NFKB2 nuclear factor kappa B subunit 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NFKB2provided by HGNC
Official Full Name: nuclear factor kappa B subunit 2provided by HGNC
Primary source: HGNC:HGNC:7795
See related: Ensembl:ENSG00000077150 MIM:164012; AllianceGenome:HGNC:7795
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: p52; p100; H2TF1; LYT10; CVID10; LYT-10; NF-kB2; p49/p100
Summary: This gene encodes a subunit of the transcription factor complex nuclear factor-kappa-B (NFkB). The NFkB complex is expressed in numerous cell types and functions as a central activator of genes involved in inflammation and immune function. The protein encoded by this gene can function as both a transcriptional activator or repressor depending on its dimerization partner. The p100 full-length protein is co-translationally processed into a p52 active form. Chromosomal rearrangements and translocations of this locus have been observed in B cell lymphomas, some of which may result in the formation of fusion proteins. There is a pseudogene for this gene on chromosome 18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
Expression: Ubiquitous expression in appendix (RPKM 21.5), bone marrow (RPKM 20.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.32

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (102394110..102402529)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (103279058..103287478)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (104153867..104162286)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RUNX1-IT1 acts as a scaffold of STAT1 and NuRD complex to promote ROS-mediated NF-kappaB activation and ovarian cancer progression.
Title: RUNX1-IT1 acts as a scaffold of STAT1 and NuRD complex to promote ROS-mediated NF-κB activation and ovarian cancer progression.
Novel NFKB2 Pathogenic Variants in Two Unrelated Patients with Common Variable Immunodeficiency.
Title: Novel NFKB2 Pathogenic Variants in Two Unrelated Patients with Common Variable Immunodeficiency.
NF-kappaB/p52 augments ETS1 binding genome-wide to promote glioma progression.
Title: NF-κB/p52 augments ETS1 binding genome-wide to promote glioma progression.
Analysis of NFKB1 and NFKB2 gene expression in the blood of patients with sudden sensorineural hearing loss.
Title: Analysis of NFKB1 and NFKB2 gene expression in the blood of patients with sudden sensorineural hearing loss.
How do nuclear factor kappa B (NF-kappaB)1 and NF-kappaB2 defects lead to the incidence of clinical and immunological manifestations of inborn errors of immunity?
Title: How do nuclear factor kappa B (NF-κB)1 and NF-κB2 defects lead to the incidence of clinical and immunological manifestations of inborn errors of immunity?
NFKB2 inhibits NRG1 transcription to affect nucleus pulposus cell degeneration and in fl ammation in intervertebral disc degeneration.
Title: NFKB2 inhibits NRG1 transcription to affect nucleus pulposus cell degeneration and inﬂammation in intervertebral disc degeneration.
An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-kappaB module.
Title: An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-κB module.
A Nonsense N -Terminus NFKB2 Mutation Leading to Haploinsufficiency in a Patient with a Predominantly Antibody Deficiency.
Title: A Nonsense N -Terminus NFKB2 Mutation Leading to Haploinsufficiency in a Patient with a Predominantly Antibody Deficiency.
Fetal lung C4BPA induces p100 processing in human placenta.
Title: Fetal lung C4BPA induces p100 processing in human placenta.
Preventing abnormal NF-kappaB activation and autoimmunity by Otub1-mediated p100 stabilization.
Title: Preventing abnormal NF-κB activation and autoimmunity by Otub1-mediated p100 stabilization.

Submit: New GeneRIF Correction See all GeneRIFs (132)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Immunodeficiency, common variable, 10 MedGen: C3809991 OMIM: 615577 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	The mRNA expression levels for alpha-tubulin, TRADD, IFN-gamma R2, GAS1, MADD, NF-kappaB, I-kappa B, 14-3-3 protein, APaf1, PARP, IGF-1 receptor, RB1, Rb2/p130, ARC, and caspase 6 are upregulated in human neuronal cells after treatment with HIV-1 gp120	PubMed
Envelope transmembrane glycoprotein gp41	env	The HIV-1 gp41 cytoplasmic domain-induced NFkappaB activation requires TAK1, RelA, and NEMO proteins	PubMed
	env	The cytoplasmic domain (residues 704-773) of HIV-1 gp41 induces NFkappaB activation. Deletion of a 12 amino-acid sequence (762CLFSYHRLRDLL) in gp41 leads to a dramatic loss of the NFkappaB activation and tyrosine 766 is particularly important	PubMed
Tat	tat	HIV-1 Tat in combination with IFN-gamma and TNF-alpha increases CXCL10 mRNA and protein in human astrocytes through the activation of the p38, Jnk, and Akt signaling pathways and their downstream transcription factors, NF-kappaB and STAT-1alpha	PubMed
	tat	Treatment of astrocytes with cell-permeable superoxide dismutase (SOD) leads to a decrease in Tat-induced ROS generation and NF-kappaB activation	PubMed
	tat	In HIV-1 Tat-expressing and HIV-infected astrocytes, endothelin-1 (ET-1) is significantly elevated through NF-kappaB (NF-kappaB)-responsive sites in the ET-1 promoter	PubMed
	tat	HIV-1 Tat has been shown to bind NFkappaB in vitro in gel shift, GST-pull down and affinity matrix assays	PubMed
	tat	NFkappaB tethers the p160 nuclear receptor co-activator GRIP1 to the HIV-1 LTR promoter, thereby regulating the full activation of this promoter by HIV-1 Tat	PubMed
	tat	HIV-1 Tat activates NFkappaB through the cellular interferon-inducible, double-stranded RNA dependent protein kinase, PKR	PubMed
	tat	p56-lck plays a critical role in the activation of NFkappaB by HIV-1 Tat	PubMed
	tat	Activation of NFkappaB by HIV-1 Tat is inhibited by Nitric Oxide	PubMed
Vpr	vpr	HIV-1 Vpr stimulates non-canonical NFKappaB pathway by inducing the phosphorylation of NFKappaB2 (p100) at serine 866, which leads to process p100 into RelB/p52 and its subsequent nuclear translocation	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI426354 (e-PCR)
- UniSTS:160850

A007E10 (e-PCR)
- UniSTS:5030

RH78118 (e-PCR)
- UniSTS:53415

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to stress	IBA Inferred from Biological aspect of Ancestor more info
involved_in extracellular matrix organization	IEA Inferred from Electronic Annotation more info
involved_in follicular dendritic cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in germinal center formation	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in non-canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in response to cytokine	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in spleen development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Bcl3/NF-kappaB2 complex	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nuclear factor NF-kappa-B p100 subunit

Names: DNA-binding factor KBF2; NFKB, p52/p100 subunit; lymphocyte translocation chromosome 10 protein; nuclear factor Kappa-B, subunit 2; nuclear factor NF-kappa-B p52 subunit; nuclear factor of Kappa light chain gene enhancer in B cells 2; nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100); oncogene Lyt-10; transcription factor NFKB2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033874.2 RefSeqGene

Range

6596..13415

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1347

mRNA and Protein(s)

NM_001077494.3 → NP_001070962.1 nuclear factor NF-kappa-B p100 subunit isoform a

See identical proteins and their annotated locations for NP_001070962.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1 and 5 both encode the same isoform (a).

Source sequence(s)

AL121928, S76638

Consensus CDS

CCDS41564.1

UniProtKB/Swiss-Prot

A8K9D9, D3DR83, Q00653, Q04860, Q9BU75, Q9H471, Q9H472

UniProtKB/TrEMBL

A0A1P8C958

Related

ENSP00000358983.3, ENST00000369966.8

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:774 → 849

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:483 → 620

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01177
Location:228 → 327

IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...

pfam12796
Location:531 → 629

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:488 → 547

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:599 → 630

ANK; ANK repeat [structural motif]
NM_001261403.3 → NP_001248332.1 nuclear factor NF-kappa-B p100 subunit isoform b

See identical proteins and their annotated locations for NP_001248332.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Variants 2, 3, and 4 encode the same isoform (b).

Source sequence(s)

AL121928

Consensus CDS

CCDS41565.1

UniProtKB/TrEMBL

A0A1P8C958

Related

ENSP00000498308.1, ENST00000652277.1

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:774 → 849

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:483 → 620

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01177
Location:228 → 327

IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...

pfam12796
Location:531 → 629

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:488 → 547

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:599 → 630

ANK; ANK repeat [structural motif]
NM_001288724.1 → NP_001275653.1 nuclear factor NF-kappa-B p100 subunit isoform b

See identical proteins and their annotated locations for NP_001275653.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Variants 2, 3, and 4 encode the same isoform (b).

Source sequence(s)

AL121928, BC002844, DB091090

Consensus CDS

CCDS41565.1

UniProtKB/TrEMBL

A0A1P8C958

Related

ENSP00000410256.1, ENST00000428099.6

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:774 → 849

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:483 → 620

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01177
Location:228 → 327

IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...

pfam12796
Location:531 → 629

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:488 → 547

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:599 → 630

ANK; ANK repeat [structural motif]
NM_001322934.2 → NP_001309863.1 nuclear factor NF-kappa-B p100 subunit isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (5) and variant 1 both encode the same isoform (a).

Source sequence(s)

AK098415, AL121928, KT935449

Consensus CDS

CCDS41564.1

UniProtKB/Swiss-Prot

A8K9D9, D3DR83, Q00653, Q04860, Q9BU75, Q9H471, Q9H472

UniProtKB/TrEMBL

A0A1P8C958

Related

ENSP00000499294.1, ENST00000661543.1

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:774 → 849

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:483 → 620

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01177
Location:228 → 327

IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...

pfam12796
Location:531 → 629

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:488 → 547

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:599 → 630

ANK; ANK repeat [structural motif]
NM_001322935.1 → NP_001309864.1 nuclear factor NF-kappa-B p100 subunit isoform c

Status: REVIEWED

Source sequence(s)

AL121928, BC002844

UniProtKB/TrEMBL

A0A1P8C958
NM_002502.6 → NP_002493.3 nuclear factor NF-kappa-B p100 subunit isoform b

See identical proteins and their annotated locations for NP_002493.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Variants 2, 3, and 4 encode the same isoform (b).

Source sequence(s)

AL121928

Consensus CDS

CCDS41565.1

UniProtKB/TrEMBL

A0A1P8C958

Related

ENSP00000189444.6, ENST00000189444.11

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:774 → 849

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:483 → 620

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01177
Location:228 → 327

IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...

pfam12796
Location:531 → 629

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:488 → 547

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:599 → 630

ANK; ANK repeat [structural motif]