We describe an ALG9 defective (Congenital Disorders of Glycosylation type IL) patient who is homozygous for the p.Y286C (c.860A>G) mutation. This patient presented with psychomotor retardation, axial hypotonia, epilepsy, failure to thrive, inverted nipples, hepatomegaly and pericardial effusion. Due to the ALG9 deficiency, the cells of this patient accumulated the lipid-linked oligosaccharides Man(6)GlcNAc(2)-PP-dolichol and Man(8)GlcNAc(2)-PP-dolichol. It is known that the oligosaccharide structure has a profound effect on protein glycosylation. Therefore we investigated the influence of these truncated oligosaccharide structures on the protein transfer efficiency, the quality control of newly synthesized glycoproteins and the eventual degradation of the truncated glycoproteins formed in this patient. We demonstrated that lipid-linked Man(6)GlcNAc(2) and Man(8)GlcNAc(2) are transferred onto proteins with the same efficiency. In addition, glycoproteins bearing these Man(6)GlcNAc(2) and Man(8)GlcNAc(2) structures efficiently entered in the glucosylation/deglucosylation cycle of the quality control system to assist in protein folding. We also showed that in comparison to control cells, patient's cells degraded misfolded glycoproteins at an increasing rate. In comparison to Man(6)GlcNAc(2), the Man(8)GlcNAc(2) isomer C on the patient's glycoproteins was found to promote the degradation of misfolded glycoproteins.