Synapse organizers are a subset of cell adhesion molecules to induce pre-and postsynaptic differentiation and whose mutations are associated with neurodevelopmental disorders such as autism spectrum disorder, intellectual disability and schizophrenia. Accumulating evidence suggests that pre-and postsynaptic organizers form complexes in various combinations to regulate several different types of synapses depending on the respective synapse organizer complex in the brain. Thus, disease-associated mutations in the synapse organizer genes may have different effects on each respective synapse organizer complex. Recent structural analyses of the synapse organizer complexes enable to design point mutations that selectively interfere the formation of the respective synapse organizer complex. The mice carrying these designed synapse organizer mutations will be useful research tools to clarify the pathogenic mechanisms of neurodevelopmental disorders.