High incidence and geographic distribution of cleft palate in Finland are associated with the IRF6 gene

Nat Commun. 2024 Nov 6;15(1):9568. doi: 10.1038/s41467-024-53634-2.

Abstract

In Finland, the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip with or without cleft palate (CL/P). This trend contrasts to that in other European countries but its genetic underpinnings are unknown. We conducted a genome-wide association study in the Finnish population and identified rs570516915, a single nucleotide polymorphism highly enriched in Finns, as strongly associated with CP (P = 5.25 × 10-34, OR = 8.65, 95% CI 6.11-12.25), but not with CL/P (P = 7.2 × 10-5), with genome-wide significance. The risk allele frequency of rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in independent cohorts of CP cases from Finland (P = 8.82 × 10-28) and Estonia (P = 1.25 × 10-5). The risk allele of rs570516915 alters a conserved binding site for the transcription factor IRF6 within an enhancer (MCS-9.7) upstream of the IRF6 gene and diminishes the enhancer activity. Oral epithelial cells derived from CRISPR-Cas9 edited induced pluripotent stem cells demonstrate that the CP-associated allele of rs570516915 concomitantly decreases the binding of IRF6 and the expression level of IRF6, suggesting impaired IRF6 autoregulation as a molecular mechanism underlying the risk for CP.

MeSH terms

  • Alleles
  • Cleft Lip / epidemiology
  • Cleft Lip / genetics
  • Cleft Palate* / epidemiology
  • Cleft Palate* / genetics
  • Estonia / epidemiology
  • Female
  • Finland / epidemiology
  • Gene Frequency
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study*
  • Humans
  • Incidence
  • Interferon Regulatory Factors* / genetics
  • Male
  • Polymorphism, Single Nucleotide*

Substances

  • Interferon Regulatory Factors
  • IRF6 protein, human