Our study screened key core genes from a human CKD dataset and constructed a CKD progression risk prediction model. The core genes associated with the occurrence and progression of CKD, such as the minimal gene set (CCL2, SUCLG1, and ACADM) and the moderate gene set (CCL2, GGT6, PCK2, SFXN2, SLC34A3, ALPL, GLTPD2, ACADM, and SUCLG1), are closely related to the progression-free survival prognosis in CKD patients. Additionally, these genes are also closely related to the overall survival prognosis in patients with renal clear cell carcinoma. We believe that the gene sets identified in this study have potential experimental research value for investigating the mechanisms in CKD and renal clear cell carcinoma.