In conclusion, we report the potential clinical usefulness of 13 ccRCC-related proteins (MITF, SHP2_pY542, IGFBP2, AMPKALPHA_pT172, ACC1, P70S6K_pT389, RRM2, PEA15, MAPK_pT202Y204, UGT1A, BRAF_pS445, 4EBP1_pT37T46 and Vinculin) that could be used as a guidance to classify patients into high- and low-risk groups, predict their clinical outcomes and strategize individualized treatments. Here, BRAF is linked to nonpapillary renal cell carcinoma.