Seizures affected children with SYNGAP1-ID (n = 11; 84.6%) more frequently than the ID-comparison group (n = 2; 7.6%, p =  < 0.001), most commonly absence seizures (n = 8; 72.7%) and atonic seizures (n = 3; 23.1%). Here, SYNGAP1 is linked to juvenile absence epilepsy.