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SCN9A should not be considered an epilepsy gene; Refuting a gene–disease association

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dc.contributor.authorGhanty, Ismael
dc.contributor.authorPerez-Palma, Eduardo
dc.contributor.authorVillaman, Camilo
dc.contributor.authorStobo, Daniel
dc.contributor.authorSymonds, Joseph
dc.contributor.authorZuberi, Sameer
dc.contributor.authorLal, Dennis
dc.contributor.authorBrunklaus, Andreas
dc.date.accessioned2026-09-08T12:53:56Z
dc.date.available2026-09-08T12:53:56Z
dc.date.issued2026
dc.description.abstractObjective The SCN9A gene is primarily expressed in nociceptive pathways within the peripheral nervous system, and pathogenic variants are associated with human pain disorders. In recent years, several studies have proposed SCN9A as a monogenic cause of epilepsy. Our objective was to critically appraise the SCN9A–epilepsy gene–disease relationship. Methods We assessed “epilepsy-associated” SCN9A variants from four sources: (1) the literature up to December 2023 (n = 27), (2) epilepsy patients referred for genetic testing at a regional service in Glasgow, UK over a 5-year period (n = 30), (3) the Human Genetics Mutation Database (n = 25), and (4) ClinVar (n = 1546). The latter two are genome-wide variant databases, accepting submissions from genetic laboratories and research groups. We checked whether each SCN9A variant is present in the Genome Aggregation Database (gnomAD) V4 (a reference population database for variant interpretation), and classified its pathogenicity based on the American College of Molecular Genetics and Genomics/Association of Molecular Pathologists guidelines. Results Only three SCN9A variants were classified as “likely pathogenic,” of which two were identified in healthy individuals in gnomAD. A total of 1540 of the 1546 SCN9A variants in ClinVar labeled as being associated with epilepsy were also reported in association with hereditary sensory and autonomic neuropathy. No further clinical data were provided in 1482 of these submissions. Significance There is no convincing genetic evidence to support SCN9A as a causative epilepsy gene. As such, the inclusion of SCN9A in epilepsy genetic testing panels should be reassessed. Research centers and genetic testing laboratories should be rigorous and consistent in their submissions to variant databases.
dc.description.versionVersión publicada
dc.format.extent12 p.
dc.identifier.citationGhanty I, Perez-Palma E, Villaman C, Stobo D, Symonds J, Zuberi S, et al. SCN9A should not be considered an epilepsy gene; Refuting a gene–disease association. Epilepsia. 2025; 66: 3516–3527. https://doi.org/10.1111/epi.18474
dc.identifier.doihttps://doi.org/10.1111/epi.18474
dc.identifier.urihttps://hdl.handle.net/11447/11080
dc.language.isoen
dc.subjectFebrile seizures
dc.subjectGEFS+
dc.subjectGenetic epilepsy
dc.subjectSCN9A
dc.subjectSodium channels
dc.titleSCN9A should not be considered an epilepsy gene; Refuting a gene–disease association
dc.typeArticle
dcterms.accessRightsAcceso abierto
dcterms.sourceEpilepsia
dspace.entity.typePublication

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