Transcription factor involved in chondrocytes differentiation and cartilage formation. Specifically binds the 5'-AACAAT-3' DNA motif present in enhancers and super-enhancers and promotes expression of genes important for chondrogenesis. Required for overt chondrogenesis when condensed prechondrocytes differentiate into early stage chondrocytes: sox5 and sox6 cooperatively bind with sox9 on active enhancers and super-enhancers associated with cartilage-specific genes, and thereby potentiate sox9's ability to transactivate. Not involved in precartilaginous condensation, the first step in chondrogenesis, during which skeletal progenitors differentiate into prechondrocytes. Expressed in migrating myoblasts during ventral body wall formation. Deletion of C-terminal sequence resulting in a frameshift at position 667.