Sleep Duration and Epilepsy Risk: Mendelian Randomization and Functional Validation of CACNA1A rs2228130-Related Inhibitory Synaptic Dysfunction.

Objectives To evaluate the causal association between sleep traits and epilepsy risk using Mendelian randomization, and to investigate the mechanism of a prioritized epilepsy-risk variant through gene-level enrichment analysis and functional validation. Methods Large-scale European GWAS datasets were analysed using multiple Mendelian randomization methods, including inverse variance weighted, MR-Egger and weighted median models, with heterogeneity and sensitivity analyses. Epilepsy-associated loci were mapped to protein-coding genes and flanking regions based on GRCh37 annotation, and primary and sensitivity-analysis gene sets were constructed from gene-level summary results for functional enrichment analysis. Guided by locus-level prioritization and the biological plausibility of CACNA1A, rs2228130 was selected for functional validation in CRISPR-ABE-edited human iPSC and knock-in mouse models to assess inhibitory synaptic transmission, sleep-related phenotypes and seizure susceptibility. Results Longer sleep duration was significantly associated with lower epilepsy risk (OR = 0.9937, p < 1 × 10⁻⁵), supporting a protective genetic causal association. The association between insomnia and epilepsy showed substantial heterogeneity (Q = 9352.91) and should be interpreted cautiously. Gene-level enrichment analysis indicated that epilepsy-associated candidate genes converged primarily on broad biological regulation, developmental processes and multicellular organismal processes, without stable dominant enrichment of GABAergic synapse or circadian rhythm pathways. Functional validation showed that rs2228130 did not affect neuronal differentiation but impaired inhibitory synaptic transmission, accompanied by abnormal network activity, altered sleep-related phenotypes and increased seizure susceptibility. Knock-in mice exhibited more frequent epileptiform discharges, reduced non-rapid eye movement sleep, decreased slow-wave activity and altered expression of rhythm-related genes. Pharmacological and sleep-related interventions partially ameliorated these abnormalities. Significance This study supports a protective genetic causal association between longer sleep duration and lower epilepsy risk, and suggests that epilepsy-related genetic risk converges primarily on broad functional networks. Within this framework, functional validation of CACNA1A rs2228130 identifies inhibitory synaptic dysfunction as a key mechanistic node linking genetic risk to sleep- and epilepsy-related phenotypes, providing a rationale for epilepsy prevention and treatment through sleep optimization and targeted modulation of critical downstream pathways. Plain Language Summary We used large-scale genetic data and experimental models to examine how sleep is related to epilepsy. Genetic evidence showed that longer sleep duration was associated with lower epilepsy risk. Although broad gene-level analyses did not identify a stable dominant signal for GABAergic synapse or circadian rhythm pathways, functional studies of the epilepsy-risk variant CACNA1A rs2228130 showed that it disrupted inhibitory synaptic transmission, altered sleep-related phenotypes and increased seizure susceptibility. In mouse models, drug treatment and sleep-related intervention partly improved these abnormalities, suggesting that sleep optimization and targeted downstream regulation may help reduce epilepsy risk.