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Background: Autophagy is an important cellular pathway in cell growth and maintenance, during which unnecessary organelles and materials in cells can be degraded. Regulation of autophagy is related to tumorigenesis. SETD2 is a histone methyltransferase and mutation of SETD2 has been identified in different human cancers, especially in clear cell renal cell carcinoma. Previous results of the laboratory showed evidence of SETD2 involvement in autophagy regulation. Therefore, the focus of this report is on autophagy regulation of SETD2 in clear cell renal cell carcinoma. Aim: To investigate the impact of SETD2 mutation in autophagy pathway in clear cell renal cell carcinoma cells Methods: Cells were cultured in standard procedure in optimal medium. Immunoblotting was used to examine protein expression level. RT-qPCR was used to determine mRNA expression level of certain gene. Localization of protein expression was detected by immunofluorescence. Results: SETD2 deficient cell lines showed less accumulation of p62 and LC3B when blocking the fusion of autophagosome and lysosome. In SETD2 deficient cell lines, an extra band and higher signal of free ATG12 were found when blotted with ATG12-ATG5. Expression of alternative splicing marker was also lower when SETD2 was mutated. Conclusion: SETD2 might be related to a lower autophagic flux and might be involved in autophagosome formation by affecting formation of ATG12-ATG5-ATG16L complex. SETD2 deficiency might also decrease alternative splicing. Further investigations are required to give solid statement.