Metachromatic leukodystrophy is a metabolic disorder caused by the deficiency of arylsulfatase A. Deficiency of this enzyme is also found in apparently healthy individuals, a condition for which the term pseudodeficiency was introduced. The arylsulfatase A (cerebroside-3-sulfate 3-sulfohydrolase; EC 3.1.6.8) (ASA) encoding gene was isolated from an individual homozygous for the ASA pseudodeficiency allele. Sequence analysis revealed two A --G transitions. One changes Arg-350 to serine, which leads to the loss of a utilized N-glycosylation site. This loss explains the smaller size of ASA in ASA pseudodeficiency fibroblasts. The introduction of Ser-350 into normal ASA cDNA does not affect the rate of synthesis, the stability, or the catalytic properties of ASA in stably transfected baby hamster kidney cells. Therefore, the loss of the N-linked oligosaccharide does not contribute to the reduction of ASA activity in ASA pseudodeficiency. The other A -* G transition changes the first polyadenylylation signal downstream of the stop codon from AATAAC to AGTAAC. The latter causes a severe deficiency of a 2.1-kilobase (kb) mRNA species. The deficiency of the 2.1-kb RNA species provides an explanation for the diminished synthesis of ASA seen in pseudodeficiency fibroblasts. Amplification of genomic DNA and hybridization with allele-specific oligonucleotides detected both mutations in four unrelated individuals with ASA pseudodeficiency.Metachromatic leukodystrophy is a lysosomal storage disorder caused by the deficiency of arylsulfatase A (cerebroside-3-sulfate 3-sulfohydrolase; EC 3.1.6.8) (ASA), which leads to the intralysosomal accumulation of cerebroside sulfate (1). The incidence of this recessively inherited disease is estimated to be 1:40,000. The sulfatide storage affects mainly the central nervous system, causing a progressive demyelination that eventually leads to the death of the patient. Based on the age of onset three clinical variants of metachromatic leukodystrophy are differentiated: late infantile,juvenile, and adult (1). The molecular basis for this heterogeneity is not known, and the determination of the residuaL ASA activity does not permit differentiation between the various forms.Occasionally, the deficiency of ASA is found in apparently healthy individuals, a condition known as ASA pseudodeficiency (2). The ASA deficiency in metachromatic leukodystrophy and pseudodeficiency are caused by allelic mutations of the same gene (3). It has been shown that the ASA synthesized in fibroblasts from individuals with ASA pseudodeficiency is reduced in quantity and smaller in size when compared to normal (4). While the size difference has been attributed to altered glycosylation, the reasons for the attenuated ASA activity remained unclear.The high frequency of the ASA pseudodeficiency allele of 7-15% (5, 6) and the inability to distinguish reliably homoand heterozygotes for nonfunctional and pseudodeficiency ASA alleles by ASA activity determinations with artificial or natural substrates pose serious pr...