en Molecular Genetics & Genomics Molecular Genetics & Genomics مقاله موردی Case Report <strong>Background: </strong>Pathogenic variants of <em>RUNX2</em>, a gene that encodes an osteoblast-specific transcription factor, have been shown as the cause of Cleidocranial dysplasia (CCD), which is a rare hereditary skeletal and dental disorder with dominant mode of inheritance and a broad range of clinical variability. Due to the relative lack of clinical complications resulting in CCD, the medical diagnosis of this disorder is challenging, which leaves it underdiagnosed. <strong>Methods: </strong>In this study, nine healthy and affected members of an Iranian family were investigated. PCR and sequencing of all exons and exon-intron boundaries of runt-related transcription factor 2 (<em>RUNX2</em>; NM_001024630) gene was performed on proband. Co-segregation analysis was conducted in the other family members for the identified variant. Additionally, a cohort of 100 Iranian ethnicity-matched healthy controls was screened by Amplification Refractory Mutation System PCR method.<strong> Results:</strong> The novel splice site variant (c.860-2A>G), which was identified in the intron 6 of <em>RUNX2</em> gene, co-segregated with the disease in the family, and it was absent in healthy controls. Pathogenicity of this variant was determined by several software, including <strong>, </strong>human splicing finder, which predicts the formation or disruption of splice donor sites, splice acceptor sites, exonic splicing silencer sites, and exonic splicing enhancer sites. <em>In silico</em> analysis predicted this novel variant to be disease causing. <strong>Conclusion: </strong>The identified variant is predicted to have an effect on splicing, which leads to exon skipping and producing a truncated protein via introducing a premature stop codon. Cleidocranial dysplasia, RUNX2, Splice site 297 302 http://ibj.pasteur.ac.ir/browse.php?a_code=A-10-1-844&slc_lang=en&sid=1 Ebrahim Jamali 0000-0002-8056-4273 No Department of Genetics, School of Basic Science, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran Raziyeh Khalesi 0000-0002-9105-5482 No Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Fatemeh Bitarafan 0000-0002-4489-2923 No Department of Cellular and Molecular Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran Navid Almadani 0000-0003-2715-5646 No Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran Masoud Garshasbi 0000-0002-5508-7903 Yes Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran