PAX9 gene is a transcription factor and member of the paired box (PAX) family, a class of genes that code for transcription factors that play major roles in fetal development and organogenesis. The PAX9 protein has been shown to interact with MSX1 to form a heterodimeric protein complex, which in turn activates the transcription of other genes, such as BMP4, that are involved in tooth development. Results obtained from animal studies show that PAX9 knocked-out mice exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and cleft secondary palate.
Mutations in the human PAX9 gene are associated with a condition known as Selective Tooth Agenesis-3, characterized by teeth agenesis and missing secondary dentition. PAX9 mutations tend to affect primarily molar development, although lateral incisors and premolars are also known to be affected.