Phosphatidylinositol 3-kinase required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific VPS34 PI3-kinase complex I. Also involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II (By similarity). a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H(+) Component of the autophagy-specific VPS34 PI3-kinase complex I composed; and of the VPS34 PI3-kinase complex II. Belongs to the PI3/PI4-kinase family.