The lysosomal catabolism of sulfatide requires arylsulfatase A and a specific sphingolipid activator protein, SAP-1. While most patients with metachromatic leukodystrophy have mutations in the gene for arylsulfatase A, some patients have deficient SAP-1, as determined by immunological techniques. We now describe the molecular findings in a patient who died at 22 years of age with SAP-1 deficiency. The DNA polymerase chain reaction was used to amplify regions of cDNA which were subcloned in M13 phage DNA and sequenced by the dideoxy chain-termination method. The patient was found to have a 33-base-pair insertion between nucleotides 777 and -778 (numbered from the A of the ATG initiation codon). No other changes were found in the coding sequence of the cDNA from this patient. At the site of the insertion some normal people have an additional 9 base pairs, which correspond to the last 9 nucleotides at the 3' end of the insertion. The cDNAs from the second-cousin parents were amplified and sequenced, and in both two alleles were identified, one with the 33-base-pair insertion and one with no insertion. Two brothers were found to have only the normal alleles and a sister was found to have the 33-base-pair insertion and a normal allele. The findings confirm studies performed on leukocyte extracts demonstrating normal antigen levels in the two brothers and a lower level in the sister. The presence of i1 additional amino acids in the coding region of mature SAP-1 in this patient causes significant changes in the hydropathy profile compatible with the previous findings at the protein level.The catabolism of most sphingolipids requires both a specific lysosomal enzyme and a specific, relatively low molecular weight protein we call sphingolipid activator protein (SAP) (1). While at least six SAPs have been identified, the exact number is not known. However, it is now obvious that, while most lysosomal disorders are due to defects in lysosomal enzymes, some very serious and fatal disorders are due to defects in SAP (2-5). These include the AB variant of GM2 gangliosidosis, a variant form of metachromatic leukodystrophy, and a variant form of Gaucher disease. While the patients have clear evidence for decreased catabolism of a specific lipid, the lysosomal enzyme activity measured in vitro is normal and there is evidence for decreased levels of a specific SAP in all cases thus far identified (2,5,6).The cDNA coding for the SAP-1 precursor species, called prosaposin by Morimoto et al. (7), has been cloned and sequenced (8,9). Most recently Nakano et al. (10) published the complete corrected sequence, which is in agreement with our unpublished data, except those authors found a 9-base-pair (bp) insertion between nucleotides 777 and 778 (counting from the A of the ATG initiation codon) in clones from normal people. The SAP-1 precursor protein contains four domains of about 80 amino acids, each with similar structural features, including glycosylation sites and proline and cysteine residues (11-13). The domains are prot...