SynGAP1 is a major signaling protein that plays a pivotal role in regulating fundamental molecular changes in dendritic spine synaptic morphological and functional modifications.

SynGAP1 functions as a downstream component of NMDA receptor-associated signaling and of AMPA receptor trafficking to excitatory postsynaptic membrane. SynGAP1 is mainly expressed in the hippocampus and cortex.

SynGAP1 is a cytosolic protein without a signal peptide or any transmembrane domain. The N-terminal half of SYNGAP1 has a Ras-GAP domain, along with the region that is loosely homologous to Pleckstrin homology and a C2 domain which is potentially involved in binding Ca²⁺ and phospholipids. Interestingly, the alignment of GAP domain of SynGAP1 with other Ras-GAPs suggests that the amino acids in the GAP domain are crucial for interacting with Ras and for stimulating Ras-GTPase activity. The C-terminal half consists of a repeat of 10 histidines that may be involved in metal chelation, several potential serine and tyrosine phosphorylation sites and a T/SXV motif necessary for interaction with SAP102 and PSD-95.

SynGAP1 has been implicated in the pathogenesis of intellectual disability. de novo out-of-frame deletions were identified in patients with intellectual disability presenting with microcephaly and generalized epilepsy while de novo microdeletions in chromosome region 6p21.3 were observed in patients with severe language impairment in addition to epilepsy. SynGAP1 may also be involved in the pathogenesis of schizophrenia through altered regulation of the NMDA receptor complex.