<p>Brain disorders caused by large effect mutations in single genes often present unexplained large symptom diversity, even among carriers of the same mutation. Here we examined genetic interactions as a possible explanation for this diversity for SNAREopathies, a group of common neurodevelopmental disorders caused by de novo genetic variation in genes that together drive secretion of chemical signals in the brain. SNAREopathies are characterized by a striking phenotypic diversity, including different types/degrees or absence of seizures, developmental delay and intellectual disability. Here, we test the hypothesis that large phenotypic diversity is caused by non-linear genetic interactions between two or more functionally related genes by combining validated SNAREopathy mouse models and comparing phenotypic diversity between single and double mutants at the synaptic, network, system and behavioral level. Single <i>Stxbp1</i> and <i>Snap25</i> mutant animals showed EEG- and motor abnormalities, but no seizures, as reported before. In contrast, double mutants exhibited extreme diversity in seizure phenotypes. Some mice had lethal generalized seizures, frequent and complex epileptiform EEG activity and thalamic hyper-excitability as indicated by increased cFos staining, while other mice of the same genotype showed no detectable abnormalities, no increased cFos staining and a normal life span. The surviving double mutant mice showed phenotypes not more severe than single mutants at the synaptic, network, and behavioral level. Finally, we present a theoretical framework to quantitatively explain our findings and extrapolate the conclusions to symptoms diversity in human patients. Taken together, this study shows that haploinsufficiency at two interacting loci leads to extreme phenotypic diversity at the systems level. These findings provide a proof of concept for how modifying genes in the patient genome enhance phenotypic diversity.</p>