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Background  Epilepsy is a heterogeneous disease with a broad phenotypic spectrum and diverse genotypes. A significant proportion of epilepsies has a genetic aetiology.  In our study, a custom designed gene panel with 112 genes known to be associated with epilepsies was used. In total, one hundred and fifty-one patients were tested (86 males / 65 females).    Results  In our cohort, the highest probability for the identification of the cause of the disease was for patients with a seizure onset within the first four weeks of life (61.9% clarification rate) – about two times more than other groups. The level of statistical significance was determined using a chi-square analysis.  From 112 genes included in the panel, suspicious and rare variants were found in 53 genes (47.3%).  Among the 151 probands included in the study we identified pathogenic variants in 39 patients (25.8%), likely pathogenic variants in three patients (2%), variants of uncertain significance in 40 patients (26.5%) and likely benign variants in 69 patients (45.7%).    Conclusion  Our report shows the utility of diagnostic genetic testing of severe childhood epilepsies in a large cohort of patients with a diagnostic rate of 25.8%. A gene panel can be considered as a method of choice for the detection of pathogenic variants within patients with unknown origin of early onset severe epilepsy.    Electronic supplementary material  The online version of this article (10.1186/s13023-018-0812-8) contains supplementary material, which is available to authorized users.

Detection rate of causal variants in severe childhood epilepsy is highest in patients with seizure onset within the first four weeks of life