Abstract
Objective
CACNA1A encodes the Cav2.1 (P/Q-type) channel whose spectrum extends from FHM1/EA2/SCA6 to epilepsy and vertigo, but penetrance—especially sex differences—remains unclear. We report a three-generation family with CACNA1A c.5610del, detail electroclinical features, assess sex-stratified penetrance, and discuss individualised therapy.
Methods
We retrospectively reviewed histories, neurological exams, EEG, treatments, and follow-up. Trio whole-exome sequencing across 13 relatives was Sanger-confirmed and interpreted per ACMG; gnomAD/ClinVar were queried. Sex-stratified penetrance was summarised with exact binomial 95% CIs.
Results
The female proband developed clinically focal seizures with preserved awareness in 2019. Valproate reduced but did not abolish seizures; after oxcarbazepine, EA2-like paroxysmal symptoms emerged and responded to acetazolamide. Since 2023, she has experienced episodic diplopia, vertigo, bilateral tinnitus, and pulsatile temporal headaches consistent with FHM-like features, typically independent of epileptic seizures. Video-EEG monitoring demonstrated generalised, bilaterally synchronous spike-and-slow-wave discharges with frontal predominance, with a reduction in interictal epileptiform burden observed after treatment optimisation. Genetic analysis identified a heterozygous CACNA1A c.5610del (p.His1871IlefsTer30) variant, absent from population databases and classified as pathogenic (PVS1 + PM2 + PP3). Segregation analysis revealed epilepsy or vestibular symptoms among female carriers, whereas male carriers were asymptomatic at last follow-up, suggesting possible sex-biased penetrance within the pedigree.
Conclusions
This pedigree supports Cav2.1 loss-of-function presenting with epilepsy, EA2, and FHM features plus BPPV. Within this family, clinical expression to date appears female-skewed while male carriers remained asymptomatic at last follow-up; this observation is hypothesis-generating. Mechanism-aware ASM selection and structured family counselling may aid management; larger cohorts and functional studies are needed.
Keywords: CACNA1A, Epilepsy, Episodic ataxia, Familial hemiplegic migraine, Benign paroxysmal positional vertigo, Sex-biased penetrance
Introduction
Epilepsy is a common and disabling neurological disorder that imposes a considerable personal and societal burden worldwide. Although its aetiology is multifactorial, genetics substantially contributes to disease risk and phenotypic expressivity. Yet, incomplete and context-dependent genotype–phenotype correlations often complicate diagnosis, prognostication, and treatment selection in suspected channelopathies [1–3].
Voltage-gated calcium channels (VGCCs) regulate neuronal excitability and synaptic transmission by controlling Ca²⁺ entry in an activity-dependent manner [1]. Structural or regulatory alterations that change gating properties can cause Ca²⁺ overload or deficiency, with downstream effects on neurotransmitter release, gene transcription, and intracellular signalling [4]. Such perturbations underpin the concept of “calcium channelopathies,” a mechanistic framework that links specific channel dysfunction to stereotyped but variably penetrant neuropsychiatric phenotypes [5].
CACNA1A encodes the α1A pore-forming subunit of the Cav2.1 P/Q-type channel (19p13), and pathogenic variants have classically been associated with familial hemiplegic migraine type 1 (FHM1; gain-of-function), episodic ataxia type 2 (EA2; loss-of-function), and spinocerebellar ataxia type 6 (SCA6; CAG-repeat expansion) [6]. Increasing clinical and molecular evidence indicates that CACNA1A-related disease extends beyond these canonical entities to include epilepsy, benign paroxysmal positional vertigo (BPPV), and cognitive impairment—thereby broadening the recognised spectrum of Cav2.1-mediated disorder [7].
Despite this expanding spectrum, epilepsy directly attributable to CACNA1A variants remains relatively uncommon, and the determinants of penetrance and expressivity—particularly potential sex-related effects—are insufficiently understood [8]. These uncertainties hinder precision counselling and tailored treatment, and they underscore the need for family-based studies that combine genetic, electroclinical, and phenotypic analyses to refine genotype–phenotype maps for Cav2.1 dysfunction [9].
Here, we report a three-generation family carrying a rare heterozygous frameshift variant in CACNA1A (c.5610del, p.His1871IlefsTer30). The female proband manifested focal epilepsy accompanied by EA2-like episodic ataxia and FHM-consistent migraine features, while additional female relatives exhibited epilepsy or BPPV; in contrast, male carriers were asymptomatic. This pedigree therefore suggests sex-biased penetrance of Cav2.1 loss-of-function. We outline the clinical, EEG, and genetic findings, discuss plausible mechanisms for sex-dependent expressivity, and consider implications for personalised therapy in calcium channelopathies.
Materials and methods
Clinical data source and phenotyping
We conducted a retrospective review of the proband’s medical records and performed structured family interviews and chart review across three generations. Extracted variables included age at onset, seizure semiology and frequency, neurological examination, comorbid paroxysmal symptoms (episodic ataxia and migraine features), electroencephalography (EEG) reports, neuroimaging where available, antiseizure medications (ASMs) and dosing regimens as documented, treatment response, and follow-up outcomes. Seizures were classified according to contemporary International League Against Epilepsy criteria. Written informed consent to participate was obtained from all participants. For participants younger than 16 years, written informed consent was obtained from their parents or legal guardians.
Clinical history was obtained using a clinician-administered structured family interview focused on epilepsy and cognition (Supplementary Materials), and global cognitive function was assessed using the Montreal Cognitive Assessment (MoCA) according to standard procedures [10].
EEG acquisition and interpretation
Long-term scalp video-electroencephalographic (EEG) monitoring was performed during the initial clinical evaluation using a digital EEG system (EEG-1200C; Nihon Kohden, Japan) with a 32-channel extended 10–20 electrode placement system, in accordance with standard clinical neurophysiological protocols. Recordings were obtained using bipolar, average reference (AV), and linked-ear reference montages. Technical parameters included a low-frequency filter of 0.53 Hz, a high-frequency filter of 70 Hz, a 50 Hz notch filter, a sensitivity of 10 µV/mm, a display speed of 30 mm/s, and a sampling rate of 2000 Hz.
Standard activation procedures, including eye opening and closure, hyperventilation, and intermittent photic stimulation, were performed during the recording session. No epileptiform abnormalities were elicited by these activation procedures.
EEG interpretation focused on background activity, interictal epileptiform discharges, and ictal patterns identified during video-EEG monitoring. Classification of clinical seizure events was based on synchronised review of EEG recordings and corresponding video data. All EEG recordings were independently reviewed by experienced clinical neurophysiologists.
Detailed EEG findings are presented in the Case Presentation section.
Genetic testing and variant interpretation
Trio whole-exome sequencing (WES) was performed for the proband and extended, where indicated, to additional relatives (13 tested in total). Variants were curated under HGVS nomenclature. The heterozygous CACNA1A frameshift c.5610del (p.His1871IlefsTer30) was identified in the proband and assessed by population databases and variant repositories (including gnomAD and ClinVar), with no prior record found. Pathogenicity was evaluated using ACMG/AMP criteria and classified as likely pathogenic based on predicted loss-of-function in a gene with established haploinsufficiency and supporting computational evidence (PVS1 + PM2 + PP3). Co-segregation within the family was assessed descriptively (see Case presentation).
Descriptive analyses
Family segregation was summarised narratively and in tabular/graphical form. Sex-stratified penetrance was estimated as the proportion of variant carriers exhibiting relevant phenotypes, with exact binomial 95% confidence intervals given the small sample size. No hypothesis-testing beyond descriptive statistics was planned.
Case presentation
Proband
The female proband developed focal seizures in August 2019, presenting with right-sided motor symptoms without impaired awareness. In addition, she reported pulsatile temporal headaches consistent with familial hemiplegic migraine (FHM) features and episodic ataxia compatible with the EA2 spectrum. Initial ASM trials included lamotrigine, which was ineffective. Following treatment optimisation, seizure control improved. Cognitive function was screened using the Montreal Cognitive Assessment (MoCA), which showed an increase in score from 21 to 26 during follow-up.
At the most recent follow-up (20 January 2025), her maintenance regimen consisted of levetiracetam 250 mg twice daily, lacosamide 50 mg twice daily, and acetazolamide 250 mg nightly, with sustained clinical benefit over the prior year and no new neurological deficits documented.
EEG findings
Electroencephalography demonstrated generalised, bilaterally synchronous spike-and-slow-wave discharges involving all scalp electrodes, with a consistent frontal predominance. Interictal epileptiform discharges were observed during wakefulness as paroxysmal spike-and-slow-wave complexes, occurring at an approximate frequency of 3–9 discharges per minute. Individual discharges had a duration of approximately 0.3–4.0 s and amplitudes of approximately 180–530 µV. Following treatment optimisation, the interictal epileptiform burden was reduced, as reflected by discharge frequencies of 0–3 discharges per minute, durations of 0.3–3.5 s, and amplitudes of approximately 70–450 µV (Fig. 1).
Fig. 1.
Representative interictal EEG recordings before and after treatment optimisation. a Background and interictal EEG in the waking state, showing generalised, bilaterally synchronous spike-and-slow-wave discharges with frontal predominance, occurring at a higher frequency and amplitude. b Background and interictal EEG after treatment in the waking state, showing only sparse generalized paroxysmal spike-and-slow-wave discharges of short duration, with reduced frequency compared to pretreatment
Genetic findings and segregation
Trio WES identified a heterozygous CACNA1A c.5610del (p.His1871IlefsTer30) frameshift variant in the proband. All family members were evaluated by a neurologist. Among 13 tested relatives across three generations, the variant segregated with paroxysmal phenotypes predominantly in females: several female carriers presented with epilepsy and/or benign paroxysmal positional vertigo (BPPV), whereas male carriers were asymptomatic at last contact. This pattern suggests sex-biased penetrance in the pedigree. The full pedigree (Fig. 2) and individual-level genotypes (Table 1) are provided.
Fig. 2.
Pedigree and sequencing results of the CACNA1A c.5610del family. a Three-generation pedigree. Orange half-filled symbols denote symptomatic individuals, blue half-filled symbols indicate asymptomatic carriers, and open symbols represent unaffected individuals. The proband is indicated by an arrow. het = heterozygous; wt = wild type; ND = not determined. b Sanger sequencing of family members. Red arrows mark the c.5610del variant site
Table 1.
Clinical phenotypes and genotypes for each family member
| Family member | Sex | Age | Relationship to proband | Main clinical phenotype | Variant status (CACNA1A c.5610del) |
|---|---|---|---|---|---|
| Ⅰ-1 | M | Not Available | Grandfather | Asymptomatic | Not Determined |
| Ⅰ-2 | F | 76 | Grandmother | Asymptomatic | Wild type |
| Ⅱ-1 | M | 44 | Father | Asymptomatic | Heterozygous |
| Ⅱ-2 | F | 41 | Mother | Asymptomatic | Wild type |
| Ⅱ-3 | F | 54 | Paternal eldest aunt | Paroxysmal vertigo with a sensation of rotation, aggravated by positional change | Heterozygous |
| Ⅱ-4 | F | 41 | Paternal second aunt | Paroxysmal vertigo with a sensation of rotation, aggravated by positional change | Heterozygous |
| Ⅱ-5 | M | 51 | Paternal uncle | Asymptomatic | Wild type |
| Ⅲ-1 | F | 14 | Proband | Episodic ataxia type 2; epilepsy; familial hemiplegic migraine | Heterozygous |
| Ⅲ-2 | M | 8 | Younger brother | Asymptomatic | Heterozygous |
| Ⅲ-3 | M | 31 | Eldest son of paternal eldest aunt | Asymptomatic | Wild type |
| Ⅲ-4 | F | 28 | Eldest daughter of paternal eldest aunt | Epilepsy; cognitive complaints | Heterozygous |
| Ⅲ-5 | M | 10 | Eldest son of paternal second aunt | Asymptomatic | Heterozygous |
| Ⅲ-6 | F | 17 | Eldest daughter of paternal second aunt | Paroxysmal vertigo with associated autonomic and motor symptoms | Heterozygous |
| Ⅲ-7 | M | 21 | Eldest son of paternal uncle | Asymptomatic | Wild type |
Results
Genetic findings
Whole-exome sequencing identified a heterozygous frameshift variant in CACNA1A, c.5610del (p.His1871IlefsTer30), which introduces a premature stop codon. The variant was confirmed by Sanger sequencing, absent from gnomAD/ClinVar, and classified as pathogenic per ACMG/AMP criteria (PVS1 + PM2 + PP3). Sequencing metrics achieved average depth > 100× with > 98% target coverage.
Family segregation and sex-biased penetrance
Across three generations, 13 relatives underwent genetic testing, and the CACNA1A c.5610del variant showed a clear sex-skewed pattern of clinical expression. Among the eight heterozygous carriers identified, all five female carriers (II-3, II-4, III-1, III-4, and III-6) manifested epilepsy and/or benign paroxysmal positional vertigo (BPPV) (penetrance 100%, 95% CI 47.8–100%), whereas the three male carriers (II-1, III-2, and III-5) were asymptomatic at last contact (penetrance 0%, 95% CI 0–70.8%). Penetrance was estimated using exact binomial (Clopper–Pearson) 95% confidence intervals, and no hypothesis testing was performed given the limited sample size. This segregation pattern supports a female-biased (potentially female-limited) penetrance in this pedigree. Individual genotypes and the pedigree are summarized in Table 1; Fig. 2.
Clinical course and current status of the proband
At the latest follow-up (20 January 2025), maintenance therapy (levetiracetam 250 mg twice daily + lacosamide 50 mg twice daily + acetazolamide 250 mg nightly) was associated with one seizure and four FHM-like attacks in the preceding year and clinically observed cognitive improvement; lamotrigine had been ineffective earlier in the course. Cognitive function was screened using the Montreal Cognitive Assessment (MoCA), with scores increasing from 21 to 26 points, suggesting improvement on this screening measure. In the absence of more extensive longitudinal neuropsychological testing, this improvement should be interpreted cautiously.
Discussion
Principal observations
We report a three-generation pedigree harbouring a heterozygous frameshift in CACNA1A (c.5610del; p.His1871IlefsTer30), in which clinical expression to date appears female-skewed. Several female carriers exhibited epilepsy or BPPV, whereas male carriers were asymptomatic at last follow-up, suggesting a possible sex-biased penetrance in this pedigree. Notably, the youngest male carrier is 8 years old, and we cannot exclude the possibility that he may develop clinical manifestations with age. The proband presented with focal epilepsy accompanied by EA2-like episodic ataxia and FHM-consistent migraine features; several female carriers exhibited epilepsy and/or BPPV, whereas male carriers were asymptomatic. EEG demonstrated generalised spike–slow-wave activity during myoclonic events and a reduction of interictal epileptiform burden after treatment optimisation, aligning the electroclinical picture with a Cav2.1-related network disorder [11]. Clinically, acetazolamide (commonly effective in EA2) together with levetiracetam and lacosamide was associated with sustained benefit, while lamotrigine was ineffective earlier in the course [6].
Genotype–phenotype correlations and mechanistic plausibility
Truncating CACNA1A variants generally imply loss-of-function (LoF) and haploinsufficiency of the presynaptic Cav2.1 (P/Q-type) channel. The present frameshift introduces a premature termination codon within the distal C-terminus, plausibly triggering nonsense-mediated mRNA decay or yielding a non-functional truncated channel [12]. Reduced Cav2.1 availability is expected to depress presynaptic Ca²⁺ influx and alter neurotransmitter release probability, perturbing cerebello-thalamo-cortical and vestibulo-cerebellar loops. This offers a unifying substrate for the triad of ataxia–migraine–epilepsy, and is also compatible with BPPV-like phenotypes via vestibular network vulnerability [13]. The observed generalised spike–wave discharges fit with established roles of P/Q-type channels in thalamocortical oscillations, where channel dysfunction can bias networks toward hypersynchrony [14].
Sex-biased penetrance: working hypotheses
In this pedigree, we observed that clinical expression has thus far been confined to female carriers, while male carriers identified in the segregation analysis were asymptomatic at last follow-up. We emphasize that this is an observational, within-family pattern that does not establish causality; age-dependent penetrance, incomplete penetrance in males, and family-specific genetic or environmental modifiers remain plausible explanations. Several non-exclusive mechanisms merit consideration:
Hormonal modulation—oestrogen and progesterone influence synaptic excitability, GABA/glutamate balance, and Ca²⁺ channel function; cyclical or life-stage–linked hormonal states may lower the threshold for phenotype expression in female carriers [15].
Genomic/epigenomic modifiers—autosomal or X-linked variants, imprinting, or methylation differences could shift penetrance [3].
Network compensation—sex-specific developmental trajectories and cerebellar–cortical plasticity might differentially buffer Cav2.1 LoF [3].
Overall, our data do not adjudicate among these possibilities and should be interpreted cautiously. The observed sex-skew in this pedigree is hypothesis-generating and may be influenced by age structure and ascertainment. Larger cohorts, longitudinal follow-up of currently asymptomatic carriers, and integration of endocrine and genetic-modifier data will be required to evaluate whether true sex-related modifiers operate in CACNA1A loss-of-function disorders [16].
Therapeutic considerations
The proband’s improvement on acetazolamide supports its continued consideration when EA2-spectrum features coexist with epilepsy or migraine in CACNA1A LoF; contemporary reviews and trial data support benefit in EA2, albeit with variable response and side effects [6]. Levetiracetam and lacosamide were compatible with seizure control in this context; lamotrigine proved ineffective here, but single-case response should not be over-generalised. In practice, phenotype-guided regimens remain prudent: targeting migraine, addressing ataxia (e.g., carbonic anhydrase inhibition), and optimising ASM choice while monitoring for inter-phenotype trade-offs. Longitudinal EEG and harmonised outcome measures are promising as biomarkers for CACNA1A trials and care pathways [17].
Clinical and counselling implications
This pedigree underscores the value of family-wide genotyping for counselling around incomplete, sex-biased penetrance, anticipating variable expressivity (epilepsy, ataxia, migraine, vestibular symptoms), and planning life-stage–aware follow-up for female carriers [3, 7, 11, 12, 17]. From a diagnostic perspective, the coexistence of EA2-like episodes and migraine in a patient with epilepsy should raise the pre-test probability of CACNA1A involvement, particularly when EEG suggests generalised spike–wave activity and when there is a family history of paroxysmal disorders [3, 7, 11, 12].
Limitations
As a single pedigree, our inference about sex bias is hypothesis-generating. Given the small n, these sex-stratified estimates should be interpreted descriptively with wide exact-binomial CIs.
Future directions
Functional characterisation of p.His1871IlefsTer30 (channel currents, trafficking, coupling to release) and patient-derived neuronal models will be informative. Prospective, sex-stratified registries with longitudinal EEG and endocrine metadata could clarify modifier landscapes. Finally, systematic trials of mechanism-aligned therapies (e.g., acetazolamide, potassium channel modulators, cerebellar-targeted approaches) in CACNA1A LoF warrant exploration.
Conclusion
This pedigree with CACNA1A c.5610del expands the spectrum of Cav2.1-related disease to include epilepsy with EA2/FHM features and BPPV. Within this family, clinical expression to date appears female-skewed, while male carriers were asymptomatic at last follow-up. This observation should be considered hypothesis-generating, and larger sex-stratified cohorts and functional studies will be needed to clarify the determinants of penetrance and potential sex-related modifiers. A mechanism-aware approach to ASM selection and structured family counselling may improve outcomes in similar channelopathies.
Acknowledgements
We gratefully acknowledge Shenzhen Aegicare Medical Laboratory for their support in performing genetic testing.
Authors’ contributions
J.Y. and Z.L. conceived the study and performed the case analysis. S.G. and Z.L. drafted the manuscript. D.J. assisted with data analysis and literature review. X.G. provided guidance on the genetic aspects of the study. X.Y., J.Y., and L.S. led the manuscript revision with critical input from all major authors. All authors read and approved of the final manuscript.
Funding
This work was supported by the National Natural Science Foundation of China (grant number 82271492).
Data availability
The datasets generated and analysed during the current study are available in the NCBI Sequence Read Archive (SRA) repository under BioProject accession number PRJNA1434109: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1434109. The data will be made publicly available upon publication. Prior to publication, de-identified data are available from the corresponding author on reasonable request.
Declarations
Ethics approval and consent to participate
This study was conducted in accordance with the Declaration of Helsinki and was approved by the Ethics Committee of Guangdong Provincial Hospital of Chinese Medicine (Approval No. G2025-23). Written informed consent to participate was obtained from all participants. For participants younger than 16 years, written informed consent was obtained from their parents or legal guardians.
Consent for publication
Written informed consent for publication of personal and clinical details, along with any potentially identifying images including pedigree information, was obtained from all participants/patients. For participants under 18 years of age, written informed consent was obtained from their parents or legal guardians.
Competing interests
The authors declare no competing interests.
Footnotes
Publisher’s note
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Contributor Information
Lisen Sui, Email: 13711580891@163.com.
Xiaofeng Yang, Email: xiaofengyang@yahoo.com.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The datasets generated and analysed during the current study are available in the NCBI Sequence Read Archive (SRA) repository under BioProject accession number PRJNA1434109: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1434109. The data will be made publicly available upon publication. Prior to publication, de-identified data are available from the corresponding author on reasonable request.