A single nucleotide A49G polymorphism (SNP) of CTLA-4 has been linked and associated with the autoimmune thyroid diseases (AITD) and thyroid autoantibody secretion. We have explored the functional mechanisms of CTLA-4 by means of recombinant human CTLA-4 expressed on transfected Jurkat T cells. Analysis of CTLA-4 transcripts with quantitative real-time PCR demonstrated similar baseline and PHA-stimulated levels for both the A49 and G49 alleles, which were markedly enhanced by anti-CTLA-4 engagement. Both alleles also coded for proteins which were expressed on the cell membrane, as measured by FACS analysis using anti-CTLA-4 (G: 34.4+/-11.9% cells, A: 27.6+/-8.6% cells) (p=ns). Baseline and PHA-stimulated IL-2 production were also similar among control and CTLA-4 clones expressing both alleles. After anti-CTLA-4 engagement, IL-2 production was markedly inhibited in a dose- and time-dependent manner but this also appeared to be similar in the A and G allele expressing cells (95.7+/-1.2% inhibition and 94.9+/-1.1% inhibition, respectively). In conclusion, both the extrinsic and intrinsic actions of human CTLA-4 were not affected by the signal peptide A49G polymorphism. Therefore, the linkage of the CTLA-4 A49G SNP to AITD is most likely secondary to linkage disequilibrium.