IKBKB

protein-coding

inhibitor of nuclear factor kappa B kinase subunit beta, the group of I kappa B kinases|IKK complex

Gene summary

The protein encoded by this gene phosphorylates the inhibitor in the inhibitor/NF-kappa-B complex, causing dissociation of the inhibitor and activation of NF-kappa-B. The encoded protein itself is found in a complex of proteins. Several transcript variants, some protein-coding and some not, have been found for this gene. [provided by RefSeq, Sep 2011]

MANE transcript

NM_001556.3

Inheritance

AR, AD

ClinVar variants

P:36U:282B:247

Top phenotype

Immunodeficiency 15A; Immunodeficiency 15B

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr8:42,271,302-42,332,460

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~61.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency 15aSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032599

Submitter: Ambry Genetics

severe combined immunodeficiency due to IKK2 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014267

Submitter: Orphanet

immunodeficiency 15aMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0032599

Submitter: ClinGen

Heterozygous germline variants in IKBKB were first reported in relationship to anhidrotic ectodermodysplasia with immunodeficiency due to IKBKB GOF mutations in 2018 (PMID: 30337470). Subsequent reports have described affected individuals presenting with variable onset of recurrent infections, progressive combined T and B cell deficiency, and immune dysregulation manifesting as autoimmunity, autoinflammation, or ectodermal abnormalities (PMID: 40403933, 32554083, 36378426, 38758301). In total, there have been a reported four different heterozygous missense gain-of-function (GOF) variants across 19 probands. IKKβ is the catalytic subunit of the IκB kinase (IKK) complex, responsible for phosphorylating IκB and triggering its degradation and activating the NF-κB pathway. GOF variants in IKBKB lead to constitutive and hyperresponsive activation of canonical NF-κB signaling, characterized by increased phosphorylation of IKKα/β and p65 with enhanced degradation of IκBα (PMID: 30337470). Functional studies using patient-derived cells demonstrate excessive NF-κB activity, impaired proliferative capacity, and abnormal B- and T-cell differentiation and function (PMID: 30337470, 40403933). Clinically affected individuals show phenotypic heterogeneity and age-related penetrance, with some patients becoming phenotypically apparent only after the age of 30 (PMID: 40403933). A mouse model harboring an IKBKB GOF mutation recapitulates key features observed reported probands (PMID: 30337470). In summary, there is moderate evidence to support this gene-disease relationship. This association has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen SCID-CID Working Group on 10/23/2025 (SOP Version 11).

immunodeficiency 15aSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032599

Submitter: Labcorp Genetics (formerly Invitae)

severe combined immunodeficiency due to IKK2 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014267

Submitter: Ambry Genetics

immunodeficiency 15aMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0032599

Submitter: Ambry Genetics

severe combined immunodeficiency due to IKK2 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014267

Submitter: Labcorp Genetics (formerly Invitae)

immunodeficiency 15aMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0032599

Submitter: Ambry Genetics

immunodeficiency 15aSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032599

Submitter: PanelApp Australia

severe combined immunodeficiency due to IKK2 deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014267

Submitter: ClinGen

IKBKB was first reported in relation to an autosomal recessive IKBKB deficiency in 2013 (Pannicke U, et al., 2013, PMID:24369076). Symptoms usually appear in the first few months of life and patients present with a wide range of recurrent infections, failure to thrive and decreased antibody levels. Most patients have normal numbers of T and B cells but these are mostly naïve. All cases reported were homozygous for nonsense mutations. The curation of IKBKB relates to autosomal recessive severe combined immunodeficiency due to IKK2 deficiency with MONDO ID 0014267 includes both case-level and experimental evidence. The first publication described four cases from four families of Northern Cree ancestry in Canada. Sixteen other cases of Northern Cree ancestry were described by Cuvelier et al. (PMID: 30391351) and all cases with genetic data available confirmed the same nonsense mutation, which suggests a possible founder mutation. Several other cases were found in other populations with different nonsense mutations (PMIDs: 24679846, 32117824, 25216719, 25139357). There are no reports of symptomatic carriers and experimental data showed no effect on heterozygous siblings cells. A maximum score of 12 points for genetic evidence has been reached. This gene-disease association is also supported by expression, functional alteration and rescue models (PMIDs: 25139357 and 24369076). Absence of protein expression in PBMCs and EBV-transformed B cell lines from patients was found in immunoblot assays, despite mRNA levels remaining high. Also, patient cells transfected with wild-type protein or empty vector and subsequently stimulated showed that cells with WT protein express IKKB protein in the cytosol whereas the ones with empty vector do not. At the same time, Nf-κB expression in the nucleus increased with stimulation when WT gene is present. A different experiment showed normal levels of NF-κB activation by TNF-α were restored in cells from the patient that re-expressed IKKB, even when expression of IKKB was low. A score of 2.5 points for experimental evidence has been reached, increasing the total score to 14.5 points. In summary, IKBKB is definitively associated with autosomal recessive severe combined immunodeficiency due to IKK2 deficiency. In summary, this curation reached a level of "Definitive" as it has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen SCID/CID GCEP on the meeting date May 25, 2023 (SOP Version 9).

severe combined immunodeficiency due to IKK2 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014267

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Immunodeficiency 15A; Immunodeficiency 15BAD/AR

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: Individuals may be susceptible to severe and recurrent infections, and prophylaxis and early and aggressive treatment of infections may be beneficial; BMT/HSCT has been described in Immunodeficiency 15B

Refs: 24369075; 25216719Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IKBKB variants in ClinVar

10 Conditions Cataloged
Severe combined immunodeficiency due to IKK2 deficiencyTotal: 753
not specifiedTotal: 75
not providedTotal: 67
Inborn genetic diseasesTotal: 58
IKBKB-related disorderTotal: 23
Immunodeficiency 15aTotal: 15
Severe combined immunodeficiency diseaseTotal: 2
Aganglionic megacolonTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001556.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
221
clinvar
2
clinvar
229
missense
1
clinvar
1
clinvar
264
clinvar
20
clinvar
3
clinvar
289
nonsense
10
clinvar
6
clinvar
3
clinvar
19
start loss
0
frameshift
7
clinvar
2
clinvar
2
clinvar
11
splice donor/acceptor (+/-2bp)
9
clinvar
7
clinvar
1
clinvar
17
Total18182822425565

Highest pathogenic variant AF is 0.000013159107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001556.3RefSeqNP_001547.121MANE Select
ENST00000520810.6EnsemblENSP00000430684.121MANE Select
NM_001190720.3RefSeqNP_001177649.220Standard
NM_001242778.2RefSeqNP_001229707.120Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ikbkbDanio rerio

Structure: cell

Quality: detached from

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Chronic myeloid leukemia - Homo sapiens (human)
  • mTOR signaling pathway - Homo sapiens (human)
  • Adipocytokine signaling pathway - Homo sapiens (human)
  • T cell receptor signaling pathway - Homo sapiens (human)

Biological Process

  • stimulatory C-type lectin receptor signaling pathway
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
  • MyD88-independent toll-like receptor signaling pathway
  • protein phosphorylation
  • inflammatory response

Molecular Function

  • protein kinase activity
  • protein serine/threonine kinase activity
  • protein binding
  • ATP binding
  • IkappaB kinase activity

Cellular Component

  • nucleus
  • cytoplasm
  • cytosol
  • IkappaB kinase complex
  • cytoplasmic side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000520810
Coding exons
21
Length
61154
Individuals with no LoFs
125736
Homozygous LoFs
0
Heterozygous LoFs
12
Defined
125748
p
0.0000477
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.592854370.6520.00002514968
Missense (PolyPhen)66148.660.443981658
Synonymous2.041401740.8030.00001041409
Loss of Function5.68954.10.1660.00000319532

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000180.00018rare
European (Non-Finnish)0.0000540.000053rare
South Asian0.0000380.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Serine kinase that plays an essential role in the NF- kappa-B signaling pathway which is activated by multiple stimuli such as inflammatory cytokines, bacterial or viral products, DNA damages or other cellular stresses. Acts as part of the canonical IKK complex in the conventional pathway of NF-kappa-B activation and phosphorylates inhibitors of NF-kappa-B on 2 critical serine residues. These modifications allow polyubiquitination of the inhibitors and subsequent degradation by the proteasome. In turn, free NF-kappa-B is translocated into the nucleus and activates the transcription of hundreds of genes involved in immune response, growth control, or protection against apoptosis. In addition to the NF-kappa-B inhibitors, phosphorylates several other components of the signaling pathway including NEMO/IKBKG, NF-kappa-B subunits RELA and NFKB1, as well as IKK-related kinases TBK1 and IKBKE. IKK-related kinase phosphorylations may prevent the overproduction of inflammatory mediators since they exert a negative regulation on canonical IKKs. Phosphorylates FOXO3, mediating the TNF- dependent inactivation of this pro-apoptotic transcription factor. Also phosphorylates other substrates including NCOA3, BCL10 and IRS1. Within the nucleus, acts as an adapter protein for NFKBIA degradation in UV-induced NF-kappa-B activation. {ECO:0000269|PubMed:11297557, ECO:0000269|PubMed:15084260, ECO:0000269|PubMed:17213322, ECO:0000269|PubMed:19716809, ECO:0000269|PubMed:20410276, ECO:0000269|PubMed:20434986, ECO:0000269|PubMed:20797629, ECO:0000269|PubMed:21138416}.;
Disease
DISEASE: Immunodeficiency 15 (IMD15) [MIM:615592]: An autosomal recessive primary immunodeficiency disorder characterized by onset in infancy of life-threatening bacterial, fungal, and viral infections and failure to thrive. Laboratory studies show hypo- or agammaglobulinemia with relatively normal numbers of B and T- cells, and impaired differentiation and activation of immune cells. {ECO:0000269|PubMed:24369075}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.811

Intolerance Scores

LoFtool
0.698
RVIS EVS
-0.75
RVIS percentile EVS
13.58

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.965

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.