Disease-associated AIOLOS variants lead to immune deficiency/dysregulation by haploinsufficiency and redefine AIOLOS functional domains.

AIOLOS, also known as IKZF3, is a transcription factor highly expressed in the lymphoid lineage and critical for lymphocyte differentiation and development. Here we report nine individuals from three unrelated families carrying AIOLOS variants Q402* or E82K leading to AIOLOS haploinsufficiency through different mechanisms of action. Nonsense mutant Q402* displayed abnormal DNA binding, pericentromeric targeting, post-transcriptional modification, and transcriptome regulation. Structurally, the mutant lacks the AIOLOS zinc finger (ZF) 5-6 dimerization domain, but is still able to homodimerize with WT AIOLOS and negatively regulate DNA binding through ZF1, a previously unrecognized function for this domain. Missense mutant E82K showed overall normal AIOLOS functions; however, by affecting a redefined AIOLOS protein stability domain, it also led to haploinsufficiency. AIOLOS haploinsufficiency patients showed hypogammaglobulinemia, recurrent infections, autoimmunity and allergy, but with incomplete clinical penetrance. Altogether, these data redefine AIOLOS structure-function relationship and expand the spectrum of AIOLOS-associated diseases.