CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1 , strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, attenuating its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22’s role in metabolism and have potential to differentially influence the human insulin response.*   CCV    :   clathrin-coated vesicles    CHC    :   clathrin heavy chain    CLC    :   clathrin light chain    GLUT4    :   glucose transporter 4    SNP    :   single nucleotide polymorphism    GFP    :   green fluorescent protein    FRAP    :   fluorescence recovery after photobleaching    GSC    :   GLUT4 storage compartment    HA    :   hemagglutinin    FACS    :   fluorescence-activated cell sorting    T2D    :   Type 2 diabetes    AFR    :   African    EUR    :   European    EAS    :   East Asian    AMR    :   Admixed American    SAS    :   South Asian    YRI    :   Yoruba from Nigeria    CEU    :   North Americans with Caucasian European ancestry    CHB    :   Han Chinese from Beijing    MSA    :   multiple sequence alignment    VCF    :   variant call format    HG    :   hunter-gatherer    EF    :   early farmer    MFI    :   mean fluorescent intensity

Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism