Chronic Myeloid Leukemia (CML) progression from chronic phase (CP) to advanced stages such as accelerated phase (AP) or blast crisis (BC) remains a major clinical challenge, particularly due to limited early detection biomarkers. In this study, we investigate the genetic mutations driving CML progression, focusing on the MUC3A gene and the downstream regulatory region of the MIR5195 gene. We identified a novel missense mutation, P258S, in MUC3A that is exclusively present in AP/BC-CML patients. Structural and physicochemical analyses revealed that the P258S mutation alters protein stability, increasing flexibility in some regions and stabilizing others, which may affect its molecular interactions. Molecular dynamics simulations and docking studies showed enhanced binding affinity of MUC3A P258S with several therapeutic agents, particularly Capmatinib, suggesting potential clinical applications in treating CML. Additionally, mutations in the MIR5195 regulatory region were found to disrupt transcription factor binding, leading to changes in gene expression patterns. MEME and TOMTOM motif analysis revealed the loss of key motifs and the emergence of new ones in the mutant sequences, indicating a shift in the transcriptional regulation landscape. These findings suggest that these mutations may influence the expression of genes involved in CML progression. This study highlights the potential of MUC3A and MIR5195 as biomarkers for CML progression and therapeutic targets for personalized treatment strategies. The identified P258S mutation in MUC3A opens new avenues for targeted therapies, while the regulatory alterations in MIR5195 offer insights into gene expression reprogramming in CML's advanced stages.