Objectives: Cleidocranial dysplasia (CCD), mainly caused by RUNX2 mutation, is a dominantly inherited skeletal disorder with many dental abnormalities, characterized by delayed permanent tooth eruption. In this study, we explored a novel RUNX2 mutation and the effect of RUNX2 mutation on osteogenic differentiation of dental follicle cells (DFCs). Design: A CCD patient with typical clinical features was involved in this study. Conservation and secondary structural-analysis-of-the-RUN. Then DFCs diet stably expressing wild-type or mutant RUNX2 were established using lentiviruses. Cell Counting Kit 8 (CCK8) assays were performed to test the proliferation of DFCs. Measurement of alkaline phosphatase (ALP) activity, ALP staining, alizarin red staining and determination of osteoblast-specific genes expression were performed to assess osteogenic capacity of DFCs. Results: A missense mutation (c.674 G > T, p. R225 L) of RUNX2 gene was identified in the CCD patient. Conservation and secondary structural analysis revealed that the mutation was located in highly conserved Runt domain and altered secondary structure of RUNX2. CCK8 assays showed that mutant RUNX2 increased the proliferation rate of DFCs compared to wild-type RUNX2. ALP activity, ALP staining and alizarin red staining results indicated that mutant RUNX2 decreased the mineralization ability of DFCs. In addition, mutant RUNX2 significantly down-regulated the expression of osteoblast-associated genes. Conclusions: RUNX2 mutation can reduce the osteogenic capacity of DFCs by inhibiting osteoblast-associated genes and then affecting bone formation, which participates in bone remodeling during tooth eruption. These effects may be partly responsible for the defects in permanent tooth eruption of CCD patients.