Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, which is still not established as the exact explanation of the illness. Identifying the target genes associated with the disorder plays a crucial part in managing PD. Different genetic experiments have established the important target genes for disease development, but this remains difficult in the drug designing area. In this research, we suggested a novel approach to disease diagnosis that classifies variant genes for PD using gene mutation, gene expression and analysis of gene deletion. The protein sequence of PD genes was retrieved from genomic databases like NCBI, Ensemble, and UniProtKB and revealed the clinical relevance of various genes mis-sense mutation and amino acid codons. Here the targeted variant genes were identified using sequence matching. Set of PARK genes were identified as target genes by integrating gene mutation and expression data. Gene deletion analysis was carried out to determine the significant target for the Parkinson’s disease. The findings from the suggested mechanism will provide additional insight for understanding the disease mechanism of PD. This changes help drug designer for specific treatment. Future enhancement of this study may help in predicting disease biomarkers as well as designing novel compounds in rational drug designing.