Based on integrative analyses of transcriptomic landscape and urinary signature, the urine-based prognostic classifier consisting of VSIG4, TGFBI, and P4HB has satisfied predictive power of survival time, pathological grade and stage in ccRCC patients, which facilitate ccRCC molecular subtyping and treatment. The gene discussed is P4HB; the disease is nonpapillary renal cell carcinoma.