In vitro and in silico analysis of three variants associated with type 2 diabetes

Common regulatory and coding variants may influence type 2 diabetes (T2D) risk by altering gene regulation or protein function. Identifying these variants and their associations with disease risk may inform disease control strategies. This study prioritized candidate variants by integrating two-group comparative genotyping with in-silico structural and dynamic analyses.

Three prioritized variants (two missense, one TF-binding-site) were genotyped in 101 T2D cases and 100 controls from the Azeri population of Iran. Variant calls were validated by Sanger sequencing. Structural modelling, ligand docking, and 100-nanosecond molecular dynamics simulations were performed to assess molecular consequences.

The TF-binding-site variant in PPP2R3A (rs184442184) was significantly associated with T2D (allelic OR ≈ 1.71, p = 0.014; TT OR ≈ 2.92, p = 0.020) and is located at a RegulomeDB 2a site overlapping EGR1/SP motifs. SLC39A11 (ZIP11) rs61736066 (A allele) was enriched in cases (allelic OR ≈ 1.87, p = 0.002; AA OR ≈ 3.49, p = 0.005), and the variant model demonstrated increased RMSD/RMSF, helix displacement, and modest destabilization. The TPCN2 missense variant exhibited only subtle in-silico effects and no genetic association.

These findings highlight PPP2R3A rs184442184 and SLC39A11 rs61736066 as promising T2D candidate variants, supported by concordant genetic signals and mechanistic in-silico effects. The TPCN2 substitution demonstrated only mild structural changes and no association in this study. Overall, these results provide testable biological hypotheses that require validation through larger replication studies and targeted functional assays.