Cav2.1. Among the various neurogenetic disorders that we follow in our clinic, CACNA1A-related disorders are somewhat unique. Even though these conditions have been known for several decades, our understanding has remained fragmented, and the functional effect of most missense variants is still not well understood. In a recent study, we contributed to a comprehensive functional assessment of 42 missense variants in CACNA1A, approaching the problem in a structured, top-down manner. Here are the main findings from our study.
Figure. Functional landscape of CACNA1A variants across structure, biophysics, and phenotype. A. Schematic of the hCaV2.1 channel topology illustrating domains DI–DIV as transmembrane segments, with S4 voltage-sensing regions highlighted in light blue. De novo missense variants are shown in red and population variants from gnomAD in gray. B. Hierarchical clustering heatmap of CACNA1A variants based on z scores of electrophysiological parameters. Each row represents a single variant and each column corresponds to an individual functional parameter. z score magnitudes are color-coded as indicated in the inset. The dendrogram groups variants with similar functional profiles. C. Forest plots showing odds ratios from logistic regression analyses for peak current density, V1/2 activation, and V1/2 inactivation across 16 phenotypes. Solid circles denote statistically significant associations and horizontal bars represent 95% confidence intervals. Analyses include data from both the GeneDx cohort and the clinically reviewed cohort. Modified from Kurganov et al., 2025. Figures used with permission as co-author of the publication.
Overview. There are three main phenotypes associated with disease-causing variants in CACNA1A, and in pediatric neurogenetics we typically encounter two of them. The most common presentation is related to loss-of-function variants, which are associated with developmental differences, ataxia, paroxysmal tonic upgaze (PTU), and absence epilepsy. In addition, we follow individuals with gain-of-function variants, which result in a spectrum of phenotypes ranging from hemiplegic migraine to developmental and epileptic encephalopathies. The one presentation we typically do not encounter in pediatrics is spinocerebellar ataxia type 6 (SCA6), which is caused by triplet-repeat expansions in CACNA1A. This slowly progressive condition usually begins in adulthood and is rarely seen in a pediatric setting.
The VUS issue. As we mentioned in a prior blog post, hemiplegic migraine (HM) is something of a misnomer from a pediatric perspective. While adult HM presentations can overlap with common migraine, hemiplegic migraine in children can represent a neurological emergency with brain swelling, coma, and status epilepticus. Disease trajectories can be unpredictable. HM rarely occurs before 24 months of age, but there are currently no reliable predictors that allow us to determine whether a child with a variant of uncertain significance in CACNA1A is at risk. Because hemiplegic migraine occurs exclusively with gain-of-function variants, functional assessment has the potential to provide important clinical insight.
In the recent study by Kurganov and collaborators, we assessed the functional consequences of 42 missense variants in CACNA1A assembled from more than 32,000 individuals with neurodevelopmental disorders. Here are three main takeaways.
1 – Loss of function is common. Nearly half of all CACNA1A missense variants in our cohort (20/42) did not produce any measurable current. From a purely electrophysiological perspective, this finding may appear straightforward. Clinically, however, it provides an important benchmark. When we evaluate a child with a novel missense variant, we often do not have a clear sense of how likely that variant is to result in loss- versus gain-of-function, especially in younger children before the phenotype has fully declared itself. The data from Kurganov and collaborators suggest that missense variants identified in neurodevelopmental disorders have approximately a 50 percent likelihood of being complete loss-of-function variants.
2 – Function is complex but driven by two main factors. Electrophysiology is inherently complex, and for non-specialists it is easy to get lost in the detail. In addition to five core electrophysiological parameters, we incorporated simulations in Purkinje cells, resulting in a broad multidimensional functional assessment. However, two principal parameters largely determine whether a variant behaves as gain- or loss-of-function in CACNA1A. Using Linear Discriminant Analysis (LDA), we found that current density (CD) and the voltage dependence of activation (V1/2 act) provide the main separation between functional classes.
Current density is intuitive: it reflects how much current passes through the channel. V1/2 activation, in contrast, is more nuanced. I sometimes describe a leftward shift in V1/2 as the channel opening more “quickly,” which electrophysiologists rightfully challenge. More precisely, a leftward shift means that the channel activates at more hyperpolarized membrane potentials, effectively opening earlier during depolarization. In practical terms, the functional abnormalities seen in CACNA1A-related neurodevelopmental disorders are largely determined by “how much” the channel opens and “how soon” it opens.
3 – Phenotypes remain challenging. We also examined the phenotypic information available for individuals carrying these variants. Two general observations emerged. First, even with limited phenotypic data, severe epilepsy and hemiplegic migraine are strongly associated with gain-of-function variants. This mirrors the clinical distinction we use in patient management and is reassuring to see replicated in this dataset.
Second, finer phenotypic distinctions are difficult to capture. Consider two established gain-of-function variants, p.A713T and p.R1349Q. In the dataset analyzed by Kurganov and collaborators, p.R1349Q is associated with hemiplegic migraine, whereas p.A713T is annotated as hemiplegia. This likely reflects differences in data sources rather than true biological divergence, but it illustrates a broader point. While we can reliably distinguish gain- from loss-of-function, phenotypic differences within the gain-of-function group are more subtle and not fully resolved. The p.A713T variant was initially reported in the Epi4K study as causing early-onset developmental and epileptic encephalopathy, whereas p.R1349Q often presents later in infancy. How specific gain-of-function properties translate into distinct clinical trajectories remains incompletely understood.
What you need to know. In a recent study by Kurganov and collaborators, we analyzed the functional consequences of 42 missense variants in CACNA1A and linked these findings to available phenotypic data. Nearly half of missense variants in neurodevelopmental disorders showed complete loss of current. Two electrophysiological parameters, current density and voltage dependence of activation, account for much of the functional distinction between gain- and loss-of-function. Clinically, hemiplegic migraine aligns strongly with gain-of-function variants, but finer phenotypic differences within this group remain difficult to resolve.
