Long QT Syndrome and Catecholaminergic Polymorphic Ventricular Tachycardia via the CALM3 Gene

Long QT syndrome (LQTS) is a heritable channelopathy characterized by prolonged cardiac repolarization that may trigger ventricular arrhythmias (torsade de pointes), recurrent syncopes, seizure, or sudden cardiac death (Alders et al. 2018. PubMed ID: 20301308). LQTS can manifest with syncope and cardiac arrest that is commonly triggered by adrenergic stress, often precipitated by emotion or exercise. Roughly 10% to 15% of patients experience symptoms at rest or during the night (Schwartz et al. 2001. PubMed ID: 11136691). The mean age of onset of symptoms is 12 years, and earlier onset usually is associated with a more severe form of the disease (Priori et al. 2004. PubMed ID: 15367556).

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmogenic heart disorder characterized by life-threatening electrical instability induced by physical or emotional stress without any structural cardiac abnormalities (Napolitano et al. 2016. PubMed ID: 20301466). The electrical instability may degenerate into cardiac arrest and sudden death. The onset of CPVT is typically during childhood and often presents as syncope. Preventative drugs (beta-blockers) and other treatments are available for susceptible individuals.

Autosomal dominant calmodulinopathies are rare adrenergically-induced arrhythmia syndromes caused by pathogenic variants in any of the three genes, CALM1, CALM2, and CALM3. The three genes are located on three different chromosomes but encode identical calmodulin proteins. Calmodulinopathies are mainly characterized by long QT syndrome (CALM-LQTS; 49%) and catecholaminergic polymorphic ventricular tachycardia (CALM-CPVT; 28%), while a small number of patients may have overlapping LQTS/CPVT phenotypes. The median age of onset for patients with CALM-LQTS is 1.5 years, while patients with CALM-CPVT have a median age of onset of 6.0 years. Additional features in calmodulinopathies include idiopathic ventricular fibrillation, sudden unexplained death, cardiac structural abnormalities, and neurological phenotypes (Crotti et al. 2019. PubMed ID: 31170290). A study that characterized the phenotypes of 74 patients with a variant in CALM1, CALM2, or CALM3 suggested no gene-specific phenotypic correlations (Crotti et al. 2019. PubMed ID: 31170290). Pathogenic variants in CALM3 have been associated with long QT syndrome 16 (LQT16) and catecholaminergic polymorphic ventricular tachycardia 6 (CPVT6). Incomplete penetrance and variable expressivity have been documented in CALM3 (Crotti et al. 2019. PubMed ID: 31170290).

Advantages of genetic testing for calmodulinopathies include confirmation of diagnosis, identification of other health risks associated with calmodulinopathies, and targeted testing of other family members.

LQT16 and CPVT6 are autosomal dominant disorders that result from heterozygous pathogenic variants in CALM3. To date, about ten variants have been reported in patients with CALM3 calmodulinopathy (Reed et al. 2015. PubMed ID: 25460178; Gomez-Hurtado et al. 2016. PubMed ID: 27516456; Chaix et al. 2016. PubMed ID: 28491681; van Lint et al. 2019. PubMed ID: 30847666; Crotti et al. 2019. PubMed ID: 31170290; Wren et al. 2019. PubMed ID: 31454269). All reported pathogenic variants are missense variants, and the majority of them occur de novo. These variants have not been reported in population databases. Pathogenic missense variants are found to cluster within the third and the fourth EF-hand calcium binding loops, which are critical for calcium binding and normal function in CALM3. Missense variant hotspots are found in the amino acid residues involved in calcium binding within EF-hand calcium binding loops (Asp96, Asn98, Asp130, and Phe142) (Crotti et al. 2019. PubMed ID: 31170290). Although a genotype-phenotype correlation between LQT16 and CPVT6 has not been well established, LQTS-associated variants are mostly located within the fourth EF-hand calcium binding loop, and CPVT-associated variants are more likely to be found in the third EF-hand calcium binding loop. Somatic mosaicism in CALM3 has also been documented (Wren et al. 2019. PubMed ID: 31454269). CALM3 is relatively intolerant to missense and loss of function variants (Genome Aggregation Database).

The CALM3 gene encodes calmodulin, a ubiquitously-expressed calcium-binding protein with four EF-hand calcium-binding motifs. Genomic redundancy in calmodulin is evidenced by the presence of three family members (CALM1, CALM2, and CALM3) each encoding an identical polypeptide. Studies in knockout mouse models are not currently available. Functional studies of LQTS-associated missense variants in induced pluripotent stem cell-derived cardiomyocytes showed impaired calcium binding affinity leading to aberrant calcium-dependent inactivation of L-type calcium channels (Wren et al. 2019. PubMed ID: 31454269). Functional studies of CPVT-associated missense variants in murine cardiomyocytes showed mild impairment of calcium binding affinity and increased spontaneous calcium release and spark activity (Gomez-Hurtado et al. 2016. PubMed ID: 27516456). CALM3 has been cited as a nonessential gene for growth of human tissue culture cells (Online Gene Essentiality, ogee.medgenius.info).

Pathogenic variants in CALM3 appear to be a rare cause of LQTS or CPVT. Up to 70% of patients with a clinical diagnosis of LQTS have identifiable pathogenic variants (Beckmann et al. 2013. PubMed ID: 23511927). The majority of LQTS cases are caused by pathogenic variants in one of three genes: KCNQ1, KCNH2, and SCN5A. Pathogenic variants in ANK2, KCNE1, KCNE2, KCNJ2, CACNA1C, CAV3, SCN4B, AKAP9, SNTA1, KCNJ5, CALM1, and CALM2 account for approximately 5% of LQTS (Lieve et al. 2013. PubMed ID: 23631430; Kapplinger et al. 2009. PubMed ID: 19716085; Alders et al. 2018. PubMed ID: 20301308). Analytical sensitivity should be high, as all reported pathogenic variants in CALM3 are detectable by sequencing.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides full coverage of all coding exons of the CALM3 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom panels).