Two independent validation datasets (GSE40435 (N = 101), GSE53757 (N = 72)) were collected for meta-analysis, suggesting that CDKN2A (log2(fold change) = 1.46, 95%CI: 1.75–2.35) showed significantly higher expression in ccRCC tissues while DLAT (log2(fold change) = −0.54, 95%CI: −0.93–−0.15) and FDX1 (log2(fold change) = −1.01, 95%CI: −1.61–−0.42) were lowly expressed. This evidence concerns the gene DLAT and nonpapillary renal cell carcinoma.