Based on our findings, we conclude that PI3K-Akt, Foxo, endocytosis, MAPK, Tight junction, and cytokine-cytokine receptor interaction pathways are among the most commonly altered pathways in renal cell carcinoma, and that MAP3K13, CHAF1A, FDX1, ARHGAP26, ITGBL1, C10orf118, MTO1, LAMP2, STAMBP, DLC1, NSMAF, YY1, TPGS2, SCARB2, PRSS23, SYNJ1, CNPPD1, and PPP2R5E are the major sources of alteration for these pathways. The gene discussed is SYNJ1; the disease is hereditary clear cell renal cell carcinoma.