Regulates autophagy by controlling the spatial distribution and levels of the intracellular phosphatidylinositol 4-phosphate (PtdIns(4)P) pools (PubMed:31806350). Modulates (PtdIns(4)P) levels by regulating the ER-to-Golgi trafficking of the phosphatidylinositide phosphatase SACM1L (PubMed:31806350). (Microbial infection) Positively regulates the replication of encephalomyocarditis virus (EMCV) via autophagy-dependent pathway. Interacts with SACM1L, SEC23A and SEC24A. (Microbial infection) Interacts with encephalomyocarditis virus (EMCV) major capsid proteins VP1 and VP2. Up-regulated in brain tumor glioblastoma multiforme cells (at protein level). Belongs to the TMEM39 family.