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Background: Factor XIII deficiency is a rare bleeding disorder (RBD) with a high incidence in Sistan and Baluchistan province, Iran. Central nervous system (CNS) bleeding is a common but life-threatening clinical presentation of severe factor XIII deficiency. This study aimed to assess the role of PAI-14G/5G polymorphism in occurrence of intra and extracranial hemorrhage in factor 13 deficiency. Methods: In this study, 64 patient with factor XIII deficiency were enrolled. Initially, according to the history of occurrence of CNS bleeding, patients were divided in two groups of case and control. At the baseline, both groups were evaluated for the Trp187Arg polymorphism in order to confirm their disorder. Then, all patients were assessed for PAI-14G/5G polymorphism. Findings: All study patients were homozygote for factor XIII polymorphism. We also found that the equal numbers of patients (4 individuals) in case and control groups were heterozygote for PAI-14G/5G polymorphism and none of patients were homozygote for this polymorphism. All heterozygote patients had intracranial hemorrhage and patients with extracranial hemorrhage had no mutation of PAI-14G/5G. Conclusion: PAI-14G/5G polymorphism did not any effect on occurrence of intra and extracranial hemorrhage in patients with factor 13 deficiency.