Distinct IRF6 dysfunction mechanisms in syndromic orofacial clefts: Computational evidence for allosteric versus...

Orofacial clefts (OC) are a congenital anomaly typically classified as syndromic or non-syndromic. Among the syndromic cases, Van der Woude syndrome (VWS) and popliteal pterygium syndrome (PPS) are primarily caused by pathogenic variants in IRF6, which encodes a transcriptional factor essential for orofacial development. Our aim is to identify and characterize IRF6 variants in two syndromic OC cases and assess their structural and functional consequences through computational modeling. Sequencing of IRF6 exons 3, 4, 7, and 9 was conducted in one proband with VWS and one proband with PPS, as well as their parents. Structural impacts were measured through comparative modeling based on the IRF4-DNA complex, followed by molecular dynamics simulations. Binding free energies and protein-DNA interactions were assessed using MM/GBSA calculations and hydrogen bond occupancy analysis. We identified two pathogenic variants: NP_006138.1:p.(Ala16Val) in a VWS proband and NP_006138.1:p.(Arg84Cys) in a PPS proband, both confirmed as de novo. Variants were classified as pathogenic by the American College of Medical Genetics and Genomics criteria, and by most pathogenicity predictors. Molecular dynamics simulations showed that NP_006138.1:p.(Ala16Val) induces long-range allosteric effects with increased structural fluctuations, while NP_006138.1:p.(Arg84Cys) directly disrupts critical DNA-binding interactions. MM/GBSA analysis demonstrated reduced DNA-binding affinity for both variants, with NP_006138.1:p.(Arg84Cys) showing the most severe electrostatic disruption. Our computational analyses suggest that pathogenic IRF6 variants may impact DNA binding through distinct molecular mechanisms: NP_006138.1:p.(Ala16Val) potentially through allosteric conformational changes and NP_006138.1:p.(Arg84Cys) likely through direct disruption of the protein-DNA interface.