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Variety of genes has been reported for intellectual disability in different ethnic group and whole exome sequencing facilitate the way of gene discovery in such heterogeneous diseases. Here, we reported a novel mutation in ELP2 gene (c.2429 G>A) in Iranian case of mental retardation. The gene ELP2 encodes acetyl transferase subunit of RNA polymerase II playing an important role in transcription elongation and chromatin remodeling. The c.2429 G>A mutation predicted as pathogenic and resulted in substitution of amino acid cysteine with tyrosine at position 811 of polypeptide chain. The proband was homozygous of the mutation and received one copy of affected allele from each parent. Although, the association of elongator proteins with neurological diseases is well established, there is only one study reported two missense mutations of ELP2 in the world which was observed in Iranian mental retarded patients. In fact, c.2429 A>G is the third report of ELP2 mutations in Iranian families suffering from mental retardation showing the importance of this gene in Iranian cases although phenotype-genotype correlation is needed.