Sequence and structural properties of identical mutations with varying phenotypes in human coagulation factor IX

Mutations in human coagulation factor IX cause an X-linked bleeding disorder Hemophilia B, which can be classified as severe, moderately severe and mild based on the plasma levels of factor IX among affected individuals with respect to normal factor IX activity assayed in the patients' plasma (<1%, 2-5%, 6-30%, respectively). Recently, we identified hemophilia B to be a disease with mutations showing clinical variation and speculated that this phenotypic heterogeneity might be a replacement-specific property. Here, we have analyzed the differences in sequence and structural properties among identical mutations with varying phenotypes (IMVPs) by comparing with mutations with uniform phenotypes (MUPs), with recurring reports in Haemophilia B mutation database. Classification of mutations into IMVPs and MUPs has been done based on rigorous systematic evaluation of the clotting activity each mutation is associated with. IMVPs (n = 51) occur in less conserved mutant sites with more tolerated substitutions compared to MUPs (n = 100). A preponderance of CpG site mutations and Arg as the mutated residue in IMVPs compared to Cys in MUPs was observed. Hence, a CpG site substitution at less conserved Arg site might have an increased propensity of expressing variable phenotypes. The changes in intrinsic properties associated with the mutation are less drastic for IMVPs than for MUPs, though no significant differences were observed in structural properties. Based on this study and available literature we speculate that modifier genes at other loci, epigenetic interactions and environment may serve individually or cumulatively to bring about the clinical variation implicating hemophilia B to be deviation from classical Mendelian disorder with complete penetrance. We demonstrate that phenotypic heterogeneity appears to be site-specific also owing to the lesser conservation of the mutant site.