Identification of functional significance of non-synonymous single nucleotide polymorphisms (nsS-NPs) is a promising area in human genetic variation that causes various diseases. In this study, the effect of nsSNPs in Btk (Bruton's tyrosine kinase) was investigated computationally by analyzing stability and efficiency of protein interactions. The consequence between the structural and functional relationship was contributed by substitution of conserved amino acid residue which leads to X-Linked Agammaglobulinemia (XLA). Hence, the most detrimental missense mutations in domains viz., PH (pleckstrin homology), SH2 (Src homology 2) and kinase domain of Btk were computationally identified. Out of 113 observed variants, 78 variants were commonly found to be less stable, deleterious and damaging by I-Mutant 2.0, SIFT and PolyPhen programs respectively. Subsequently, in-silico modeling was performed and RMSD (root mean square deviation) was computed for these 78 variants to understand the structural deviation with respect to three native domains of Btk.In addition, the native PH domain and its 13 mutants were docked with substrate, phosphotidylinositol 3,4,5-triphosphate (PI(3,4,5)P3). Similarly, the native SH2 domain and its 13 mutant were docked with its interacting partner, BLNK (B-cell linker protein). Also, the native kinase domain and its 52 variants were docked with its inhibitor, Dasatinib. Based on these computational analyses, it was observed that the majority of amino acids in mutants of PH and SH2 domain lost the interacting efficiency with their substrate, PI(3,4,5)P3 and BLNK respectively, whereas, Dasatinib was found as a potential inhibitor for several mutants of kinase domain which could be used for the treatment of imatinib-resistance chronic myelogenous leukemia (CML). Moreover this work could pave the way for aiding nanotechnology based targeted drug delivery. Copyright © 2015 American Scientific Publishers.