<p>The family of deubiquitinating enzymes is primarily involved in the removal of ubiquitin chains from specific target proteins. Among these proteins, ubiquitin-specific protease 12 (USP12 protein) has been identified as a key molecule in regulating cellular homeostasis, cancer progression, and immune regulation. This protein is reportedly associated with colorectal cancer, prostate cancer, and breast cancer, along with neurodegenerative disorders like Huntington’s disease. The study of mutations in USP12 could be crucial for understanding its impact on cancer and neurodegeneration, making it a potential target for therapeutics against such diseases. Our study uses a sequence-based and a structure-based screening method to identify a mutation in USP12 having the most deleterious and destabilizing effect. The mutation Y49N was found to significantly alter structural and biological functions of USP12 protein while compromising its stability. A total of 5000 conformations were generated for wild-type and Y49N_USP12 structures through normal mode analysis and a comparative study was conducted. We evaluated parameters like RMSD and <i>R</i>_g values to study structural divergence and reduced compactness in mutant protein conformations. Analysis of RMSF values of mutant protein showed significant structural deviations hinting at its increased flexibility. Further, heavily modified surface charge distributions were found through electrostatic surface charge mapping and fluctuations in energetic distribution indicated conformational perturbation. Moreover, the study shows how Y49N mutation could induce a helix to coil conversion in the N-terminal region of mutant protein structures throughout 5000 cycles of simulation. Our work helps advance our understanding of USP12 and its clinical value which needs to be explored further.</p>