Structural modelling of germline FOXA1 variants identified in Asian participants with incident gastrointestinal cancers from the UK Biobank.

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Background: Interpretation of rare germline missense variants identified through population-scale exome sequencing remains challenging, particularly in under-represented ancestries. Such variants are often observed in individuals who later develop cancer, yet their biological relevance is difficult to infer from sequence data alone. FOXA1 is a pioneer transcription factor involved in chromatin regulation and epithelial differentiation, and its dysregulation has been implicated in gastrointestinal (GI) carcinogenesis. Methods: Whole-exome sequencing data from the UK Biobank were analysed to identify FOXA1 missense variants in Asian participants with incident GI cancers. Among these, 77 individuals carried one or more FOXA1 variants. Four variants (p.A83T, p.L148V, p.H387R, p.S448N), absent in Asian healthy controls, were prioritised. AlphaFold-based structural models were used to evaluate single-, dual- and multi-variant configurations using global and domain-restricted RMSD, local interaction mapping, and in silico stability prediction. Results: Across all models, the global FOXA1 architecture, including the forkhead DNA-binding domain, remained preserved, indicating structural robustness to multiple substitutions. Each variant induced localized perturbations affecting residue packing, polarity, and interaction networks without evidence of global unfolding. Variants in flexible regulatory regions (A83T, S448N) altered local interaction environments, while substitutions near structured regions (L148V) and in loop-proximal segments (H387R) modulated hydrophobic packing and surface electrostatics. Combined variant models demonstrated spatially segregated effects without additive destabilisation. Conclusions: Structural modelling provides mechanistic context for germline FOXA1 variants identified in the UK Biobank cohort. The preserved global fold with localized perturbations is consistent with region-specific conformational modulation rather than global structural collapse. Such structure-based interpretation may help prioritise rare germline variants for downstream functional investigation and improve understanding of how these variants may contribute to cancer biology within precision oncology frameworks.