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Vitamin D deficiency has adverse effects on renal allograft outcomes, and polymorphisms of genes encoding vitamin D-binding protein (VDBP) and vitamin D receptor (VDR) are defined to play a role in these conditions. The goal of the current investigation was to evaluate the connection between those polymorphisms with acute rejection, viral infection history, and recipients’ vitamin D status. In this study, 115 kidney transplant recipients and 100 healthy individuals were included. VDR polymorphisms including <i>Fok</i>I (rs2228570), <i>Apal</i> (rs7975232), <i>BsmI</i> (rs1544410), as well as VDBP (rs7040) polymorphisms were studied using high resolution melting (PCR-HRM) analysis among the studied groups. The frequency of G allele in <i>Apal</i> rs7975232 polymorphism in the kidney transplant recipients was 0.63 times lower than healthy individuals (<i>p</i> = 0.026). Further, the G allele frequency in VDBP rs7040 polymorphism was significantly lower in patients with allograft rejection (<i>p</i> = 0.002). Considering the incidence of viral infection, significant differences were identified between the frequencies of VDR <i>Fok</i>I (OR = 2.035; 95% CI 1.06–2.89, <i>p</i> = 0.030) and VDBP rs7040 (OR = 0.40; 95% CI 0.24–0.67, <i>p</i> < 0.001) T alleles in the studied groups. Moreover, the VDBP rs7040 GG genotype distribution was low in the recipients with a history of viral infection (<i>p</i> = 0.004). VDR (<i>Fok</i>I) and VDBP (rs7040) alleles and their genotype distribution are significantly associated with allograft outcomes including allograft rejection and viral infection in the studied population.