A genomic phage library was constructed using lymphocyte DNA from a patient with cross-reacting material-positive, moderately severe hemophilia B. The library was screened by using a full-length factor IX cDNA as a hybridization probe. DNA sequence analysis of the factor IX exons and intron/exon junctions revealed a single point mutation at nucleotide 31,311 of the gene. This mutation occurs in the protease domain of factor IXa and changes the codon for isoleucine 397 (ATA) to a threonine codon (ACA). The resulting abnormal protein has been named factor IXVancouver. Factor IXVancouver was isolated from the patient's plasma by barium citrate adsorption, affinity chromatography on a Ca2+-dependent antibody bound to agarose, and anion-exchange chromatography. On gel electrophoresis, the purified protein exhibited a normal molecular weight and a normal pattern of activation cleavages with bovine factor XIa. Kinetic studies on the purified protein indicated that the Km of factor IXaVancouver for human factor X was 3.4 times higher than that of normal factor IXa. The kcat of factor IXaVancouver was 12.5% of the kcat of normal factor IXa. Structural models of the protease domain of human factor IXa and of factor IXaVancouver were constructed, based on the homology of factor IXa with related serine proteases of known structure. The factor IXaVancouver model suggests that hydrogen bonding between the side chain hydroxyl group of threonine 397 and the carbonyl oxygen of tryptophan 385 reduces the ability of factor IXaVancouver to bind factor X in a configuration favoring catalysis.