Autism Spectrum Disorders (ASDs) are likely to be associated with impaired central nervous development, however the molecular and cellular pathogenesis of ASDs remains largely unknown. In this study, we focused on POGZ, one of the most recurrently mutated genes in patients with ASDs. To elucidate the molecular and cellular pathogenesis underlying POGZ mutation-mediated neural developmental abnormalities, comprehensive RNA expression analysis was conducted using samples derived from neural stem cells and neurons from a patient with POGZ mutation and control individuals. We performed gene ontology (GO) enrichment analysis on genes that exhibited significant differences in expression between patients and healthy individuals and found that the differentially expressed genes in neural stem cells and neurons were enriched for GO terms involving neural development. Furthermore, phospho-proteome analysis suggested that several signal transduction pathways potentially implicated in neural development were impaired in iPS cell-derived neurons from the patient. Our current results will help to clarify the pathogenesis of the de novo mutation in the POGZ gene locus, providing crucial insights into understanding the molecular and cellular pathogenesis underlying ASDs.