How Rare is Rare? TNFAIP3 Variants and the High Collective Burden of Haploinsufficiency

BackgroundMonogenic diseases are considered rare, yet many remain underdiagnosed when clinical manifestations are heterogeneous. A20 haploinsufficiency (HA20) is an early-onset inborn error of immunity (IEI) caused by heterozygous TNFAIP3 variants that dysregulate inflammatory signaling, producing diverse immune phenotypes. MethodsWe analyzed variants in all human haploinsufficiency (HI) disease genes in gnomAD, All of Us (AoU), and UK Biobank (UKBB), applying refined loss-of-function predictors. Rare TNFAIP3 variants (allele frequency <0.01%) were classified as predicted loss-of-function (pLOF) or functionally validated highly predicted pathogenic missense (fHPPM). Clinical associations were tested through meta-phenome-wide association studies (PheWAS) and phenome-set enrichment analysis (PSEA) and, for TNFAIP3, validated in a University of Pittsburgh referral cohort and a single center biobank at Mass General Brigham (MGB). FindingsDeleterious variants in human HI disease genes, including IEI-HI genes, occurred frequently despite strong constraint and were significantly associated with immune disease risk. TNFAIP3 pLOF variant prevalences were as high as [~]1:24,000; combined pLOF + fHPPM prevalences reached [~]1:9,000. PheWAS and PSEA linked rare TNFAIP3 variants to diverse immune phenotypes. In a referral cohort (18 patients, 9 families), missense variants conferred hypomorphism with intermediate immunophenotypes. In the MGB biobank, 29 individuals carried hypomorphic TNFAIP3 variants without a HA20 diagnosis; nearly two-thirds had phenotypes consistent with or plausibly related to A20 hypomorphism, suggesting penetrance exceeds 50%. Only 4 had received HA20-directed immunomodulatory therapy. InterpretationDeleterious IEI-HI variants are far more common than reported and are associated with immune dysregulation; hypomorphic TNFAIP3 variants are common and highly penetrant with variable expressivity. Genotype-first analysis of institutional biobanks can identify untreated IEI-HI patients. These findings establish proof-of-concept that haploinsufficiency diseases are pervasively underrecognized. Patients with early-onset or treatment-refractory immune disease should be prioritized for genetic testing; biobank callback amendments may expedite diagnosis, monitoring, and precision therapy.