Structural and Functional Characterization of the Rare GNAT1 Variant p.Gly4Trp Reveals Impaired GDP Binding and Potential Pathogenic Association with Congenital Stationary Night Blindness

Abstract

Background: Congenital stationary night blindness (CSNB) is a genetically heterogeneous retinal disorder associated with defects in rod phototransduction signaling. GNAT1 encodes the α-subunit of rod transducin, a G-protein essential for visual signal transduction in photoreceptor cells. In this study, we investigated the structural and functional consequences of the rare GNAT1 missense variant rs1699413898 (p.Gly4Trp), currently classified as a variant of uncertain significance. Methodology: The variant was retrieved from the gnomAD database with an extremely low allele frequency (0.000002056). Computational pathogenicity prediction tools, including PolyPhen-2, SIFT, and MutationTaster, consistently classified the variant as deleterious. Structural analysis was performed using the wild-type GNAT1 crystal structure (PDB ID: 1TAD), while the mutant model was generated using AlphaFold3. Molecular docking analysis of GDP with both wild-type and mutant proteins was performed to evaluate binding affinity and interaction changes. Results: Molecular docking analysis of GDP with both wild-type and mutant proteins revealed reduced binding affinity in the mutant structure (-9.1336 kcal/mol) compared with the wild type (-9.4581 kcal/mol). The mutant protein exhibited loss of critical interactions with ASP268, and P-loop residues involved in nucleotide stabilization, along with a reduced hydrogen-bonding network and altered binding geometry. Novel interactions with THR177 and GLN200, a residue previously associated with CSNB, were also observed. Conclusion: Collectively, these findings suggest that the p.Gly4Trp substitution may destabilize GDP binding and impair GNAT1 function, supporting its potential pathogenic role in recessive CSNB.