Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants

Mutations in the transcription factor PAX6 cause eye development defects, including aniridia, microphthalmia and coloboma. To understand the molecular mechanisms, we combined saturation mutagenesis of the paired domain of PAX6 with a yeast one-hybrid (Y1H) assay in which expression of a PAX6-GAL4 fusion gene drives antibiotic resistance. We quantified binding of more than 2,700 single amino-acid variants to two DNA sequence elements. Mutations in DNA-facing residues of the N-terminal subdomain and linker region were most detrimental, as were mutations to prolines and to negatively charged residues. Some variants, including Ile71Tyr, increased binding to one of the DNA elements. In the absence of antibiotic selection, variants that retained DNA binding slowed yeast growth, likely because such variants perturbed the yeast transcriptome. Benchmarking against known patient variants, we obtained supporting-to-moderate evidence that 977 variants are likely pathogenic and 1,306 are likely benign. Our analysis shows that most pathogenic mutations in PAX6 can be explained by effects on PAX6:DNA association, and establishes Y1H as a generalisable assay for the interpretation of variant effects in transcription factors.