A human specific CCG repeat in the RBFOX1 promoter is implicated in speech and autism

Human speech likely arose from regulatory changes for speech-related brain regions, yet causal variants and mechanisms remain unclear. RBFOX1 is a prime candidate, showing specialized expression in vocal learning circuits of human and zebra finch brains and carrying a promoter deletion linked to autism spectrum disorder (ASD) with language dysfunction. Here, we perform integrative analyses with cross-species brain single-cell multi-omic data and the more complete genomes of the Vertebrate Genomes Project. We identify a human-specific CCG insertion in the RBFOX1 promoter, creating a human-unique CCG-repeated motif. This motif is fixed in both archaic and modern humans but is disrupted by rare clinical variants that exhibit language-related phenotypes and autism. Binding motif models predicted, and reporter assays reveal that this human allele drives stronger EGR1-dependent transcription than its chimpanzee allele. Genome-wide, 107 other genes have core promoters with the identical motif; enriched for postsynapse and implicated in ASD, including PTCHD1. At the PTCHD1 promoter, an ASD-causative CCG-repeated variant enhances EGR1-dependent promoter activity, and its activating effects are predicted in human brain regions using AlphaGenome. Our findings suggest that small variations in the number of CCG repeats in promoters can exert a large regulatory effect on complex traits and their associated disorders.