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Cardiovascular disease (CVD) is a leading global cause of mortality, and understanding its underlying mechanisms is crucial for developing effective interventions. The liver-derived protein PCSK9 (proprotein convertase subtilisin/kexin-type-9) plays a vital role in regulating lipoprotein metabolism by binding to the low-density lipoprotein receptor (LDLR) and promoting its lysosomal degradation, ultimately reducing low-density lipoprotein (LDL) clearance. Loss-of-function (LOF) variants in PCSK9 are associated with decreased LDL cholesterol (LDL-C) levels, suggesting that these variants may contribute to a lower risk of cardiovascular events. Our computational analysis of PCSK9 LOF variants revealed significant alterations in stability, flexibility, and free energy compared to the native protein. Protein-protein docking studies of both wildtype and mutant PCSK9 with LDLR demonstrated variations in binding energy and interacting residues. Notably, while the binding cavity remained the same as that of the wildtype, all variants exhibited distinct binding interactions. Molecular dynamics simulations further highlighted increased flexibility and solvent exposure in the mutant protein complexes. These findings indicate that LOF variants in PCSK9 induce substantial structural changes, leading to a decreased affinity for LDLR binding.