chr6-118559037-T-G

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_StrongPP5_Very_Strong

The NM_002667.5(PLN):c.116T>G(p.Leu39*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000192 in 1,610,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000021 ( 0 hom. )

Consequence

PLN
NM_002667.5 stop_gained

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:21

Conservation

PhyloP100: 6.64

Variant links:

Genes affected

PLN (HGNC:9080): (phospholamban) The protein encoded by this gene is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase in cardiac muscle. The encoded protein is an inhibitor of cardiac muscle sarcoplasmic reticulum Ca(2+)-ATPase in the unphosphorylated state, but inhibition is relieved upon phosphorylation of the protein. The subsequent activation of the Ca(2+) pump leads to enhanced muscle relaxation rates, thereby contributing to the inotropic response elicited in heart by beta-agonists. The encoded protein is a key regulator of cardiac diastolic function. Mutations in this gene are a cause of inherited human dilated cardiomyopathy with refractory congestive heart failure, and also familial hypertrophic cardiomyopathy. [provided by RefSeq, Apr 2016]

PLN links:

CEP85L (HGNC:21638): (centrosomal protein 85 like) The protein encoded by this gene was identified as a breast cancer antigen. Nothing more is known of its function at this time. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

CEP85L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.27 CDS is truncated, and there are 3 pathogenic variants in the truncated region.

PP5

Variant 6-118559037-T-G is Pathogenic according to our data. Variant chr6-118559037-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 13637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-118559037-T-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLN	NM_002667.5 link	c.116T>G	p.Leu39*	stop_gained	Exon 2 of 2	ENST00000357525.6	NP_002658.1	P26678Q5R352
CEP85L	NM_001042475.3 link	c.1020+6492A>C		intron_variant	Intron 3 of 12	ENST00000368491.8	NP_001035940.1	Q5SZL2-1Q3ZCQ5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLN	ENST00000357525.6 link	c.116T>G	p.Leu39*	stop_gained	Exon 2 of 2	1	NM_002667.5	ENSP00000350132.5		P26678
CEP85L	ENST00000368491.8 link	c.1020+6492A>C		intron_variant	Intron 3 of 12	1	NM_001042475.3	ENSP00000357477.3		Q5SZL2-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000159

AC:

AN:

251234

Hom.:

AF XY:

0.0000147

AC XY:

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000352

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000206

AC:

AN:

1458766

Hom.:

Cov.:

AF XY:

0.0000262

AC XY:

AN XY:

725946

show subpopulations

Gnomad4 AFR exome

AF:

0.00

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:

0.0000252

Gnomad4 OTH exome

AF:

0.0000332

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152226

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000558

Hom.:

Bravo

AF:

0.0000189

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:21

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:6

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 18, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Reported in association with DCM and HCM (Haghighi et al., 2003; Chiu et al., 2007; Landstrom et al., 2011; Medeiros et al., 2011; Sanoudou et al., 2015; Walsh et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); Functional studies show significantly reduced expression of the p.(L39*) protein (Haghighi et al., 2003; Kelly et al., 2008); Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 14 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 26917049, 17010801, 31402444, 23861362, 26535225, 16829191, 16432188, 22427649, 23139254, 23989713, 21332051, 18287099, 12724757, 25928149, 17655857, 25611685, 28102477, 27532257, 21167350, 12639993, 16235537, 30259183, 28986455, 28600387, 28449774, 28790153, 34426522, 31589614, 22137083) -

Clinical Genetics, Academic Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 27, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 02, 2021

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dilated cardiomyopathy 1P

Pathogenic:4

Aug 30, 2019

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

Sep 09, 2022

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PM2, PP5 -

Jan 15, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Leu39*) in the PLN gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 14 amino acid(s) of the PLN protein. This variant is present in population databases (rs111033560, gnomAD 0.004%). This premature translational stop signal has been observed in individuals with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) (PMID: 12639993, 17655857, 21167350, 25611685, 26535225, 27532257). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13637). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects PLN function (PMID: 12639993). For these reasons, this variant has been classified as Pathogenic. -

Jan 01, 2011

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Cardiomyopathy

Pathogenic:2

Sep 20, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0104 - Dominant negative is a known mechanism of disease for missense variants in this gene, and is associated with dilated cardiomyopathy 1P (MIM#609909), and hypertrophic cardiomyopathy 18 (MIM#613874) (PMID: 16432188). The mechanism of truncating variants is unclear. (I) 0107 - This gene is associated with autosomal dominant disease. Rare reports of biallelic individuals has also been reported (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 22820313, PMID: 16432188). (I) 0205 - Variant is predicted to result in a truncated protein (premature termination codon is NOT located at least 54 nucleotides upstream of the final exon-exon junction) with less than 1/3 of the protein sequence affected. (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (4 heterozygotes, 0 homozygotes). (SP) 0600 - Variant is located within the annotated phospholamban domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as likely pathogenic and pathogenic, and observed in individuals with hypertrophic cardiomyopathy, dilated cardiomyopathy and cardiac arrest, with incomplete penetrance (ClinVar). (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

May 02, 2023

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy 18

Pathogenic:2

May 25, 2022

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2011

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Cardiac arrest

Pathogenic:1

Oct 14, 2014

Blueprint Genetics

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Intrinsic cardiomyopathy

Pathogenic:1

Sep 06, 2023

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The PLN c.116T>G (p.Leu39Ter) nonsense variant occurs in the only coding exon of the gene and may escape nonsense-mediated decay. Across a selection of available literature, this variant has been identified in a heterozygous state in eight unrelated individuals with cardiac phenotypes (hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), left ventricular hypertrophy (LVH), and cardiac arrest) and in a homozygous state in two individuals with severe DCM, LVH and heart failure requiring cardiac transplantation. This variant has been shown to segregate with disease in multiple families, with reduced penetrance (PMID: 12639993; 17655857; 21167350; 22137083; 25611685; 28600387; 28986455). Functional studies conducted in human cell lines demonstrated that this variant resulted in mislocalization of the protein, and examination of heart tissue from a homozygous patient showed reduced mRNA expression and no detectable protein product (PMID: 12639993). This variant is not observed at a significant frequency in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant has been classified as pathogenic by at least three submitters in ClinVar. Based on the available evidence, the c.116T>G (p.Leu39Ter) variant is classified as pathogenic for intrinsic cardiomyopathy. -

Dilated cardiomyopathy 1P;C3151265:Hypertrophic cardiomyopathy 18

Pathogenic:1

Jun 19, 2020

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.116T>G (p.Leu39Ter) variant identified in the PLN gene is a nonsense variant predicted to lead to the premature termination of the protein at amino acid 39/53 (exon 2/2). This variant is absent from gnomAD(v3.0) suggesting it is not a common benign variant in the populations represented in that database. The c.116T>G (p.Leu39Ter) variant is reported as Likely Pathogenic/Pathogenic in ClinVar (VarID:13637), and functional studies suggest the p.Leu39Ter variant leads to significantly reduced or absent protein expression [PMID:12639993]. The p.Leu39Ter variant has been identified in many affected individuals with dilated cardiomyopathy, cardiac hypertrophy, and arrhythmias [PMID:12639993;PMID:17655857;PMID:26535225;PMID:28600387]. Given its deleterious nature, absence in population databases, functional studies suggesting altered protein expression, and observation in many affected individuals in the literature, the c.116T>G (p.Leu39Ter) variant identified in the PLN gene is reported as Pathogenic. -

Primary dilated cardiomyopathy

Pathogenic:1

Jun 24, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Sudden cardiac death

Pathogenic:1

Oct 14, 2014

Blueprint Genetics

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy

Pathogenic:1

Jun 11, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Leu39X variant in PLN leads to a premature termination codon at position 3 9 which is predicted to lead to a truncated or absent protein. This variant has been identified in 1/66694 European chromosomes by the Exome Aggregation Consort ium (ExAC, http://exac.broadinstitute.org; dbSNP rs111033560). It has been repor ted in 4 families with cardiomyopathy (2 families with HCM and conduction system disease; 2 families with DCM and LVH) (Haghighi 2003, Chiu 2007, Landstrom 2011 ). In one family, 2 individuals with severe DCM were homozygous for the variant (Haghighi 2003), and heterozygous family members presented with a range of featu res including LVH, HCM +/- conduction system disease, or DCM. Across these 4 fam ilies, this variant segregated with disease in 8 affected relatives. The increas ed severity in homozygosity lends additional support for a pathogenic role. In s ummary, the p.Leu39X variant meets our criteria to be classified as pathogenic f or HCM in an autosomal dominant manner (http://www.partners.org/personalizedmedi cine/LMM) based upon segregation studies, virtual absence in the general populat ion and the predicted severe impact on the protein. -

Cardiovascular phenotype

Pathogenic:1

Feb 09, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.L39* pathogenic mutation (also known as c.116T>G), located in coding exon 1 of the PLN gene, results from a T to G substitution at nucleotide position 116. This changes the amino acid from a leucine to a stop codon within coding exon 1. This alteration has been previously reported in association with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) and demonstrated segregation with disease in families with variable expression and reduced penetrance (Haghighi K et al. J Clin Invest. 2003 Mar;111(6):869-76; Chiu C et al. J Mol Cell Cardiol. 2007 Sep;43(3):337-43; Landstrom AP et al. Am Heart J. 2011 Jan;161(1):165-71). Two homozygous siblings with severe DCM requiring transplantation were reported, one of whom had only mild left ventricular hypertrophy that progressed to left ventricular dilation and cardiac failure; their heterozygous family members exhibited a range of clinical features from some with DCM, to those with left ventricular hypertrophy and normal ejection fractions, and others with no reported findings (Haghighi K et al. J Clin Invest. 2003 Mar;111(6):869-76). This alteration was reported in an individual with unexplained sudden cardiac arrest and no detectable cardiac findings; however, she remained under the age of 18 at time of follow-up (Mellor G et al. Circ Cardiovasc Genet, 2017 Jun;10). In addition, one study reported this alteration to result in reduction of detectable mRNA, no detectable protein product, and loss of normal protein-protein interaction in a sample from a homozygous individual with DCM (Haghighi K et al. J Clin Invest. 2003;111(6):869-76). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.49

BayesDel_noAF

Pathogenic

0.55

CADD

Pathogenic

DANN

Uncertain

0.97

Eigen

Pathogenic

0.75

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Uncertain

0.93

Vest4

0.79

GERP RS

5.6

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over