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M ucolipidosis IIIC, or variant pseudo-Hurler polydystrophy, is an autosomal recessive disease of lysosomal hydrolase trafficking. Unlike the related diseases, mucolipidosis II and IIIA, the enzyme affected in mucolipidosis IIIC (N-Acetylglucosamine-1-phosphotransferase [GlcNAc-phosphotransferase]) retains full transferase activity on synthetic substrates but lacks activity on lysosomal hydrolases. Bovine GlcNAc-phosphotransferase has recently been isolated as a multisubunit enzyme with the subunit structure α₂β₂γ₂. We cloned the cDNA for the human γ-subunit and localized its gene to chromosome 16p. We also showed, in a large multiplex Druze family that exhibits this disorder, that MLIIIC also maps to this chromosomal region. Sequence analysis of the γ-subunit cDNA in patients from 3 families identified a frameshift mutation, in codon 167 of the γ subunit, that segregated with the disease, indicating MLIIIC results from mutations in the phosphotransferase γ-subunit gene. This is to our knowledge the first description of the molecular basis for a human mucolipidosis and suggests that the γ subunit functions in lysosomal hydrolase recognition.