Pathogenic Epilepsy Gene Variant Prevalence and Penetrance Among U.S. Military Veterans in the Million Veteran Program Cohort

Background and Objectives: Genetic causes of epilepsy are well-established in children, but the genetics of adult-onset epilepsy is not well understood. There are few studies of epilepsy genetics in older adults, U.S. military Veterans, and people with acquired causes of epilepsy like traumatic brain injury (TBI) and stroke. To test if rare gene variants that cause pediatric epilepsy are associated with adult-onset epilepsy, we determined the prevalence of pathogenic germline variants (PGVs) in epilepsy-associated genes in an ancestrally diverse cohort of older Veterans and examined the penetrance of epilepsy among PGV carriers. We evaluated the effect of mode of inheritance (MOI), variant selection, single gene-level factors, and gene-disease relationship validity on prevalence and penetrance estimates. Methods: This retrospective cohort study used electronic health record (EHR) data from Veterans enrolled in the Million Veteran Program (MVP) biobank who had whole genome sequencing (WGS) data available. We identified Veterans with one or more rare (variant allele frequency [VAF] <0.01) pathogenic/likely pathogenic single nucleotide variants (SNVs) within one or more of 165 expert-curated epilepsy genes. Epilepsy phenotype was defined using a validated algorithm, and penetrance estimates were calculated using Bayes theorem and compared to civilian cohorts. Results: There were 102,624 MVP participants with WGS data. Mean age at censorship or death was 74.6 years, 6.1% were female and 6.3% had epilepsy. Among participants, 1.9% (n=1,955) carried at least 1 rare PGVs and 1.0% (n=1,041) carried ultrarare PGVs. Most carriers of autosomal dominant (AD) PGVs (89.7%) were not diagnosed with epilepsy, though carriers of both AD and autosomal recessive (AR) ultrarare PGVs had increased odds of epilepsy (odds ratios of 1.72 and 1.45, respectively) compared to non-carriers. Penetrance estimates were low for AD PGVs (8.2%), but similar to estimates from civilian biobanks. Discussion: Veterans carrying PGVs in AD-labeled epilepsy genes had increased risk for epilepsy, but only 10.3% were diagnosed. Unexpectedly, Veterans heterozygous for AR-labeled PGVs also had increased risk of epilepsy. Potential reasons for this include latent compound heterozygosity, misclassification of variant pathogenicity or gene MOI, or the possibility that PGVs in AR genes may be risk alleles for adult-onset epilepsy.