During our study, through joint analysis of the data from GEO and TCGA-KIRC databases, we found that IRF6 expression was significantly decreased in ccRCC than that in adjacent normal renal tissues, and decreased IRF6 expression was associated with advanced tumor stage, distant metastasis, higher histological grade and pathological stage, and worse prognosis. Here, IRF6 is linked to nonpapillary renal cell carcinoma.