The most noteworthy coding SNP contained in the HA LD structure is rs16969968, a nonsynonymous α5 coding variant (p.Asp398Asn) resulting in substitution of a negatively charged residue within the M3–M4 intracellular loop, a region thought to be involved with receptor trafficking. The local amino acid context surrounding the p.Asp398Asn variant also displays accelerated protein evolution (higher lineage-specific Ka/Ks) in primate lineages within a class of genes related to nervous system development [53]. In mouse brain, α5 is a widely distributed minor subunit within heteromeric brain nAChRs, and incorporation of an α5 subunit into brain nAChRs leads to changes in receptor-level function [54]. The association of HA and the p.Asp398Asn variant with a nicotine dependence phenotype in humans suggests further research, such as an engineered mouse model, to explore the functional role and developmental expression of these variants within the process leading to chronic nicotine dependence. Both rs16969968 and rs1051730, a synonymous α3 variant, are in nearly complete linkage disequilibrium and, along with the HA LD structure, occur at significantly higher frequencies in European-American populations based on HapMap allele frequencies.
