CXCR4, a chemokine receptor known as Fusin or CD184, spans the outer membrane of various human cells, including leukocytes. This receptor is essential for HIV infection as well as for many vital cellular processes and is implicated to be associated with multiple pathologies, including cancers. This study employs various computational tools to investigate the molecular effects of disease-vulnerable germ-line missense and non-coding SNPs of the CXCR4 gene. In this investigation, the tools SIFT, PROVEAN, PolyPhen-2, PANTHER, SNAP 2.0, PhD-SNP, and SNPs&GO were used to predict potentially harmful and disease-causing nsSNPs in CXCR4. Additionally, their impact on protein stability was examined by I-mutant 3.0, MUpro, Consurf, and Netsurf 2.0, combined with conservation and solvent accessibility analyses. Structural analysis with normal and mutant residues of the protein harboring these disease-associated functional SNPs was conducted using TM-align and SWIS MODEL, with visualization aided by PyMOL and the BIOVINA Discovery Studio Visualizer. The functional impact of wild-type and mutated CXCR4 variants was evaluated through molecular docking with its natural ligand CXCR4-modulator 1, using the PyRx tool. Non-coding SNPs in the 3' -UTR were investigated for their regulatory effects on miRNA binding sites using PolymiRTS. Five non-coding SNPs were identified in the 3'-UTR that can disrupt existing miRNA binding sites or create new ones. Non-coding SNPs in the 5' and 3'-UTRs, as well as in intronic regions, were also examined for their potential roles in gene expression regulation. Furthermore, RegulomeDB databases were employed to assess the regulatory potential of these non-coding SNPs based on chromatin state and protein binding regulation. In the mostly annotated variant (ENSP00000241393) of the CXCR4 gene, we found 23 highly deleterious and pathogenic nsSNPs and these were selected for in-depth analysis. Among the 23 nsSNPs, five (G55V, H79P, L80P, H113P, and P299L) displayed notable structural alternation, with elevated RMSD values and reduced TM (TM-score) values. A molecular docking study revealed the significant impact of the H113P variant on the protein-ligand binding affinity, supported by MD simulation over 100 nanoseconds, which highlighted substantial stability differences between wild-type and H113P mutated proteins during ligand binding. This comprehensive analysis shed light on the potential functional consequences of genetic variation in the CXCR genes, offering valuable insights into the implications of disease susceptibility and may pave the way for future therapeutic interventions.