In this study, we investigated the distribution of rare variants in CHRNA4 in more than 2000 ND cases and comparison subjects. Compared to cases, controls had a significantly higher frequency of rare nonsynonymous variants located in the exon 5 region encoding the cytoplasmic loop of the α4 nAChR (FET p=0.009; association test p=0.009, OR=0.43, 95%CI=0.23-0.81; WSM p=0.014). Functional in-silico analysis (PolyPhen) further demonstrated that the comparison subjects carried significantly more potentially damaging rare nonsynonymous variants than the cases (FET p=0.005; association test p=0.008, OR= 0.29, 95%CI=0.11-0.72; WSM p=0.005), suggesting that some rare functional variants exert a protective effect against ND. In addition, although we observed that comparison subjects had a higher frequency of rare nonsynonymous variants in the exon 5 cytoplasmic loop region in both EAs and AAs, the difference was significant only in AAs.
