Estimation of a potential functional significance for the IVS2(+4) t/c, IVS4(-44) t/c и IVS5(-47) a/g polymorphisms of the HFE human hereditary hemochromatosis gene

We tried to undermine the functional significance of the intronic polymorphisms of the HFE gene. The HFE protein is the main regulator of the iron metabolism in human. We investigated haplotype frequencies for the IVS2(+4)t/c, IVS4(-47)t/c, and IVS5(-44)a/g polymorphisms and their linkages with C282Y, H63D, and S65S mutations of the HFE gene. Only four intronic haplotype variants (TTG, TTA, CTA, and CCA) were identified in various ethnic backgrounds in Russia. We found the linkage for the C282Y mutation with the TTG haplotype, H63D with CTA, and S65C with CCA. Context analysis was performed to reveal a potential influence of the intronic polymorphisms in splicing. The IVS2(+4)t/c polymorphism is located near the donor splice site junction and it is supposed to able to affect the choice of the 5${}'$ splice site by the U1 RNP. The IVS4(-44)t/c polymorphism is located at position -5 of a possible donor splice site. Predicted pre mRNA variants from different HFE alleles containing the retained 4-th intron sequences would generate soluble protein. The IVS5(-44)a/g polymorphism is located in the nucleotide block, which is homologous to the U6 snRNA and at the same time is complementary to the U2 snRNA fragment. The HFE intronic haplotype frequencies in hemochromatosis and iron overload patients and in a long-livers cohort were examined. Significant decrease ($\chi^2={}$6.335, p${}={}$0.012) of the ССА haplotype frequency in iron overload patients cohort was found.