A mutant low density lipoprotein (LDL) receptor with abnormal ligand binding and recycling abilities was found in a patient with familial hypercholesterolemia. The molecular weights of the precursor and the mature form of the receptor were 72,000 and 115,000, respectively, which were about 45,000 smaller than those of the normal receptor. The mutant receptor was concluded to be present on the cell surface because the mature form was susceptible to Pronase digestion, and specific monoclonal antibody against the LDL receptor (IgG-C7) could bind to the cell surface. This mutant receptor could not bind LDL, but could bind other ligands for the LDL receptor, beta-migrating very low density lipoprotein, and the apolipoprotein E-lipid complex. After the receptor bound to the ligand, it disappeared from the cell surface of the mutant cells faster than that of normal cells, showing that, in the mutant cells, the receptor was not efficiently recycled back to the cell surface. Southern blotting of the genomic DNA from the patient showed a large deletion of about 12 kilobases around the epidermal growth factor precursor homology domain. For further characterization of the mutant, we cloned a 9.4-kilobase EcoRI/XbaI fragment, which was expected to contain the deletion joint. Mapping and sequencing analyses of the receptor gene showed that exons 7-14 were deleted. The nucleotide sequence suggested that this mutation may have occurred by recombination between repetitive Alu sequences in introns 6 and 14 of the receptor gene. The recombination brought about a complete deletion of the gene coding the epidermal growth factor precursor homology domain. The characteristics of the receptor protein produced by this mutation were similar to those of an artificial mutation constructed by Davis et al. (Davis, C. G., Goldstein, J. L., Südhof, T. C., Anderson, R. G. W., Russell, D. W., and Brown, M. S. (1987) Nature 326, 760-765) in which the whole gene coding this domain was deleted. The clinical phenotype of the patient having this mutation was similar to that of so-called "receptor-defective" type familial hypercholesterolemia, in which cells show detectable, but markedly reduced activity of the LDL receptor.