A non-coding variant at 2p24.2 confers susceptibility to non-syndromic cleft lip and palate through LLPS-dependent regulation of MYCN

Non-syndromic cleft lip and palate (NSCLP) represents the most prevalent and clinically severe subtype within non-syndromic orofacial cleft (NSOFC), and 2p24.2 is the most significant reported risk locus for NSCLP. However, the causal variant at 2p24.2 and the underlying pathogenic mechanism remain unclear, limiting clinical translation. Here, we defined a 104-kb linkage disequilibrium (LD) block tagged by the lead SNP rs7552 at 2p24.2. Through a two-stage genetic screen within this block, including targeted sequencing and replication involving 2,437 Chinese NSCLP patients and 2,391 unaffected individuals, we identified a common non-coding single-nucleotide polymorphism, rs4263114, at 2p24.2 as the causal variant that confers susceptibility to NSCLP by residing within a previously unrecognized enhancer. Mechanistically, this enhancer physically bridges to the MYCN promoter through distal spatial contact, implicating MYCN as the pathogenic gene at this locus. Specifically, the rs4263114 risk variant reduces the recruitment of FOXP2 to the enhancer and disrupts liquid-liquid phase separation (LLPS)-driven droplet assembly. This biophysical defect impairs MYCN transcriptional activation and subsequently suppresses cranial neural crest cell (cNCC) differentiation. Notably, MYCN expression in cNCCs carrying homozygous risk alleles were partially restored by promoting FOXP2 LLPS. Collectively, our study functionally annotates the 2p24.2 locus and identifies a mechanism by which a non-coding variant disrupts transcription factor phase separation to increase susceptibility to NSCLP, providing a basis for future clinical translation.