Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee

1Inborn errors of immunity, also referred to as primary immunodeficiencies, manifest as increased susceptibility to infectious diseases, autoimmunity, autoinflammatory diseases, allergy, and/or malignancy. These conditions are caused by monogenic germline mutations that result in loss of expression, loss-of-function (LOF; amorphic/hypomorphic), or gain-of-function (GOF; hypermorphic) of the encoded protein. Heterozygous lesions may underlie autosomal dominant traits by GOF, haploinsufficiency, or negative dominance. Biallelic lesions typically cause autosomal recessive traits by LOF of the encoded protein (rarely GOF), while X-linked recessive traits arise from LOF of genes on the X chromosome, either in the hemizygous state in males or in the homozygous state in females. Rare X-linked dominant traits can also arise from LOF or GOF variants. This results in aberrant immunity due to the critical roles of these proteins in the development, maintenance and function of cells of the immune system, or cells other than leukocytes that contribute to immunity, during homeostasis and in response to external (e.g., infectious agents or environmental antigens) and internal (e.g., cytokines, self-antigens and cancer cells) stimuli. Inborn errors of immunity were traditionally considered to be rare diseases, affecting ~ 1 in 10,000 to 1 in 50,000 births. However, with ongoing discovery of novel inborn errors of immunity (Fig. 1a) and improved definition of clinical phenotypes, the collective prevalence of these conditions is more likely to be at least 1/1000–1/5000. Indeed, more common inborn errors have recently been described. Regardless of their exact incidence and prevalence, inborn errors of immunity represent an unprecedented model to link defined monogenic defects with clinical phenotypes of immune dysregulation, in a broad sense of the term. As a committee, we are aware that human immunity involves cells other than circulating or tissue leukocytes and that it can be scaled up from the immune system to the whole organism. Inborn errors of immunity have unequivocally revealed non-redundant roles of single genes and their products in immune function, formed the basis of improved mechanism-based therapies for the immunopathology underlying many diseases, established immunological paradigms representing the foundations of basic, clinical and translational immunology, and provided insights into the molecular pathogenesis of more common diseases. Clear examples of these include:The initial description by Bruton of X-linked agammaglobulinemia (XLA) and the ability to treat this condition with antibody replacement therapy (the mainstay treatment for antibody deficiency diseases such as CVID)The discovery of mutations in BTK and the subsequent development of BTK-inhibitors such as ibrutinib for the treatment of B cell malignanciesProgressive CD4 T cell deficiency explains opportunistic infections secondary to HIV infection.

2The initial description by Bruton of X-linked agammaglobulinemia (XLA) and the ability to treat this condition with antibody replacement therapy (the mainstay treatment for antibody deficiency diseases such as CVID)

3The discovery of mutations in BTK and the subsequent development of BTK-inhibitors such as ibrutinib for the treatment of B cell malignancies

4Progressive CD4 T cell deficiency explains opportunistic infections secondary to HIV infection.

5Thus, the study of inborn errors of immunity has provided profound advances in the practice of precision molecular medicine.

6Since the early 1950s, when XLA was one of the first primary immune deficiencies to be described, clinical immunology has leveraged advances in the development of new methods to expedite the identification of defects of the immune system and the cellular, molecular, and genetic aberrations underlying these conditions. Indeed, the completion of the Human Genome Project in the early 2000s, coupled with rapid developments in next generation DNA sequencing (NGS) technologies, enabled the application of cost-effective and time-efficient sequencing of targeted gene panels, whole exomes, or whole genomes to cohorts of patients suspected of having a monogenic explanation for their disease. These platforms have led to a quantum leap in the identification and diagnosis of previously undefined genetically determined defects of the immune system (Fig. 1a, b;).

7The International Union of Immunological Societies Expert Committee of Inborn Errors of Immunity comprises pediatric and adult clinical immunologists, clinician/scientists and researchers in basic immunology from across the globe (https://iuis.org/committees/iei/). A major objective and responsibility of the committee is to provide the clinical and research communities with an update of genetic causes of immune deficiency and dysregulation. The committee has existed since 1970 and has published an updated report approximately every 2 years to inform the field of these advances (Fig. 1a). In March 2019, the committee met in New York to discuss and debate the inclusion of genetic variants published over the preceding 2 years (since June 2017), as well as gene mutations that had appeared in the literature earlier but, based on newly available evidence, were now substantiated (Fig. 1b).

8Rather than simply including every gene variant reported, the committee applies very stringent criteria such that only those genes with convincing evidence of disease pathogenicity are classified as causes of novel inborn errors of immunity. The Committee makes informed judgments for including new genetic causes of immunological conditions based on what we believe is most useful for practitioners caring for patients. Our current, and continuously evolving, practice is that criteria for inclusion can be met by several ways, for instance peer-reviewed publication of (1) multiple cases from unrelated kindreds, including detailed immunologic data, or (2) very few cases, or even a single case (see below), for whom compelling mechanistic/pathogenic data is also provided, generally from parallel studies in an animal or cell culture model.

9Herein, we provide this latest update. The inborn errors of immunity are listed in 10 tables: Combined immunodeficiencies (Table 1), Combined immunodeficiencies with syndromic features (Table 2), Predominantly antibody deficiencies (Table 3), Diseases of immune dysregulation (Table 4), Congenital defects of phagocytes (Table 5), Defects in intrinsic and innate immunity (Table 6), Autoinflammatory diseases (Table 7), Complement deficiencies (Table 8), and Phenocopies of inborn errors of immunity (Table 10) (Fig. 1b). Since the last update (published January 2018), we have added a new table to consolidate genes that cause bone marrow failure (Table 9). Our division into phenotypes does not imply that the presentation is homogeneous. Rather, we recognize that substantial phenotypic and clinical heterogeneity exists within groups of patients with mutations in the same gene and even between individuals from the same pedigree with the identical gene mutation. To simplify the classification, each disorder has been listed only once, although distinct disorders due to mutations in the same gene, but with different modes of inheritance and pathogenic mechanisms are listed individually. Thus, several genes appear more than once in this update (some examples are listed below). Sub-divisions within each table segregate groups of disorders into coherent phenotypic sets. OMIM numbers are also provided within each table. If a OMIM number has not yet been issued for a particular genetic condition, then the number provided generally refers to the OMIM for that gene. Beneath each table, the new disorders added to this update are highlighted for easy reference.

10The advances in our understanding of clinical immunology continue to expand at a vast and remarkable rate, with the addition in this update of many—64, distributed across all tables (Fig. 1b)—novel genetic defects underlying inborn errors of immunity. Perhaps not surprisingly, most if not all of these new variants were identified by NGS, thus highlighting that whole exome/whole genome sequencing has become the gold standard for identifying novel pathogenic gene variants. Indeed, since the first application of NGS to identify novel inborn errors of immunity was published in 2010, ~ 45% of all currently known disease-causing variants have been discovered by whole exome/genome sequencing. Thus, a typical approach to identifying a pathogenic variant in a new patient might now consist of first sequencing a phenotype-driven panel of genes and advancing to whole exome/genome sequencing if the cause of disease remains elusive.

11In this update, we increase the list of immunological diseases to 404, with 430 known genetic defects identified as causing these conditions. The unbiased application of NGS to the discovery and characterization of novel inborn errors of immunity continues to inform clinical and basic immunology. Thus, additional phenotypes have been identified for conditions resulting from variants in known and novel genes; the penetrance of genetic variants on clinical phenotypes has been shown to be highly variable; and clinical entities sharing common phenotypes have been discovered. For example, this update includes the findings that bi-allelic mutations in ZNF341, IL6ST (encoding gp130, a common component of the receptors for IL-6, IL-11, IL-27, LIF, OSM, CNTF), or IL6R all cause conditions that resemble autosomal dominant hyper-IgE syndrome due to dominant negative mutations in STAT3. Detailed analyses of these patients revealed a novel mechanism of regulating STAT3 signaling (via the transcription factor ZNF341) and defined the exact consequences of impaired IL-6/IL-6R/gp130 and putatively IL-11/IL-11R/gp130 signaling to the phenotype of AD-HIES.

12Furthermore, key findings over the past 2 years continue to reveal that distinct mechanisms of disease (GOF, LOF, dominant negative, haploinsufficient), as well as different modes of inheritance (autosomal recessive, autosomal dominant) of variants in the same gene can cause disparate clinical conditions. This is a fascinating aspect of the genetics of human disease, and a salient reminder to be cognizant of the nature of the genetic variants identified from NGS. It is these genes that have several entries in this update. A few recent examples include:Heterozygous variants in CARD11 or STAT5B can be pathogenic due to negative dominance. This was potentially unexpected because autosomal recessive LOF variants in both of these genes were previously reported to cause combined immunodeficiency and severe immune dysregulation, respectively, yet heterozygous relatives of these affected individuals were healthy.While heterozygous dominant negative mutations in TCF3, encoding the transcription factor E47, cause B cell deficiency and agammaglobulinemia, nonsense mutations in TCF3 have now been identified that are pathogenic only in an autosomal recessive state, as heterozygous carriers of these particular allelic variants remained healthy.A heterozygous hypermorphic variant in IKBKB was found to cause a combined immunodeficiency not too dissimilar to the original description of bi-allelic, recessive variants in IKBKB. Similarly, bi-allelic LOF mutations in PIK3CD are now known to cause B cell deficiency and agammaglobulinemia, which is quite distinct from the immune dysregulated state of individuals with monoallelic activating PIK3CD mutations. This observation nicely parallels the earlier findings of either homozygous or heterozygous mutations in PIK3R1 that clinically phenocopy recessive or activating mutations in PIK3CD respectively.Distinct diseases can result from heterozygous mutations in IKZF1 (Ikaros): combined immunodeficiency due to dominant negative alleles or CVID due to haploinsufficiency.Similar to STAT1, variants in RAC2 or CARD11 can be pathogenic either as monoallelic GOF or LOF or bi-allelic recessive LOF.

13Heterozygous variants in CARD11 or STAT5B can be pathogenic due to negative dominance. This was potentially unexpected because autosomal recessive LOF variants in both of these genes were previously reported to cause combined immunodeficiency and severe immune dysregulation, respectively, yet heterozygous relatives of these affected individuals were healthy.

14While heterozygous dominant negative mutations in TCF3, encoding the transcription factor E47, cause B cell deficiency and agammaglobulinemia, nonsense mutations in TCF3 have now been identified that are pathogenic only in an autosomal recessive state, as heterozygous carriers of these particular allelic variants remained healthy.

15A heterozygous hypermorphic variant in IKBKB was found to cause a combined immunodeficiency not too dissimilar to the original description of bi-allelic, recessive variants in IKBKB. Similarly, bi-allelic LOF mutations in PIK3CD are now known to cause B cell deficiency and agammaglobulinemia, which is quite distinct from the immune dysregulated state of individuals with monoallelic activating PIK3CD mutations. This observation nicely parallels the earlier findings of either homozygous or heterozygous mutations in PIK3R1 that clinically phenocopy recessive or activating mutations in PIK3CD respectively.

16Distinct diseases can result from heterozygous mutations in IKZF1 (Ikaros): combined immunodeficiency due to dominant negative alleles or CVID due to haploinsufficiency.

17Similar to STAT1, variants in RAC2 or CARD11 can be pathogenic either as monoallelic GOF or LOF or bi-allelic recessive LOF.

18Thus, these findings have revealed the fundamental importance of elucidating the impact of a novel variant on the function of the encoded protein and thus the mechanism of pathogenicity. Furthermore, these new entries are an important reminder not to overlook the potential significance of identifying heterozygous variants in genes previously believed to cause disease only in a biallelic manner or to result in a previously defined specific clinical entity. Indeed, there are now at least 35 genes that have multiple entries in the current update, reflecting the distinct mechanisms by which variants result in or cause disease (e.g., STAT1, STAT3, NLRP1, RAC2, ZAP70, CARD11, IKBKB, WAS, JAK1, IFIH1, C3, C1R, C1S–GOF or LOF; STAT5, STAT1, CARD11, ACD, CFH, CFHR1–5, FOXN1, RAC2, TCF3, AICDA, PIK3R1, IFNGR1, TREX1, TICAM1, IRF8–AD or AR; PIK3CD–AD GOF, AR LOF; IKZF1–AD, or haploinsufficient; NLRP3—distinct disease phenotypes despite all resulting from GOF alleles).

19As noted above, genetic, biochemical, and functional analyses of putative novel pathogenic variants need to meet stringent criteria to be considered for inclusion in this update. These criteria can make reporting genetic findings from single cases challenging, as often the best evidence that a novel variant is disease-causing is to identify additional, similarly affected but unrelated individuals with the same variants, or functionally similar variants in the same gene. While this can be challenging, particularly in light of the rarity of individual inborn errors of immunity, robust mechanistic laboratory investigations continue to provide compelling data from single patients, with or without evidence from animal models. Specifically, homozygous LOF mutations in IRF9 and IL18BP were identified and rigorously characterized in single patients and found to be the molecular cause of life-threatening influenza and fulminant viral hepatitis, respectively.

20The study and discovery of novel inborn errors of immunity can also enable improved patient management by implementing gene-specific targeted therapies. Thus, JAK inhibitors are being used to treat disorders of immune dysregulation resulting from GOF mutations in JAK1, STAT1 or STAT3, while mTOR inhibitors such as rapamycin or PI3K p110δ-specific inhibitors have been reported for the treatment of individuals with PIK3CD GOF or PIK3R1 LOF mutations. Regarding novel gene defects, immune dysregulation due to DEF6 deficiency was successfully treated with abatacept (CTLA4-Ig). This correlated with impaired CTLA4 expression and function in DEF6-deficient T cells and parallels the therapeutic use of abatacept and belatacept for LRBA-deficiency and CTLA4 haploinsufficiency, both of which are characterized by reduced CTLA4 expression in affected regulatory T cells. From a theoretical perspective, the finding that MSMD can be caused by mutations in IL12RB2, IL23R or SPPL2A and that these mutations are associated with impaired production of IFNγ—a requisite of anti-mycobacterial immunity—implies that IFNγ administration could be therapeutically beneficial in these clinical settings. Similarly, recombinant IL18BP could potentially ameliorate viral-induced liver toxicity due to IL18BP deficiency.

21The goals of the IUIS Expert Committee on Inborn Errors of Immunity are to increase awareness, facilitate recognition, promote optimal treatment, and support research in the field of disorders of immunity. Thus, this 2019 Update and the accompanying “Phenotypical IUIS Classification” publications are intended as resources for clinicians and researchers. Importantly, these tables underpin the design of panels used for targeted gene sequencing to facilitate genetic diagnoses or inborn errors. In the past 5 years, the number of gene defects underlying inborn errors of immunity has nearly doubled from ~ 250 to 430 (Fig. 1a). The human genome contains 1800–2000 genes that are known to be involved in immune responses. Thus, the discovery and study of inborn errors of immunity has elegantly illustrated that > 20% of these immune genes play non-redundant roles in host defense and immune regulation. With the improved identification and phenotyping of patients with rare diseases, combined with high throughput genome sequencing, the number of genes fundamentally required for immunity will no doubt continue to increase, further revealing critical and novel roles for specific genes, molecules, pathways and cell types in immune responses, as well as mechanisms of disease pathogenesis and targets for immunotherapies. The field of inborn errors of immunity, and the global clinical and research communities, will therefore continue to provide key insights into basic and clinical immunology.