Biallelic structural variations within <i>FGF12</i> detected by long-read sequencing in epilepsy

We discovered biallelic intragenic structural variations (SVs) in <i>FGF12</i> by applying long-read whole genome sequencing to an exome-negative patient with developmental and epileptic encephalopathy (DEE). We also found another DEE patient carrying a biallelic (homozygous) single-nucleotide variant (SNV) in <i>FGF12</i> that was detected by exome sequencing. <i>FGF12</i> heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of <i>FGF12</i> are known causes of epilepsy, but biallelic SNVs/SVs have never been described. <i>FGF12</i> encodes intracellular proteins interacting with the C-terminal domain of the alpha subunit of voltage-gated sodium channels 1.2, 1.5, and 1.6, promoting excitability by delaying fast inactivation of the channels. To validate the molecular pathomechanisms of these biallelic <i>FGF12</i> SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and <i>Drosophila</i> in vivo functional analysis of the SNV were performed, confirming loss-of-function. Our study highlights the importance of small SVs in Mendelian disorders, which may be overlooked by exome sequencing but can be detected efficiently by long-read whole genome sequencing, providing new insights into the pathomechanisms of human diseases.