NFKBID

protein-coding

NFKB inhibitor delta, the group of Ankyrin repeat domain containing

Gene summary

Predicted to enable NF-kappaB binding activity. Predicted to be involved in T cell receptor signaling pathway; positive regulation of T-helper 17 cell differentiation; and regulation of gene expression. Predicted to act upstream of or within several processes, including negative regulation of canonical NF-kappaB signal transduction; obsolete negative regulation of NF-kappaB transcription factor activity; and positive regulation of thymocyte apoptotic process. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_139239.5

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

Immunodeficiency, common variable, 12

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr19:35,887,630-35,902,303

External References & Databases

Ensembl (ENSG00000167604)

Transcript & Mutation Effects

hg38 • Region Span ~14.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NFKBID variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 37

Immunodeficiency, common variable, 12Total: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139239.5. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			37 clinvar	2 clinvar		39
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	39	2	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139239.5	RefSeq	NP_640332.2	12	MANE Select
ENST00000641389.3	Ensembl	ENSP00000493265.2	12	MANE Select
NM_001321831.2	RefSeq	NP_001308760.1	9	Standard
NM_001365705.1	RefSeq	NP_001352634.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

inflammatory response
negative regulation of NF-kappaB transcription factor activity
negative regulation of T cell differentiation in thymus
negative regulation of I-kappaB kinase/NF-kappaB signaling
T cell receptor signaling pathway

Molecular Function

protein binding
NF-kappaB binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396901
Coding exons: 9
Length: 14651
Individuals with no LoFs: 124641
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124647
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.03	124	206	0.602	0.0000132	1957
Missense (PolyPhen)		38	92.223	0.41205		973
Synonymous	0.217	89	91.6	0.971	0.00000611	714
Loss of Function	2.94	4	17.2	0.233	0.00000100	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000035	0.000029	rare
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates the expression of IL-2, IL-6, and other cytokines through regulation on NF-kappa-B activity. Functions in the regulation of inflammatory responses. Involved in the induction of T helper 17 cells (Th17) differentiation upon recognition of antigen by T cell antigen receptor (TCR). May also regulate TCR-induced negative selection of thymocytes. {ECO:0000250|UniProtKB:Q2TB02}.;

Recessive Scores

pRec: 0.0946

Intolerance Scores

LoFtool: 0.317
RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.421

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium