By integrating WES with radiologic and histopathologic data, we identified brain pathogenic somatic variants in the following, already well-established lesional epilepsy genes of the PI3K-AKT-mTOR axis: MTOR (in patient 3 with HMEG), PIK3CA (in patient 4 with focal megalencephaly), and TSC2 (in patient 5 with FCD), highlighting their role in focal cortical dysplasia and in other epilepsy-related malformations. Here, AKT1 is linked to epilepsy.