CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive glucose transporter GLUT4, and so in post-prandial clearance of glucose from human blood. We performed population genetic and phylogenetic analyses of the CLTCL1 gene, encoding CHC22, to gain insight into its functional evolution. Analysis of 58 vertebrate genomes showed independent loss of CLTCL1 in at least two lineages after it arose from a gene duplication during the emergence of jawed vertebrates. All vertebrates studied retain the parent CLTC gene encoding CHC17 clathrin, which mediates endocytosis and other housekeeping pathways of membrane traffic, as performed by the single type of clathrin in non-vertebrate eukaryotes. For those species retaining CLTCL1, preservation of CHC22 functionality was supported by strong evidence for purifying selection over phylogenetic timescales, as seen for CLTC. Nonetheless, CLTCL1 showed considerably greater allelic diversity than CLTC in humans and chimpanzees. In all human population samples studied, two allelic variants of CLTCL1 segregate at high frequency, encoding CHC22 proteins with either methionine or valine at position 1316. Balancing selection of these two allotypes is inferred, with V1316 being more frequent in farming populations, when compared to hunter-gatherers, and originating an estimated 500-50 thousand years ago. Functional studies indicate that V1316-CHC22 is less effective at controlling GLUT4 membrane traffic than M1316-CHC22, leading to an attenuated insulin-regulated response, consistent with structural predictions and measurable differences in cellular dynamics of the two variants. These analyses suggest that CHC22 clathrin was subject to selection in humans with different diets, leading to allotypes that affect its role in nutrient metabolism and have potential to differentially influence the human insulin response.
