Transcription factor, which play a role in limb development. Is an essential player in the regulatory network governing transcription of genes implicated in limb morphogenesis. Heterodimer (PubMed:25466284). Efficient DNA binding requires dimerization with another bHLH protein. Interacts with TCF3, TCF4, and TCF12 (PubMed:25466284). Disease susceptibility may be associated with variants affecting the gene represented in this entry. A copy number variation (CNV) resulting in BHLHA9 duplications is a necessary but not sufficient susceptibility factor for Split-hand/foot malformation with long bone deficiency, a highly variable phenotype with reduced penetrance, particularly in females (PubMed:22147889). The disease is caused by variants affecting the gene represented in this entry. The disease may be caused by variants affecting the gene represented in this entry. Extended N-terminus.