A Novel CFA3 Locus Encompassing KCNIP4 Is Associated with Idiopathic Epilepsy in Siberian Huskies

Background/Objectives: Idiopathic epilepsy is a lifelong neurologic disorder in dogs, but its genetic basis remains incompletely understood in many breeds. This study aimed to identify risk-associated markers in Siberian Huskies, quantify their effects, assess potential risk modifiers, and characterize the shared haplotype background of the associated signal. Methods: A genome-wide association study was conducted in 113 Siberian Huskies genotyped on the Illumina CanineHD array, integrating association, regression, and haplotype/IBD analyses. An independent follow-up cohort of 57 additional dogs was genotyped at the lead marker by Sanger sequencing. Sex and gonadectomy status/timing were also evaluated as potential modifiers of risk, using multivariable regression and time-to-event analyses. Results: A strong, localized association was identified on canine chromosome 3 (CFA3) within KCNIP4. The lead intronic marker was significantly enriched in cases, with all risk-allele homozygotes affected, most heterozygotes affected, and no control homozygotes observed. Risk-associated chromosomes shared extended haplotypes across the region, consistent with carriers inheriting a common risk haplotype from a relatively recent shared ancestor. Among carriers, male sex was associated with higher odds of epilepsy and earlier seizure onset, with more tentative evidence for a similar association with gonadectomy before 5 years of age. Conclusions: These findings prioritize a CFA3 region encompassing KCNIP4 as a major risk locus for idiopathic epilepsy in Siberian Huskies. Fine-mapping with high-coverage sequencing and functional follow-up will be required to pinpoint the causal variant(s) and support development of risk assessment tools. Until those studies are completed, this marker should be regarded as a research finding rather than a predictive test.