Systematic analysis of naturally occurring missense mutations in human manganese transporters: prediction and structural insights

Manganese (Mn) homeostasis in humans is tightly regulated by the transporters ZIP8, ZIP14, and ZnT10, and pathogenic mutations in these proteins cause systemic Mn dysregulation, leading to severe disorders in multiple systems. Here, we performed a systematic survey of naturally occurring missense variants in these transporters. Pathogenicity was assessed with two widely used computational tools, CADD and AlphaMissense (AM), and results were integrated with AlphaFold-predicted structural models. Although the prediction methods showed general agreement, substantial discrepancies were observed, with CADD tending to overpredict deleteriousness and AM failing to identify a portion of confirmed pathogenic variants. Structural mapping revealed that predictions were more accurate for amino acid substitutions in structured and buried residues than for solvent-exposed loops and flexible regions. Mechanistic insights further highlighted variants at functionally important regions as critical. Our study helps prioritize Mn transporter variants for future experimental validation and provides a framework for bridging computational predictions with structure-guided mechanistic studies.