Cells possess several quality control mechanisms for a proper folding and function of protein. Malfunction of the mechanisms causes some protein folding diseases. Many proteins are modified with a glycosylphosphatidylinositol (GPI) anchor in the endoplasmic reticulum (ER), but the quality control mechanisms of GPI-anchored proteins are not clear, so far. We developed a model misfolded GPI-anchored protein (Gas1^*p). Gas1^*p can be modified with a GPI anchor in ER, however, the modified Gas1^*p was excreted and degraded rapidly via a proteasome. We found that deacylation of GPI by an enzyme (Bst1p) plays important role in the quality control of GPI-anchored proteins.