Biallelic structural variations within<i>FGF12</i>detected by long-read sequencing in epilepsy
Sachiko Ohori, Akihiko Miyauchi, Hitoshi Osaka, Charles Marques Lourenço, Naohiro Arakaki, Toru Sengoku, Kazuhiro Ogata, Rachel Sayuri Honjo, Chong Ae Kim, Satomi Mitsuhashi, Martin C. Frith, Rie Seyama, Naomi Tsuchida, Yuri Uchiyama, Eriko Koshimizu, Kohei Hamanaka, Kazuharu Misawa, Satoko Miyatake, Takeshi Mizuguchi, Kuniaki Saito, Atsushi Fujita, Naomichi Matsumoto
Abstract
We discovered biallelic intragenic structural variations (SVs) in FGF12 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 FGF12 that was detected by exome sequencing. FGF12 heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of FGF12 are known causes of epilepsy, but biallelic SNVs/SVs have never been described. FGF12 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 FGF12 SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and Drosophila 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.