Motivated by the specific clinical need of biomarkers specific to rare subtypes of renal cell carcinoma, we carried out multi-omics analyses to identify protein/mRNA biomarkers to distinguish benign ROs from chRCC (MAPRE3, ADGRF5, GPNMB), pRCC from MTSCC (SOSTDC1, PIGR), and tumors with high wGII (PYCR1, IGF2BP3). The gene discussed is MAPRE3; the disease is hereditary clear cell renal cell carcinoma.