Encephalopathy is a syndrome of overall brain dysfunction with unknown causes despite its well-recognized etiology. This study reports clinical laboratory, radiological, and magnetic resonance imaging (MRI) findings as well as whole-exome sequencing (WES) of a female patient aged 19 months and 7 days with encephalopathy. To this end, the documented files of the hospitalized encephalopathy patients in Ayat Allah Mosavi hospital (Zanjan, Iran), referred from Khodabandeh city, Zanjan, Iran, were investigated. The initial symptoms, laboratory tests, computerized tomography (CT) scans, MRI, WES, and the course of disease were reported. The laboratory examination revealed mild anemia, and the normal range of the CSF, ESR, and CRP. Brain CT indicated brain edema while the MRI analysis of the brain revealed hypersignality. The c. 352G>A heterozygote variant was diagnosed in the PPP2RIA gene in exon four of chromosome 19. According to the observations, the frequency of this disorder was higher in this region of Zanjan province than other areas. The limitation of this study such as lack of access to the patients or biological samples of other similar patients hindered further evaluation. Hence, comprehensive research must be conducted to reveal the underlying etiology.