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To analyze the promoter region of PIP5K2A, a phosphatidylinositol 4-phosphate 5-kinase that maps to 10p in a region linked to both bipolar disorder and schizophrenia.The promoter region was screened by single-strand conformation polymorphism analysis and DNA sequencing. Allele frequencies were determined in a case–control study. Functional significance of a promoter variant was determined by electromobility gel shift assays.Homozygosity for a rare putative promoter variant, −1007C→T, was found in only two patients with schizophrenia and in no controls or bipolar patients. The variant forms a 7/8 base match for the binding site of Oct-1, a member of the POU homeodomain family. Electromobility gel shift assays revealed increased binding of a brain-specific nuclear protein to the −1007T allele compared with −1007C.The data suggest that homozygosity for −1007T could be a rare genetic factor in the development of schizophrenia.