Catalysis of the reaction: N-acetyl-D-glucosaminylphosphatidylinositol + H2O = D-glucosaminylphosphatidylinositol + acetate. This reaction is the second step of the biosynthesis of glycosylphosphatidylinositol (GPI), used to anchor various eukaryotic proteins to the cell-surface membrane.
GlcNAc-PI de-N-acetylase activity