Central glutamatergic synapses and the molecular pathways that control them are emerging as common substrates in the pathogenesis of mental disorders. Genetic variation in the contactin associated protein-like 2 (CNTNAP2) gene, including copy number variations, exon deletions, truncations, single nucleotide variants, and polymorphisms have been associated with intellectual disability, epilepsy, schizophrenia, language disorders, and autism. CNTNAP2, encoded by Cntnap2, is required for dendritic spine development and its absence causes disease-related phenotypes in mice. However, the mechanisms whereby CNTNAP2 regulates glutamatergic synapses are not known, and cellular phenotypes have not been investigated in Cntnap2 knockout neurons. Here we show that CNTNAP2 is present in dendritic spines, as well as axons and soma. Structured illumination superresolution microscopy reveals closer proximity to excitatory, rather than inhibitory synaptic markers. CNTNAP2 does not promote the formation of synapses and cultured neurons from Cntnap2 knockout mice do not show early defects in axon and dendrite outgrowth, suggesting that CNTNAP2 is not required at this stage. However, mature neurons from knockout mice show reduced spine density and levels of GluA1 subunits of AMPA receptors in spines. Unexpectedly, knockout neurons show large cytoplasmic aggregates of GluA1. Here we characterize, for the first time to our knowledge, synaptic phenotypes in Cntnap2 knockout neurons and reveal a novel role for CNTNAP2 in GluA1 trafficking. Taken together, our findings provide insight into the biological roles of CNTNAP2 and into the pathogenesis of CNTNAP2-associated neuropsychiatric disorders.A bnormalities in excitatory synapses of cortical pyramidal neurons have emerged as key cellular substrates in the pathogenesis of several psychiatric disorders. Disease-specific disruptions in synaptic morphology or number and glutamate receptors accompany several neuropsychiatric disorders, particularly those that involve deficits in information processing (1). In support of this view, postmortem neuropathological studies found altered dendritic spine density on cortical pyramidal neurons in individuals with intellectual disability (2), autism spectrum disorders (3), and schizophrenia (4). Dendritic spines are the sites of the majority of excitatory glutamatergic synapses in the mammalian brain and represent the postsynaptic compartment of these synapses. Spines are rich in actin, and their morphology changes during development and in various physiological conditions (5). Spines contain glutamate receptors, of which the AMPA subtype are the ones responsible for fast neurotransmission (6). AMPA receptors, like other membrane proteins, are processed in the endoplasmic reticulum and the Golgi complex, then delivered to synapses by forward trafficking mechanisms (7). At the synapse, they undergo constitutive and regulated exo-and endocytosis, known to modulate synapse strength (6). Together, changes in spine number and morphology, along with glutam...