Acid phosphatase 5 (ACP5) gene plays a vibrant role in the synthesis of a tartrate-resistant acid phosphatase (TRAP5) enzyme. TRAP5 is ~35 KD glycosylated di-iron metalloenzyme responsible for the regulation of osteopontin (protein) activity. There are two isoforms of TRAP5, TRAP5a, and TRAP5b. TRAP5a functions with low enzymatic activity due to a loop interacting with the active site and the more active TRAP5b is generated upon proteolytic cleavage of this loop. TRAP5a works as a marker for systematic macrophage function and chronic inflammation activity, while TRAP5b for osteoclast activity. ACP5 is evolutionarily conserved in nature and acts as a multifunctional protein that involves generations of reactive oxygen species, normal bone development, macrophage function, and osteoblast regulation, affecting a series of pathways, as well as reflecting bone resorption and osteoclast activity. To understand its fundamental role, a functional investigation of missense mutations of the ACP5 gene was carried out through an in-silico approach. Two nsSNPs G109R and L201P were predicted to be deleterious using multiple computational tools like SIFT, Polyphen-1, PolyPhen-2, MAPP, SNAP, Predict SNP and PhD-SNP. Additionally, the structural analysis was performed. The result is that there was no similarity between the native and mutant structures. Therefore, these reported mutations in ACP5 modify the expression, function, and structure of a TRAP5 protein. These findings suggest that TRAP5 can be a therapeutic target in immunological disorders, cancer, a n d metabolic bone diseases. These deleterious mutations can be lethal to its function and may hamper its therapeutic strategy leading to various diseases such as autoimmune cytopenia, systemic lupus erythematosus (SLE) immune-osseous dysplasia, spasticity with leukodystrophy, moyamoya syndrome, and sjogren's syndrome.