Abstract: Objective To investigate the association between single nucleotide polymorphisms (SNPs) of the transmembrane
protein 39A (TMEM39A) at the loci 1880G/A, 2442T/G, and 2456A/T and systemic lupus erythematosus (SLE) in Chinese Han
patients. Methods TMEM39A gene polymorphisms at 3 loci (1880G/A, 2442T/G, 2456 A/T) were analyzed using polymerase
chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 110 Chinese Han patients with SLE and 80 normal
control subjects, and the allele and genotype frequencies were compared by Chi-square test between the two groups. Results
Both the genotype frequencies (AA, GA and GG) and allele frequencies (A and G) at 1880G/A differed significantly between
SLE cases and the normal controls (P=0.002 and P=0.044, respectively). The two groups also showed significant differences in
the genotype frequencies (GG, TG and TT) (P=0.001) and allele frequencies (G and T) (P=0.041) at 2442T/G. No significant
differences were found in the genotype frequencies (TT, AT and AA) or allele frequencies (T and A) at 2456A/T between the
two groups (P>0.05). The allele and genotype frequencies of the 3 SNPs showed no significant differences between lupus
nephritis (LN) patients and non-LN patients. Conclusion The TMEM39A polymorphisms at 1880G/A and 2442T/G, but not at
2456 A/T gene, may be associated with the susceptibility to SLE in Chinese Han population. The genotype or allele frequencies
of the 3 SNPs have no effect on the incidence of lupus nephritis.