ClinVar Genomic variation as it relates to human health

The CACNA1C Arg518His variant had been identified in a few probands with mixed phenotypes of Long QT, congenital heart defects and HCM (Boczek NJ, et al., 2015; Genedx, personal communication) and has been found to segregate in 2 families with varying phenotypes (Boczek NJ, et al., 2015). In vitro functional analysis using whole cell patch clamping confirmed the loss of current density and inactivation in combination with increased window and later voltage gated calcium channel current (Boczek NJ, et al., 2015), however this study may not necessarily reflect biological function and future studies will be useful to validate these findings. The variant is present a singleton event in the Exome Aggregation Consortium dataset (MAF= 0.00003230, http://exac.broadinstitute.org/). We identified this variant in a patient diagnosed with HCM in their adoloscence, the patient had a known family history of disease and a prolonged QT was noted when the patient was in his 40s. The probands affected son also harbours this variant. He was diagnosed with HCM at 2 months. Computational tools SIFT, PolyPhen-2 and MutationTaster predict this variant to have deleterious effect. In summary, based on a few proband's reported with similar phenotypes, strong segregation data, rarity in general population databases, as well supportive in silico tools in combination with a functional study suggestive of an affect on protein function, we classify the CACNA1C Arg518His as "likely pathogenic".

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 518 of the CACNA1C protein (p.Arg518His). This variant is present in population databases (no rsID available, gnomAD 0.3%). This missense change has been observed in individuals with long QT syndrome or a complex phenotype of long QT syndrome and hypertrophic cardiomyopathy (PMID: 26253506, 30025578, 31408100, 32161207). ClinVar contains an entry for this variant (Variation ID: 372313). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CACNA1C protein function. Experimental studies have shown that this missense change affects CACNA1C function (PMID: 26253506). This variant disrupts the p.Arg518 amino acid residue in CACNA1C. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26253506; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Published functional studies demonstrate reduction in current density combined with increased window current and loss of inactivation (PMID: 26253506); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27390944, 30984024, 30025578, 30027834, 35862440, 32161207, 30681346, 34079780, 35352813, 31110529, 31408100, 36252119, 34999275, 36578016, 37614386, 26253506, 31430211)

Variant summary: CACNA1C c.1553G>A (p.Arg518His) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 219196 control chromosomes. c.1553G>A has been reported in the literature in individuals affected with Arrhythmia. These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and showed that this variant disrupts the normal function. 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 pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The p.R518H pathogenic mutation (also known as c.1553G>A), located in coding exon 12 of the CACNA1C gene, results from a G to A substitution at nucleotide position 1553. The arginine at codon 518 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported in multiple unrelated probands with mixed cardiac phenotypes, including long QT syndrome, hypertrophic cardiomyopathy, cardiac conduction defects, and congenital heart disease, and limited segregation data suggest that this variant co-segregates with disease (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32; Bagnall RD et al. J. Am. Coll. Cardiol., 2018 Jul;72:419-429; Bonaventura J et al. Arch Med Sci, 2019 May;15:641-649; Mellor GJ et al. Europace, 2019 Aug; epub ahead of print; Fukuyama M et al. Circ J, 2020 03;84:559-568; GeneDx pers comm; Invitae pers comm). Functional studies performed in vitro indicate that R518H leads to a decrease in peak channel current density but an increase in the late calcium current (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32). Another pathogenic alteration, p.R518C, has been described in the same codon, with additional functional studies demonstrating the pathogenic impact of alterations at this site (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32; Estes SI et al. Circ Genom Precis Med, 2019 08;12:e002534). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

PS3, PM5, PM2, PP3