Variants in SBF1, CELSR2, and TENM1 are associated with childhood epileptic encephalopathies

Epileptic encephalopathy is a common devastating epilepsy with etiologies remain largely elusive, despite application of whole gene/exon sequencing on large cohorts. This study targeted on childhood epileptic encephalopathy, typically Lennox-Gastaut syndrome that is featured by age-dependent onset and characteristic clinical manifestations. Trio-based whole-exome sequencing with individualized analysis before statistic studies was employed, including individualized analysis on each trio by explainable inheritance origin and stratified frequency filtration and on each gene from four aspects. This study identified three novel candidate genes in 235 patients, including SBF1 with de novo variants in three cases, CELSR2 with biallelic recessive variants in eight cases, and TENM1 with X-linked recessive variants in six cases. These genes presented significant repetitiveness, including significant higher excess of de novo variants in SBF1 and excess of biallelic variants in CELSR2 , and aggregated frequencies of variants in SBF1 , CELSR2 , and TENM1 . The frequency of compound heterozygous/homozygous CELSR2 variants in the cases was significantly higher than that in the asymptomatic parent-controls. Further experiments with knock-down/knock-out of these genes showed increased seizure-like behavior and increased firing of excitatory neurons. This study highlights the implication of phenotype sub-classification, individualized analysis in combination with statistic studies, and use of controls for compound heterozygous variants. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the National Natural Science Foundation of China (grant Nos. 82171439, 82271505, and 81971216), and Guangdong Basic and Applied Basic Research Foundation (grant No. 2021A1515010986). The funders had no role in study design, data collection, and analysis, or in the decision to publish or the preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All procedures performed were in accordance with the ethical standards of the institutional committee. Ethical approval was approved by the ethics committee of the Second Affiliated Hospital of Guangzhou Medical University (approval ethics number 2020-hs-49). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors