The function of TMEM39A (transmembrane protein 39A, ENSG00000176142) is as follows. 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. .