Comprehensive Bioinformatics Analysis of AGAP6: Linking Protein Networks, Genetic Variants, and Clinical Significance

Background: AGAP6 belongs to ArfGAP proteins that have an important role in GTPase activity, membrane transport, cellular trafficking, and organization of the cytoskeleton. AGAP6 is crucial for cellular functions, but little is known about its true roles, interactions, and any clinical significance it may have. Methods: ArfGAP6 interaction data were recovered from the STRING database and visualized using Cytoscape. Enrichment analysis was performed to determine the pathways and biological processes of AGAP6. Protein domains were analyzed using InterPro and Pfam. SIFT, PolyPhen, and Combined Annotation Dependent Depletion were used for variant pathogenicity predictions. All statistical analyses were done using Python and R. Results: The ArfGAP6 PPI network comprised 11 nodes and 18 edges and contained >0.0144 in enrichment P values. Membrane trafficking, cytoskeletal reconstruction, and GTPase Activator Protein were the pathways identified during the enrichment analysis. The key domains having the highest statistical significance were the ArfGAP superfamily and the Plekstrin homology domain, which had false discovery rates of 0.0034 and 0.0050, respectively. Variants with SIFT scores <0.05 and PolyPhen scores >0.85 were predicted to disrupt ArfGAP6’s function. Conclusion: ArfGAP6 is a central regulator in essential cellular pathways and exhibits potential as a biomarker and therapeutic target in conditions such as cancer, neurodegeneration, and immune dysfunctions. This study provides a foundational framework for further experimental validation and clinical research.