We have identified several mutations causing beta-glucuronidase (beta Gl) deficiency in three cases with mucopolysaccaridosis type VII (MPS VII). Enzyme assay of lysates of these lymphocytes or cultured fibroblasts showed little residual activity and that the beta Gl-specific mRNA levels were normal, as revealed by Northern blot analysis. Mutated cDNA clones including the entire coding sequencing were isolated from a library in case 1 and PCR (polymerase chain reaction) products in case 2 and 3 derived from cultured fibroblasts. Sequencing of the full-length mutated cDNA revealed C----T transitions, an event causing a single Ala619----Val change (cases 1 and 2) and Arg382----Cys and Pro649----Leu changes (case 3). The former change is detected by loss of the cleavage site for the enzyme Fnu 4 HI in the mutated cDNA. On the basis of the loss of Fnu 4 HI restriction site, the patients (cases 1 and 2) were shown to be a homozygote with this mutation and the parents and brother in case 1 were heterozygotes. The Ala619----Val and Arg382----Cys mutations disrupt a functional domain consisting of a region of sequence highly conserved among human, rat and bacterial beta Gl's, and they lower the enzyme activity, as tested by transfection of COS cells with expression vectors harboring the mutated cDNA. However the Pro649----Leu mutation does not lower the enzyme activity.