presence in multiple affected individuals, low frequency in the general population and the predicted impact to the protein. -

Cardiomyopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Jan 05, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 15, 2023	This variant causes a G to A nucleotide substitution at the +1 position of intron 12 splice donor site of the PKP2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. This variant has been reported in over twenty individuals affected with arrhythmogenic right ventricular cardiomyopathy (PMID: 15489853, 17010805, 20031616, 20031617, 21822014, 22214898, 23871674, 28523642, 32916635, 36225810). An RT-PCR of an affected carrier individual has shown that this variant causes either skipping of PKP2 exon 12 or, alternatively, activates a cryptic splice donor site in intron 12 (PMID: 15489853). This variant has been identified in 8/282816 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PKP2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Aborted sudden cardiac death Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Agnes Ginges Centre for Molecular Cardiology, Centenary Institute

Feb 09, 2018

PKP2 c.2489+1G>A has been previously reported in multiple ARVC probands (Gerull B, et al., 2004; Dalal D, et al., 2006; van Tintelen JP, et al., 2006; Watkins DA, et al., 2009; Fressart V, et al., 2010; van der Werf C, et al., 2010; Tan BY, et al., 2010; Quarta G, et al., 2011; Palmisano BT, et al., 2011; Cox MG, et al., 2011; Nakajima T et al., 2012; Baskin B, et al., 2013) and in at least one family, has been found to segregate to an affected family member (Dalal D, et al., 2006). We identified this variant in a proband who presented with aborted cardiac arrest, but has no cardiac features suggestive of ARVC. The proband has a family history of sudden death however segregation was not possible. The variant is present at a low frequency in the Genome Aggregation Database (MAF=0.00002; http://gnomad.broadinstitute.org/). In summary, the variant has been reported in numerous ARVC cases, is rare in the general population and PKP2 loss of function variants are an established cause of disease, therefore we classify PKP2 c.2489+1G>A as "pathogenic". -

Arrhythmogenic ventricular cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Royal Brompton Clinical Genetics And Genomics Laboratory, NHS South East Genomic Laboratory Hub

Aug 21, 2017

This variant has previously been reported in multiple patients with ARVC (Gerull et al. Nat Genet. 2004 Nov;36(11):1162-4; Dalal et al. J Am Coll Cardiol. 2006 Oct 3;48(7):1416-24; Nakajima et al. Circ J. 2012;76(3):737-43; Olfson et al. PLoS One. 2015 Sep 2;10(9):e0135193; Walsh et al. Genet Med. 2017 Feb;19(2):192-203; Xiong et al. Science. 2015 Jan 9;347(6218):1254806; Palmisano et al. Cardiology. 2011;119(1):47-53; Cox et al. Circulation. 2011 Jun 14;123(23):2690-700; Quarta et al. Circulation. 2011 Jun 14;123(23):2701-9; Tan et al. J Cardiovasc Transl Res. 2010 Dec;3(6):663-73; Fressart et al. Europace. 2010 Jun;12(6):861-8; den Haan et al. Circ Cardiovasc Genet. 2009 Oct;2(5):428-35; Bhuiyan et al. Circ Cardiovasc Genet. 2009 Oct;2(5):418-27; Dalal et al. J Am Coll Cardiol. 2009 Apr 14;53(15):1289-99; van Tintelen et al. Circulation. 2006;113(13):1650-8; Dalal et al. Circulation. 2006 Apr 4;113(13):1641-9; ClinVar variation ID 6757). It has been detected at a very low allele frequency in control populations (6/277168; 0.0022%; gnomAD database). Algorithms predict this variant will disrupt the canonical donor splice site and lead to an aberrant splice transcript and premature termination of translation, leading to an abnormal or absent protein. Premature truncation of PKP2 is a known disease mechanism in ARVC (Gerull et al Nat Genet. 2004 Nov;36(11):1162). -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 24, 2021

The c.2489+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 12 of the PKP2 gene. This alteration occurs at the 3' terminus of the PKP2 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 12.9% of the protein. The exact functional effect of this alteration is unknown; however, the impacted region is critical for protein function, and a significant portion of the protein is affected (Ambry internal data). This alteration has been detected in multiple patients with arrhythmogenic right ventricular cardiomyopathy, and was reported to segregate with the disease in some of the families (Gerull B et al. Nat. Genet., 2004 Nov;36:1162-4; van Tintelen JP et al. Circulation, 2006 Apr;113:1650-8; Dalal D et al. J. Am. Coll. Cardiol., 2006 Oct;48:1416-24; Nakajima T et al. Circ. J., 2012 Dec;76:737-43; Walsh R et al. Genet Med, 2017 02;19:192-203; Orgeron GM et al. J Am Heart Assoc, 2017 Jun;6:[ePub ahead of print]; Haggerty CM et al. Genet Med, 2017 11;19:1245-1252; Truszkowska GT et al. Sci Rep, 2017 Jun;7:3362; Andrews CM et al. Circ Arrhythm Electrophysiol, 2017 Jul;10:). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial isolated arrhythmogenic right ventricular dysplasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 31, 2021

Variant summary: PKP2 c.2489+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing by skipping of PKP2 exon 12 or, alternatively, activate a cryptic splice donor site in intron 12 (Gerull_2004). The variant allele was found at a frequency of 3.1e-05 in 255982 control chromosomes. c.2489+1G>A has been reported in the literature in multiple individuals affected with Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (example, Gerull_2004, Dalal_2006, Dalal_2009, vanTintelen_2006, Cox_2011, Palmisano_2011, Quarta_2011, Fressart_2010, Bhuiyan_2009, denHaan_2009, Wlodarska_2008, Nakajima_2012, Tan_2010). These data indicate that the variant is very likely to be associated with disease. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.17
CADD	Pathogenic	28
DANN	Uncertain	0.99
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Uncertain	0.91	D
MutationTaster	Benign	1.0	D;D
GERP RS		5.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.96		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.96		Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs111517471; hg19: chr12-32949042;