We identified the PACS2 gene responsible for the multifunctional sorting protein that play a role in nuclear gene expression as well as pathway trafic regulation. Diseases associated with PACS2 include early infantile epileptic encephalopathy (EIEE66), alacrima, achalasia, and mental retardation syndrome. Whole exome sequencing (WES) technique was used for the identification of variants that may lead to the disease. We identified a consanguineous Saudi family segregating developmental delay, mental retardation and epilepsy. Our results showed a heterozygous missense variant PACS2 gene leading to intellectual disability, epilepsy and cause epileptic encephalopathies (EIEE66) disorder. WES data was analyzed and identified variants were further confirmed by Sanger sequencing validation technique. We identified a heterozygous missense c.625G>A p.Glu209Lys in exon-6 of PACS2. The detected heterozygous mutation in the exon-6 region of PACS2 gene change the protein features and may cause disease. Further, explain the possibility that PACS2 gene play important role to cause intellectual disability, epilepsy and epileptic encephalopathies in this Saudi family.