Phosphatase that acts on lipids with a phosphoinositol headgroup. Dephosphorylates phosphatidylinositol 3-phosphate (PtdIns(3P and phosphatidylinositol 3,5-bisphosphate (Probable. Binds with high affinity to phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5P2 but also to phosphatidylinositol 3-phosphate (PtdIns(3P, phosphatidylinositol 4-phosphate (PtdIns(4P, and phosphatidylinositol 5-phosphate (PtdIns(5P, phosphatidic acid and phosphatidylserine. Negatively regulates ER-Golgi protein transport (By similarity. Probably in association with MTMR9, plays a role in the late stages of macropinocytosis by dephosphorylating phosphatidylinositol 3-phosphate in membrane ruffles. Acts as a negative regulator of KCNN4/KCa3.1 channel activity in CD4(+ T-cells possibly by decreasing intracellular levels of phosphatidylinositol 3-phosphate. Negatively regulates proliferation of reactivated CD4(+ T-cells. In complex with MTMR9, negatively regulates DNA damage-induced apoptosis. The formation of the MTMR6-MTMR9 complex stabilizes both MTMR6 and MTMR9 protein levels.