Severe Multisystem Autoimmunity and Atopy in a Child with a Loss-of-Function IKAROS Variant

The IKAROS family of zinc finger transcription factors (IKZF1–4) plays a central role in lymphocyte development and immune regulation. Pathogenic IKZF1 variants produce a wide phenotypic spectrum related to whether the variant causes haploinsufficiency, dominant-negative effects, dimerization defects, or gain-of-function disease. Gain-of-function variants are typically associated with multisystem autoimmunity, allergic disease, and lymphoproliferation. Loss-of-function variants typically manifest with recurrent infections and hypogammaglobinemia. We describe a child with extensive autoimmunity and atopy who carried a novel loss-of-function IKZF1 variant, despite a clinical presentation that closely resembled gain-of-function disease. A previously healthy girl with a benign family history presented to the gastroenterology clinic at age 6 for workup of frequent postprandial epigastric pain, diarrhea, and decreased appetite. She was previously diagnosed with polyarticular juvenile idiopathic arthritis (JIA) one month prior and was followed by allergy/immunology for eczema, asthma, and eosinophilic esophagitis. Laboratory evaluation demonstrated lymphopenia, reduced T, B, and natural killer (NK) cell subsets, elevated IgE, anemia, hypoalbuminemia, and elevated inflammatory markers. She was treated with infliximab, then transitioned to ustekinumab, methotrexate, and corticosteroids with partial improvement. At age 8, she developed periorbital, abdominal, and lower extremity edema. Renal biopsy confirmed class IV/V lupus nephritis, requiring therapy with corticosteroids, rituximab, and mycophenolate mofetil. Persistent secondary hypogammaglobulinemia led to the initiation of immunoglobulin replacement therapy. Whole-exome sequencing identified a de novo IKZF1 c.378C>G (p.C126W) likely pathogenic variant affecting the first zinc finger DNA-binding domain. Functional testing showed diffuse nuclear localization on immunofluorescence and markedly reduced DNA binding on electrophoretic mobility shift assay, consistent with a loss-of-function mechanism through haploinsufficiency, as co-transfection of the wild-type and mutant constructs did not demonstrate a dominant-negative effect (Figure 1). Despite this, her clinical course was dominated by multisystem autoimmunity, severe allergic disease, and immune dysregulation, features which, in combination and severity, more closely resemble the gain-of-function IKZF1 phenotype. Figure 1. Functional analysis of IKAROS C126W mutation. (Left) Immunofluorescence analysis of pericentromeric heterochromatin localization (PC-HC) demonstrating nuclear distribution of wild-type (WT) and C126W IKAROS. WT IKAROS shows the characteristic punctate nuclear pattern, whereas the C126W variant displays diffuse nuclear staining, indicating impaired DNA binding and altered pericentromeric localization with no evidence of a dominant-negative effect on the WT/Mutant co-transfection experiment. (Right) Electrophoretic mobility-shift assay (EMSA) using IKBS1, IKBS4, and gSat8 probes demonstrates that wild-type IKAROS binds consensus DNA sequences, whereas the C126W variant fails to bind or is markedly reduced. Together, these findings confirm that the C126W mutation disrupts IKAROS pericentromeric heterochromatin localization and DNA-binding capacity, consistent with a loss-of-function, haploinsufficiency mechanism. This case illustrates a gain-of-function-like phenotype arising from a confirmed loss-of-function IKZF1 allele. The discordance between molecular mechanism and clinical presentation suggests additional genetic or epigenetic modifiers and underscores the importance of early genetic testing and functional validation in children with unexplained multisystem autoimmunity.