Dissection of pleiotropic effects of missense mutations, scarcely investigated in inherited diseases, is fundamental to understanding genotype-phenotype relationships. Missense mutations might impair mRNA processing in addition to protein properties. As a model for haemophilia A (HA) we investigated the highly prevalent F8 p.R2016W/c.6046c>t (exon 19) mutation. In expression studies exploiting lentiviral vectors, we demonstrated that the aminoacid change impairs both secretion (FVIII:Ag 11.0+/-0.4% of wild-type) and activity (FVIII:C 6.0+/-2.9%). Investigations in patients' ectopic F8 mRNA and with minigenes showed that the corresponding nucleotide change also decreases correct splicing to 70+/-5%, which is predicted to lower further FVIII:C (4.2+/-2%), consistently with FVIII:C levels observed in patients (1-5%). Masking the mutated exon 19 region by antisense U7snRNA supported the presence of a splicing regulatory element, potentially affected by several HA-causing missense mutations. Among these, the c.6037g>a (p.G2013R) reduced exon inclusion to 41±3% and the c.6053a>g (p.E2018G) to 28+/-2%, similarly to a variant affecting the 5' splice site (c.6113a>g, p.N2038S, 26+/-2%), which displayed normal protein features upon recombinant expression. The p.G2013R remarkably reduced both FVIII:Ag (7.0+/-0.9%) and FVIII:C (8.4+/-0.8%), while the p.E2018G produced a dysfunctional molecule (FVIII:Ag, 69.0+/-18.1%; FVIII:C, 19.4+/-2.3%). In conclusion, differentially altered mRNA and protein patterns produce a gradient of residual FVIII:C, and clarify genotype-phenotype relationships. The integrated approach details pathogenic mechanisms that, only in combination, account for symptomatic HA and thus determine the HA mutation profile. Overall data provide a clear example of interplay between mRNA and protein mechanisms of disease that certainly operate in shaping many other inherited disorders.