ClinVar Genomic variation as it relates to human health

The A519T variant of uncertain significance in the CACNA1C gene has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. A519T was not observed with any significant frequency in the NHLBI Exome Sequencing Project or the Exome Aggregation Consortium (ExAC), indicating it is not a common benign variant in these populations. The A519T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Moreover, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function.Nevertheless, additional evidence is needed to determine whether this variant is pathogenic or benign. This result cannot be used for diagnosis or family member screening at this time.

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 519 of the CACNA1C protein (p.Ala519Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with sudden unexplained death or long QT syndrome (PMID: 28704380, 31737537). ClinVar contains an entry for this variant (Variation ID: 392350). 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 not expected to disrupt CACNA1C protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

The CACNA1C c.1555G>A; p.Ala519Thr variant (rs371702432) is reported in the literature in a victim of sudden unexpected death syndrome, but this individual carried other variants in different genes as well (Suktitipat 2017). This variant is also reported in ClinVar (Variation ID: 392350). It is observed in the general population with an overall allele frequency of 0.002% (6/250334 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.595). Due to limited information, the clinical significance of this variant is uncertain at this time. References: Suktitipat B et al. Molecular investigation by whole exome sequencing revealed a high proportion of pathogenic variants among Thai victims of sudden unexpected death syndrome. PLoS One. 2017 Jul 13;12(7):e0180056. PMID: 28704380.

The p.A519T variant (also known as c.1555G>A), located in coding exon 12 of the CACNA1C gene, results from a G to A substitution at nucleotide position 1555. The alanine at codon 519 is replaced by threonine, an amino acid with similar properties. According to data from gnomAD, the frequency for this variant is above the maximum credible frequency for a cardiac disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the supporting evidence, the association of this alteration with CACNA1C-related neurodevelopmental disorder is unknown; however, the association with CACNA1C-related Timothy syndrome or long QT syndrome is unlikely.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with Long QT syndrome 8 (MIM #618447), and Timothy syndrome (MIM#601005). Missense variants result in loss of channel inactivation, and increased current (OMIM, PMID: 25260352). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from alanine to threonine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (6 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (2 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0809 - Previous evidence of pathogenicity for this variant is inconclusive. This variant has been reported multiple times as VUS in ClinVar, and also in one individual who suffered a sudden death who also harboured two other potential causative variants (PMID: 28704380). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign