The results indicated that VHL and PBRM1 genes were the most frequently mutated genes in ccRCC, and Cluster A showed a relatively higher mutation rate than Clusters B and C. We also performed subgroup analysis of ccRCC and found significantly differential heterogeneity in methylation, miRNA, and mRNA levels among the three subgroups (p < 0.05). This evidence concerns the gene PBRM1 and nonpapillary renal cell carcinoma.