Molecular analysis of the glycoasparaginase gene was performed on two Japanese siblings with aspartylglucosaminuria. The cDNA from one patient contained 7 additional bases between exons 3 and 4 (3'-terminal sequence of intron 3). This insertion resulted in a frame shift, and a termination codon appeared at amino acid 146. Amplification and sequencing of genomic DNA detected a single base transition (A-->G) at the 5' side adjacent to the insertion sequence. This mutation created a consensus AG dinucleotide in the splice acceptor site, and produced almost exclusively an abnormal mRNA containing the insertion by alternative splicing. The calculation of the sample score of the acceptor site supported this analytical result. BsmAI restriction site analysis of amplified cDNA and genomic DNA showed that these patients were homozygotes for this mutation. We conclude that the splicing defect in intron 3 causes glycoasparaginase deficiency in these patients.