Clinical and molecular characterisation of KCNT1-related severe early onset epilepsy

Objective: To characterise the phenotypic spectrum, molecular genetic findings and\ud functional consequences of pathogenic variants in early onset KCNT1-epilepsy.\ud Methods: We identified a cohort of 31 patients with epilepsy of infancy with\ud migrating focal seizures (EIMFS) and screened for variants in KCNT1 using direct\ud Sanger sequencing, a multiple gene next generation sequencing panel and whole\ud exome sequencing. Additional patients with non-EIMFS early onset epilepsy in\ud whom we identified KCNT1 variants on local diagnostic multiple gene panel testing\ud were also included. Where possible, we performed homology modelling to predict\ud putative effects of variants on protein structure and function. We undertook\ud electrophysiological assessment of mutant KCNT1 channels in a Xenopus oocyte\ud model system.\ud Results: We identified pathogenic variants in KCNT1 in 12 patients, four of which\ud are novel. Most variants occurred de novo. Ten had a clinical diagnosis of EIMFS\ud and the other two presented with early onset severe nocturnal frontal lobe seizures.\ud Three patients had a trial of quinidine with good clinical response in one.\ud Computational modelling analysis implicates abnormal pore function (F346L) and\ud impaired tetramer formation (F502V) as putative disease mechanisms. All evaluated\ud KCNT1 variants resulted in marked gain-of-function, with significantly increased\ud channel amplitude and variable blockade by quinidine.\ud Conclusions: Gain-of-function KCNT1 pathogenic variants cause a spectrum of\ud severe focal epilepsies with onset in early infancy. Currently, genotype-phenotype\ud correlations are unclear, though clinical outcome is poor for the majority of cases.\ud Further elucidation of disease mechanisms may facilitate the development of\ud targeted treatments, much needed for this pharmacoresistant genetic epilepsy.