Systematic and proactive evaluation of AIRE missense variant effects

Pathogenic variants in the autoimmune regulator (AIRE) cause autoimmune polyendocrine syndrome type 1 (APS-1), a rare primary immunodeficiency disease with symptoms including hypoparathyroidism, adrenal insufficiency, and chronic mucocutaneous candidiasis. AIRE increases the expression and presentation of tissue-specific genes expressing "self" antigens in the developing T cell niche, thus triggering the elimination of self-reactive T cells and preventing autoimmunity. Earlier diagnoses can benefit those with APS-1, and APS-1 diagnosis by AIRE sequencing is increasingly common. However, two-thirds of reported clinical variants are missense, and more than half of these are variants of uncertain significance (VUSs). Cell-based variant functional assays can provide strong evidence toward more informative variant classification, but these are carried out reactively, often years after clinical presentation. By contrast, proactively assessing all possible missense variants could provide immediate evidence to guide genetic diagnosis, even for never-before-seen variants. Here, we used an insulin-promoter-driven reporter to proactively assess the function of 9,790 AIRE missense variants. The resulting AIRE variant effect map both validates and extends current biochemical knowledge, concords with pathogenicity annotations, and provides proactive evidence for 70% of previously reported VUSs. Placing our map in the context of both an international APS-1 cohort and the UK Biobank revealed quantitative genotype-phenotype correlations. Moreover, evidence from our variant effect map resolved 32% of current VUSs. Together, our proactive resource of AIRE variant impacts offers the potential to improve outcomes via more rapid and definitive APS-1 diagnosis.