MSX1 is a transcriptional repressor that functions as a homeobox-containing DNA-binding protein regulating craniofacial and dental development 1. It binds consensus sequences in gene promoters to repress transcription of developmental factors and acts as a stage-specific regulator during odontogenesis, controlling odontoblast differentiation and dental mesenchymal cell proliferation 2. MSX1 phase separation, regulated by PRMT1-catalyzed methylation of its intrinsically disordered region, is essential for embryonic palatal fusion; hypomethylated MSX1 forms abnormal condensates impairing palatal mesenchymal cell proliferation 3. Beyond dentition, MSX1 plays critical roles in heart valve cell differentiation as a key transcription factor mediating endocardial-mesenchymal transition 4, and influences cardiac development through regulation of downstream signaling pathways 5. Clinically, MSX1 mutations cause non-syndromic orofacial clefts, the most common craniofacial birth defect, with specific SNPs showing varying risk associations across populations 67. MSX1 mutations also cause selective tooth agenesis and Witkop syndrome (dental-nail dysplasia), representing major genetic contributions to odontogenic anomalies 28. These findings establish MSX1 as a central developmental regulator with phase separation-dependent mechanisms underlying craniofacial and dental pathologies.