Simplified schematic illustrating molecular mechanisms of neurite regulation. Extracellular events such as cell contact , guidance cues , neurotransmitter release , and interactions with extracellular matrix components  are detected by receptors and cell adhesion molecules at the membrane surface and are transduced via cytoplasmic terminals and multidomain scaffolding proteins  to downstream signalling molecules [81–83]. Polarity and directional navigation is achieved by coordinating local calcium concentration , Src family kinases , cyclic nucleotide activation (cAMP and cGMP) , and phosphoinositide signalling molecules which affect the spatial distribution and membrane recruitment of proteins that regulate the neuronal cytoskeleton . Chief among these regulators are the small Rho family GTPases RhoA, Rac and Cdc42, which serve as molecular 'switches' to activate downstream effectors of cytoskeletal remodelling . In developed neurons, this pathway further regulates the formation of actin-dependent microarchitecture such as mushroom-like dendritic spines at the postsynaptic terminals of excitatory and inhibitory synapses . This simplified schematic presents components in an exploded format for tractability, and includes an abridged set of interactions. Additional File 9 presents autism candidate genes identified by GWAS-NR having known roles in neurite regulation. RPTP (receptor protein tyrosine phosphatase); EphR (Eph receptor); FGFR (fibroblast growth factor receptor); EphR (Eph receptor); PLXN (plexin); NRP (neuropilin); Trk (neurotrophin receptor); ECM (extracellular matrix); NetR (netrin receptor); NMDAR (NMDA receptor); mGluR (metabotropic glutamate receptor); AA (arachidonic acid); PLCγ (phospholipase C, gamma); MAGI (membrane associated guanylate kinase homolog); IP3 (inositol 1,4,5-trisphosphate); DAG (diacylglycerol); PIP2 (phosphatidylinositol 4,5-bisphosphate); PIP3 (phosphatidylinositol 3,4,5-trisphosphate); PI3K (phosphoinositide-3-kinase); nNOS (neuronal nitric oxide synthase); NO (nitric oxide); IP3R (inositol trisphosphate receptor); RyR (ryanodine receptor); GEF (guanine exchange factor); GAP (GTPase activating protein); MAPK (mitogen-activated protein kinase); and JNK (c-Jun N-terminal kinase).