Pérez‐Palma, Eduardo

Abstract Epilepsy affects more than 50 million individuals globally and has a substantial genetic component that remains to be completely understood. Traditional studies have focused on severe, early onset cases enrolled through clinical or research settings. Recent biobank‐based approaches, leveraging large‐scale population datasets, offer opportunities to explore genetic associations in broader epilepsy phenotypes, including milder, later onset forms. We analyzed data from more than 750 000 individuals across the UK Biobank, All of Us, and Massachusetts General Brigham Biobank, including 20 026 individuals with epilepsy. Rare coding variant burden testing revealed a significant association with LGI1 , a known epilepsy gene. Among the other top 10 associated genes, seven had prior evidence linking them to epilepsy ( GABRG2 , ATP1A3 ), neurological disorders with comorbid seizures ( HTRA2 , KRIT1 , STAG1 ), possible involvement in seizure phenotypes ( ADAM23 ), or roles in neuronal function ( PDCD4 ). Thus, we provide the first statistical evidence for ADAM23 as a candidate gene for epilepsy, based on the suggestive association signal combined with prior biological evidence from both animal (canine and murine) and one recent human epilepsy case study, potentially contributing to human epilepsy through its direct interaction with LGI1 . Phenome‐wide analyses highlighted the pleiotropic effects of epilepsy genes, with LGI1 and ADAM23 predominantly associated with epilepsy, whereas other genes such as KRIT1 , TSC1 , and TSC2 exhibited broader systemic involvement. Our study shows the potential of population‐scale genomic data and suggests that integrating these datasets with deep phenotyping will uncover more novel insights into epilepsy genetics in the future.

Abstract Rare Mendelian disorders affect 300-400 million people globally. Although genetic testing has become widely adopted, gene-specific evidence for tailored variant interpretation remains scattered across resources. We present Gene Portals, a framework for gene-centered multimodal knowledge bases that co-localize expert-harmonized clinical data, functional assays, population variation, structural annotations and gene-specific ACMG/AMP specifications within a single resource. A modular interface integrates this unified evidence with VCEP-refined ACMG specifications to enable automated gene-specific variant classification, infer molecular mechanisms, and support cross-gene analyses. We demonstrate the framework’s utility across five Gene portals spanning eleven neurodevelopmental disorder-associated genes, integrating data from 4,423 individuals with 2,838 unique variants, 36,149 ClinVar submissions, and 1,044 expert-curated molecular readouts. By organizing evidence that is otherwise dispersed across multiple sources into a unified, queryable framework, the SCN, GRIN, CACNA1A, SATB2 and SLC6A1 Gene Portals became widely used community resources and provide an extensible template for standardized rare-disease variant interpretation and mechanism-aware discovery.

Abstract Background The majority of missense variants in clinical genetic tests are classified as variants of uncertain significance. Prior research has shown that the deleterious effects and the subsequent molecular consequence of variants are often conserved among paralogous protein sequences within a gene family. Here, we systematically quantified on an exome-wide scale if the existence of pathogenic variants in paralogous genes at a conserved position could serve as evidence for the pathogenicity of a new variant. For the gene family of voltage-gated sodium channels where variants and expert-curated clinical phenotypes were available, we also assessed whether phenotype patterns of multiple disorders for each gene were also conserved across variant positions within the gene family. Methods We developed a framework that assesses the presence of pathogenic missense variants located in conserved residues across paralogous genes. We systematically mapped 2.5 million pathogenic and general population variants from the ClinVar, HGMD, and gnomAD databases onto a total of 9,990 genes and aligned them by gene families. We evaluated the quantity of classifiable amino acids by utilizing pathogenic variants identified in databases alone and then compared this assessment to the inclusion of paralogous pathogenic variants. We validated and quantified the evidence of conserved pathogenic paralogous variants in variant pathogenicity classification. Results Considering conserved pathogenic variants in paralogous genes, increased the number of classifiable variants 2.8-fold across the exome, compared to pathogenic variants in the gene of interest alone. The presence of a pathogenic variant in a paralogous gene is associated with a positive likelihood ratio of 8.32 for variant pathogenicity. The likelihood ratio was gene family-specific. Across ten genes encoding voltage-gated sodium channels and 22 expert-curated disorders, we identified cross-paralog correlated phenotypes based on 3D structure spatial position. For example, the established loss-of-function disorders SCN1A-associated Dravet syndrome, SCN2A-associated autism, SCN5A-associated Brugarda Syndrome, and SCN8A-associated neurodevelopmental disorder without seizures were correlated in their spatial variant position on structure. Finally, we show that phenotype integration in paralog variant selection improves variant classification. Conclusion Our results show that paralogous variants, in particular with phenotype information can enhance our understanding of variant effects.

Abstract Brain voltage-gated sodium channel NaV1.1 (SCN1A) loss-of-function variants cause the severe epilepsy Dravet syndrome, as well as milder phenotypes associated with genetic epilepsy with febrile seizures plus. Gain of function SCN1A variants are associated with familial hemiplegic migraine type 3. Novel SCN1A-related phenotypes have been described including early infantile developmental and epileptic encephalopathy with movement disorder, and more recently neonatal presentations with arthrogryposis. Here we describe the clinical, genetic and functional evaluation of affected individuals. Thirty-five patients were ascertained via an international collaborative network using a structured clinical questionnaire and from the literature. We performed whole-cell voltage-clamp electrophysiological recordings comparing sodium channels containing wild-type versus variant NaV1.1 subunits. Findings were related to Dravet syndrome and familial hemiplegic migraine type 3 variants. We identified three distinct clinical presentations differing by age at onset and presence of arthrogryposis and/or movement disorder. The most severely affected infants (n = 13) presented with congenital arthrogryposis, neonatal onset epilepsy in the first 3 days of life, tonic seizures and apnoeas, accompanied by a significant movement disorder and profound intellectual disability. Twenty-one patients presented later, between 2 weeks and 3 months of age, with a severe early infantile developmental and epileptic encephalopathy and a movement disorder. One patient presented after 3 months with developmental and epileptic encephalopathy only. Associated SCN1A variants cluster in regions of channel inactivation associated with gain of function, different to Dravet syndrome variants (odds ratio = 17.8; confidence interval = 5.4–69.3; P = 1.3 × 10−7). Functional studies of both epilepsy and familial hemiplegic migraine type 3 variants reveal alterations of gating properties in keeping with neuronal hyperexcitability. While epilepsy variants result in a moderate increase in action current amplitude consistent with mild gain of function, familial hemiplegic migraine type 3 variants induce a larger effect on gating properties, in particular the increase of persistent current, resulting in a large increase of action current amplitude, consistent with stronger gain of function. Clinically, 13 out of 16 (81%) gain of function variants were associated with a reduction in seizures in response to sodium channel blocker treatment (carbamazepine, oxcarbazepine, phenytoin, lamotrigine or lacosamide) without evidence of symptom exacerbation. Our study expands the spectrum of gain of function SCN1A-related epilepsy phenotypes, defines key clinical features, provides novel insights into the underlying disease mechanisms between SCN1A-related epilepsy and familial hemiplegic migraine type 3, and identifies sodium channel blockers as potentially efficacious therapies. Gain of function disease should be considered in early onset epilepsies with a pathogenic SCN1A variant and non-Dravet syndrome phenotype.