Many studies have demonstrated a role for alternative polyadenylation (APA) of the 3'UTR region in the subcellular localization of mRNA in neurons, but to date, there has been little evidence of a link to psychiatric disorders, particularly schizophrenia.However, our group has recently demonstrated an alteration of polyadenylation in a large cohort of iPSC-derived cortical glutamatergic neurons from healthy controls and schizophrenic (SCZ) patients as well as from post-mortem brains.104 iPSCs-derived cortical glutamatergic neurons were characterized by RNA-Seq, revealing that the use of the canonical polyadenylation site is reduced in favor of the upstream site in SCZ patients, resulting in a shorter 3'UTR, with a particular enrichment for genes involved in synaptic signaling.Among them, the SHANK3 gene showed an intracellular shift in transcript and protein localization associated with a reduction in the number of synapses and microcircuit connectivity in iPSC-derived neurons. In this follow-up study, we investigated the downstream biological effects of altered polyadenylation of the 3'UTR regions by compartment-specific RNA-seq in 56 donors. Subsequently, we performed deep cellular phenotyping in a subset of 20 donors by qPCR, Western blot, RNA-FISH, and immunofluorescence. To validate these results, we generated and characterized two SHANK3 long-3'UTR knocked-out cell lines from healthy controls using CRISPR-Cas9.Our results point to a novel aspect of synaptic and molecular alterations in schizophrenia. The alteration in mRNA and protein localization of Shank3 caused by differential 3’UTR usage in SCZ patients represents a potential mechanism contributing to the changes in synapse biology in neuropsychiatric disorders.