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. Here, MTO1 is linked to hereditary clear cell renal cell carcinoma.