NFKBIB

NFKB inhibitor beta, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 19:38899699-38908893

Links

ENSG00000104825 ∙ NCBI:4793 ∙ OMIM:604495 ∙ HGNC:7798 ∙ Uniprot:Q15653 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NFKBIB gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFKBIB gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	14	2	0

Variants in NFKBIB

This is a list of pathogenic ClinVar variants found in the NFKBIB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-38900175-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-38905077-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-38905364-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-38905365-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-38905388-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-38905391-G-A		not specified	Likely benign (Jul 26, 2022)
19-38905392-A-C		not specified	Uncertain significance (Dec 07, 2021)
19-38905415-G-A		not specified	Uncertain significance (Jul 05, 2022)
19-38905419-G-A		not specified	Likely benign (May 27, 2022)
19-38905520-G-A		not specified	Uncertain significance (Jul 27, 2022)
19-38907238-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-38907309-G-A			Likely benign (Jan 01, 2023)
19-38907558-G-A		not specified	Uncertain significance (May 27, 2022)
19-38907561-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-38907615-G-A		not specified	Uncertain significance (Dec 14, 2022)
19-38908731-G-A		not specified	Uncertain significance (Jul 22, 2022)
19-38908740-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-38908764-C-T		not specified	Uncertain significance (Jul 20, 2022)
19-38908768-G-A		not specified	Uncertain significance (Aug 23, 2021)
19-38908821-C-T		not specified	Uncertain significance (Feb 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFKBIB	protein_coding	protein_coding	ENST00000313582	6	9194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.422	0.576	125703	0	18	125721	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.970	203	246	0.826	0.0000169	2261
Missense in Polyphen		66	96.268	0.68558		976
Synonymous	-0.0624	110	109	1.01	0.00000813	774
Loss of Function	2.72	3	13.9	0.215	7.74e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000192	0.000192
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000529	0.0000462
European (Non-Finnish)	0.0000776	0.0000703
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits NF-kappa-B by complexing with and trapping it in the cytoplasm. However, the unphosphorylated form resynthesized after cell stimulation is able to bind NF-kappa-B allowing its transport to the nucleus and protecting it to further NFKBIA- dependent inactivation. Association with inhibitor kappa B- interacting NKIRAS1 and NKIRAS2 prevent its phosphorylation rendering it more resistant to degradation, explaining its slower degradation.
• Pathway: Adipocytokine signaling pathway - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Influenza A - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Cytosolic DNA-sensing pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Shigellosis - Homo sapiens (human);Measles - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);IL-1 signaling pathway;TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;Prolactin Signaling Pathway;IL17 signaling pathway;TNF alpha Signaling Pathway;Apoptosis;Hair Follicle Development- Induction (Part 1 of 3);Apoptotic Signaling Pathway;RIG-I-like Receptor Signaling;Chemokine signaling pathway;TLR NFkB;Toll Like Receptor 7/8 (TLR7/8) Cascade;Signaling by Interleukins;hypoxia and p53 in the cardiovascular system;tumor suppressor arf inhibits ribosomal biogenesis;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;B cell receptor signaling;ZBP1(DAI) mediated induction of type I IFNs;Toll-Like Receptors Cascades;TRAF6 mediated NF-kB activation;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Activation of NF-kappaB in B cells;Signaling by the B Cell Receptor (BCR);Interleukin-1 signaling;TCR;Innate Immune System;Immune System;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);IL-1 NFkB;RIP-mediated NFkB activation via ZBP1;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;BCR signaling pathway;TNFalpha;Cytosolic sensors of pathogen-associated DNA ;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;TNF;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

• pRec: 0.640

Intolerance Scores

• loftool: 0.149
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.512
• hipred: Y
• hipred_score: 0.701
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfkbib
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; skeleton phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: transcription, DNA-templated;signal transduction;cellular response to lipopolysaccharide;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;cytosol
• Molecular function: transcription coactivator activity;protein binding