The RUNX2 gene is a physiological regulatory gene implicated in the development of cleidocranial dysplasia (CCD). A 13-month-old child presented with clinical features of CCD. At the age of 3 years the diagnosis was corroborated by clinical genetic assessment and DNA analysis, revealing a missense mutation p.R131C (c.391C>T) in RUNX2. At the age of 8 years the child was found to have a unique dental phenotype, represented by lack of supernumerary teeth and congenital absence of one tooth. A simple therapeutic approach was adopted, consisting of interceptive orthodontic treatment. The presence of this specific missense mutation in RUNX2, associated with the lack of typical supernumerary teeth may suggest a phenotype-genotype association.