We observed association of six marker diplotype ATTGCT/ATTGCT (rs746203-rs10828317-rs7094131-rs2296624-rs11013052-rs1409396) of PIP4K2A gene with an estimated odds ratio of OR = 3.19 (95%-CI = 1.46–6.98) in severely ill schizophrenia patients who had inadequate response for antipsychotics irrespective of treatment in the study population. Here, PIP4K2A is linked to schizophrenia.