Missense mutations on SynGAP C2 domain impair membrane diffusion

SYNGAP1 mutations have been linked to a range of neuropathological disorders and, more recently, to the insurgence of cancer. Despite its emerging relevance, the molecular basis of SynGAP’s action remains poorly understood. Here, using extensive molecular dynamics simulations integrated with structural analysis, we define how the SynGAP C2 domain associates with lipid bilayers. In particular, we observed spontaneous membrane binding of the domain in two distinct orientations, top and side, defined by the relative positioning of the C2 domain to its fold. These modes display markedly different dynamical properties: the top mode enables faster lateral diffusion on the membrane surface, whereas the side mode establishes more stable but less mobile contacts. Interestingly, pathogenic missense mutations mapping to the membrane-facing loops of SynGAP C2 disrupt these dynamics, leading to reduced diffusivity and altered membrane avidity. Our findings reveal a dual binding mechanism that underlies SynGAP’s membrane versatility and offer a general framework for how diverse mutations may perturb SynGAP activity across its polyedric biological functions.