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A comparison of TPP\u2010I amino acid sequences with sequences derived from an EST database suggested that TPP\u2010I is identical to a pepstatin\u2010insensitive carboxyl proteinase of unknown specificity which is mutated in classical late infantile neuronal ceroid lipofuscinosis (LINCL), a lysosomal storage disease. Both TPP\u2010I and the carboxyl proteinase have an <jats:italic>M<\/jats:italic>\n<jats:sub>r<\/jats:sub> of about 46 kDa and are, or are predicted to be, resistant to inhibitors of the four major classes of proteinases. Fibroblasts from LINCL patients have less than 5% of the normal TPP\u2010I activity. The activities of other lysosomal enzymes, including proteinases, are in the normal range. LINCL fibroblasts are also defective at degrading short polypeptides and this defect can be induced in normal fibroblasts by treatment with a specific inhibitor or TPP\u2010I. 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