Long‐read sequencing of recurrent FGF12 duplications in epilepsy: Insights into structural mechanisms and aberrant isoforms

Abstract Objective Fibroblast growth factor 12 ( FGF12 ), a member of the fibroblast homologous factor family, plays a key role in the modulation of voltage‐gated sodium (Nav) channels. Pathogenic variants in the FGF12 gene leading to a gain‐of‐function mechanism and partial duplication encompassing the FGF12 gene leading to a loss‐of‐function mechanism are associated with developmental and epileptic encephalopathy (DEE), characterized by developmental delay, intellectual disability, ataxia, and drug‐resistant epilepsy. We report two patients with DEE harboring de novo recurrent intragenic duplications of FGF12 identified by long‐read sequencing (LRS). Methods We applied LRS to the DNA and cDNA of patients with FGF12 duplication to fully characterize the DNA's structural organization and its transcriptional consequences. Additionally, we reanalyzed electroencephalographic (EEG) data from patients at different timepoints to identify phenotypical specificities and refine the electroclinical spectrum. Results These duplications, spanning approximately 536 kbp, were mediated by nonallelic homologous recombination between L1PA2 elements (LINE‐1 Primate‐specific subfamily A, number 2). cDNA analysis revealed aberrant transcripts, one predicted to encode an elongated FGF12 protein and another leading to premature termination. Both patients shared overlapping clinical features, including postepilepsy onset regression, global developmental delay, and ataxia. EEG studies revealed a marked early encephalopathic pattern with disorganized and high‐voltage slow background activity with multifocal spikes at onset evolving later into subcontinuous generalized spike and wave activation. Significance Our findings are consistent with previous reports linking structural variants to functional disruption, suggesting impaired Nav channel activity due to a shift in inactivation to hyperpolarized potential, leading to a loss‐of‐function effect. These findings underscore the utility of LRS for DNA and cDNA analysis in resolving structural variants and expanding the electroclinical spectrum of patients with FGF12 duplications.