Biochemically deleterious human NFKB1 variants underlie an autosomal dominant form of common variable immunodeficiency

Abstract

Autosomal dominant (AD) NFKB1 deficiency is thought to be the most common genetic etiology of common variable immunodeficiency (CVID). However, the causal link between NFKB1 variants and CVID has not been demonstrated experimentally and genetically, as there has been insufficient biochemical characterization and enrichment analysis. We show that the cotransfection of NFKB1-deficient HEK293T cells (lacking both p105 and its cleaved form p50) with a κB reporter, NFKB1/p105, and a homodimerization-defective RELA/p65 mutant results in p50:p65 heterodimer–dependent and p65:p65 homodimer–independent transcriptional activation. We found that 59 of the 90 variants in patients with CVID or related conditions were loss of function or hypomorphic. By contrast, 258 of 260 variants in the general population or patients with unrelated conditions were neutral. None of the deleterious variants displayed negative dominance. The enrichment in deleterious NFKB1 variants of patients with CVID was selective and highly significant (P = 2.78 × 10−15). NFKB1 variants disrupting NFKB1/p50 transcriptional activity thus underlie AD CVID by haploinsufficiency, whereas neutral variants in this assay should not be considered causal.

Vulnerability to Meningococcal Disease in Immunodeficiency Due to a Novel Pathogenic Missense Variant in NFKB1

“…Recently, Li et al evaluated the functional impact of 365 NFKB1 variants utilizing a reporter assay and showed that deleteriousness of monoallelic variants in NFKB1 lies on haploinsufficiency. Characterized NFKB1 variants included missense LOF or hypomorphic variants, which allsimilar to the variant presented in the present workwere localized at the RHD domain of p105/p50 (17).…”

Establishing the Molecular Diagnoses in a Cohort of 291 Patients With Predominantly Antibody Deficiency by Targeted Next-Generation Sequencing: Experience From a Monocentric Study

“…This mutation is also predicted to disrupt both, the precursor p105 and the mature form p50 of NF-kB1. In analogy to other well-known severely truncating mutations (63), we consider this newly identified variant as pathogenic, although we have not explicitly confirmed its deleterious effect. Patients P005, P156 and P192 (all unrelated) carried splice-altering mutations: The splice-donor change c.1066+1G>C (which was found in P005) results in a shift of the reading frame and a premature termination of translation (p.Phe310Ilefs*76); however, other splice defects are also conceivable.…”

“…Although functional in vitro testing, as previously described (23), indicated that none of these four variants cause a detrimental protein loss, we could not exclude a hypomorphic reduction of protein function (data not shown). Using reporter assays, a recent study demonstrated a loss-of-function for p.Arg57Cys, whereas a functional defect associated with p.Tyr90Ser, p.Arg214Gln, and p.Met216Val, remained obscure (63). P134 presented with splenomegaly, pneumonias and psoriatic dermatitis.…”

Common Variable Immunodeficiency and Neurodevelopmental Delay Due to a 13Mb Deletion on Chromosome 4 Including the NFKB1 Gene: A Case Report

“…Most pathogenic variants are predicted to cause loss of function, but only a few missense variants are truly pathogenic. In a large and comprehensive functional study, Li et al found that only 57% of published NFKB1 variants were deleterious, whereas 43% were neutral (22). These authors also demonstrated that deleterious heterozygous NFKB1 variants cause disease by haploinsufficiency.…”

“…To date, more than 100 heterozygous NFKB1variants have been reported in patients with a CVID-like phenotype (13,22). Most pathogenic variants are predicted to cause loss of function, but only a few missense variants are truly pathogenic.…”