Computational analysis identifies six deleterious nsSNPs in p47ING1a's PHD domain, disrupting tumor-suppressor function

The p47ING1a isoform of the ING1 gene functions as a crucial tumor suppressor, primarily by regulating cellular senescence through Rb-dependent pathways. Its activity hinges on a specialized plant homeodomain (PHD) zinc-finger, which specifically recognizes the H3K4me3 histone mark, a key epigenetic signal. Despite its critical role, the full spectrum of mutations in p47ING1a and the functional consequences of nonsynonymous single-nucleotide polymorphisms (nsSNPs) within its PHD domain remain largely uncharacterized. Understanding these variants is vital for clarifying their potential impact on ING1's tumor-suppressor activity and its implications for cancer development.

Researchers retrieved a total of 347 missense nsSNPs for the p47ING1a isoform from the NCBI dbSNP database. These variants were initially screened using 12 distinct sequence-based computational tools to predict deleteriousness. Variants consistently predicted as deleterious underwent further evaluation through I-Mutant stability analysis and ConSurf evolutionary conservation profiling. Three-dimensional structural modeling was performed using AlphaFold3, subsequently refined via GalaxyRefine, and validated using ERRAT, PROCHECK, and TM-align. Mutation-induced structural and binding effects were assessed using Missense3D, mCSM, and BeAtMuSiC. Post-translational modification sites were predicted using NetPhos 3.1, GPS 3.0, BDM-PUB, and NetOGlyc 4.0. Protein-protein interaction networks were constructed with STRING and Gene MANIA, while pan-cancer expression was analyzed via UALCAN and the Human Protein Atlas.

Twelve computational tools converged on six high-priority variants: C358S, C374G, W378G, F379V, S382L, and R400P. All six of these identified mutations were exclusively localized within the critical PHD zinc-finger domain, specifically spanning residues 353-402. Across multiple stability analyses, all six mutations were consistently predicted to destabilize the p47ING1a protein, suggesting a significant impact on its structural integrity. This destabilization is crucial because the PHD domain's stability is directly linked to its ability to bind H3K4me3. The study concluded that these nsSNPs are predicted to disrupt protein stability, impairing H3K4me3 binding, and consequently interfering with Sin3A/HDAC complex interactions. This disruption is a key mechanism by which ING1 exerts its tumor-suppressor function. > The six identified nsSNPs (C358S, C374G, W378G, F379V, S382L, R400P) were consistently predicted to destabilize the p47ING1a protein and disrupt its critical H3K4me3 binding and Sin3A/HDAC interactions.