Pycnodysostosis (Pycno) is a rare, autosomal recessive sclerosing skeletal dysplasia with features that include short stature, osteosclerosis, frequent fractures, and bony abnormalities. Linkage analysis, physical mapping and the positional candidacy approach mapped the Pycno locus to 1q21, and identified specific gene defects in three Pycno families in cathepsin K (Cat K), a lysosomal protease (Science 1996, 273: 1236). Nine additional Pycno families were analyzed for Cat K mutations and molecular modeling approaches were used to study their functional consequences. Mutations were identified by amplifying and sequencing the seven exons containing the entire coding region, and confirmed using PCR-based restriction polymorphisms. Seven Cat K mutations were found- a proregion nonsense (K52X), a proregion missense (G79E), and five mature enzyme missense lesions (G146R, Y212C, R241X, A277E, and R312G). Including three families studied previously, the ancestors of nine of 12 families were from the Iberian peninsula and two mutations, G146R and R241X, were each found in four of these families, indicating a possible common origin for these mutations. Molecular modeling of the G79E proregion mutation revealed that a charge change was introduced at position 6 within a conserved GxNxFxD motif which was predicted to cause significant conformational alteration of this region, probably resulting in improper folding and/or protein instability. A three-dimensional molecular model of the mature enzyme was constructed based on known structures of other papain family members. The R146 and E277 mutant residues were buried within the active cleft but could be accommodated. The R146 mutation appeared to shift the pK's of the active site Cys-His sufficiently to preclude the proton transfer required for catalysis. The effects of the E277 mutation seemed to be primarily steric due to the bulky side group. Y212 was a surface residue but C212 might interfere with the C170-C210 disulfide bridge, potentially destabilizing the molecule. Future studies of Cat K mutations should facilitate development of inhibitors useful for the treatment of bone diseases with relatively excessive bone degradation such as osteoporosis.