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 germline TNFAIP3 variants, resulting in dysregulated inflammatory signaling and diverse immune phenotypes. MethodsWe analyzed variants in all human haploinsufficiency disease genes in gnomAD v4, applying refined loss-of-function predictors to estimate population frequencies. We assessed rare TNFAIP3 variants (allele frequency <0.01%) in All of Us (AoU), UK Biobank (UKBB), and gnomAD. Variants were classified as predicted loss-of-function (pLOF) or high predicted pathogenic missense (HPPM). Clinical associations were tested through phenome-wide association studies (PheWAS) and validated in a University of Pittsburgh referral cohort. FindingsHigh-confidence deleterious variants in human haploinsufficiency disease genes, including IEI haploinsufficiency genes, occur frequently at the population level despite strong constraint. Across datasets, TNFAIP3 pLOF variants corresponded to estimated prevalences of [~]1:14,400 (U.S.) and [~]1:23,700 (global); combined pLOF + HPPM prevalences were [~]1:2,800 (U.S.) and [~]1:4,900 (global). PheWAS linked rare TNFAIP3 variants to immune phenotypes with large effect sizes. In a referral cohort (18 patients, 9 families), missense variants conferred hypomorphism with intermediate immunophenotypes. InterpretationDeleterious TNFAIP3 variants are over 100-fold more common than reported cases suggest and are associated with immune dysregulation spanning variable expressivity and severity. These findings establish proof-of-concept that haploinsufficiency diseases may be pervasively underrecognized. Patients with early-onset or treatment-refractory autoimmune disease should be considered for genetic testing, as precision therapies are available and commercial panels already incorporate TNFAIP3. FundingThis work was supported by NIAID (T32-AI074490, T32-GM144300), the Jeffrey Modell Foundation, Rheumatology Research Foundation, Samuel and Emma Winters Foundation, University of Pittsburgh Competitive Medicine Research Fund, Sobi, and Eli Lilly. Research in Context Evidence before this studyPrior database analyses estimated that pathogenic variants in constrained haploinsufficiency genes may occur more frequently than case reports suggest, but these observations have not been validated clinically or for specific genetic diseases. Haploinsufficiency of A20 (HA20) is a monogenic immune disorder caused by deleterious variants in TNFAIP3, with fewer than 200 cases reported worldwide. Previous studies characterized clinical phenotypes and treatment responses but did not systematically assess population-level prevalence. Added value of this studyThis is the first study to establish that a monogenic immune disease is substantially underrecognized at the population level. We first show that predicted deleterious variants in haploinsufficiency disease genes, including inborn errors of immunity, occur at unexpectedly high frequencies in population databases. We then demonstrate that predicted and functionally validated deleterious TNFAIP3 variants occur at over 100-fold higher frequencies than reported case numbers suggest. We further validate this through phenome-wide association studies showing that variant carriers have significantly elevated rates of immunologic disease, and through deep phenotyping of a referral cohort. Implications of all the available evidenceThese findings indicate that HA20, and likely other haploinsufficiency diseases, represent a substantial burden of undiagnosed monogenic disease. Clinicians evaluating patients with early-onset or treatment-refractory autoimmune and autoinflammatory conditions should consider genetic testing for inborn errors of immunity including HA20. The high prevalence of pathogenic variants, combined with the availability of targeted therapies, underscores the clinical urgency of improved recognition and diagnosis.