NFKB1 (nuclear factor kappa B subunit 1)

Gene

• Entrez ID: 4790
• Gene name: Nuclear factor kappa B subunit 1
• Gene symbol: NFKB1
• Synonyms: CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1, NF-kappaB, NF-kappabeta, NFKB-p105, NFKB-p50, NFkappaB
• Chromosome: 4
• Chromosome location: 4q24
• Summary: This gene encodes a 105 kD protein which can undergo cotranslational processing by the 26S proteasome to produce a 50 kD protein. The 105 kD protein is a Rel protein-specific transcription inhibitor and the 50 kD protein is a DNA binding subunit of the NF-kappa-B (NFKB) protein complex. NFKB is a transcription regulator that is activated by various intra- and extra-cellular stimuli such as cytokines, oxidant-free radicals, ultraviolet irradiation, and bacterial or viral products. Activated NFKB translocates into the nucleus and stimulates the expression of genes involved in a wide variety of biological functions. Inappropriate activation of NFKB has been associated with a number of inflammatory diseases while persistent inhibition of NFKB leads to inappropriate immune cell development or delayed cell growth. NFKB is a critical regulator of the immediate-early response to viral infection. Alternative splicing results in multiple transcript variants encoding different isoforms, at least one of which is proteolytically processed. [provided by RefSeq, Aug 2020]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs773694113	->T	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant
rs869320688	A>G	Pathogenic	Intron variant
rs869320689	T>C,G	Likely-pathogenic, pathogenic	Splice donor variant
rs869320754	->A	Pathogenic	Frameshift variant, coding sequence variant
rs939459600	C>G,T	Likely-pathogenic	Missense variant, stop gained, coding sequence variant
rs1553934187	C>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1553934395	G>A	Likely-pathogenic	Splice donor variant
rs1560679469	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1560706306	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1578735709	G>A	Likely-pathogenic	Splice acceptor variant
rs1578735747	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1578771120	T>G	Pathogenic	Coding sequence variant, missense variant
rs1578771197	T>A	Pathogenic	Coding sequence variant, missense variant
rs1578771211	C>T	Pathogenic	Coding sequence variant, stop gained
rs1578785260	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1578787945	A>-	Likely-pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1578790573	->A	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant
rs1578793298	C>G	Pathogenic	Coding sequence variant, missense variant
rs1578793312	C>T	Likely-pathogenic, pathogenic	Coding sequence variant, stop gained
rs1578795536	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1578805410	AGAA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1578809017	->AG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1578809101	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1578811073	TGCCA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1578811245	GA>-	Pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT003193	hsa-miR-9-5p	qRT-PCR, Luciferase reporter assay, Western blot	19702828
MIRT003193	hsa-miR-9-5p	GFP reporter assay, qRT-PCR, Western blot	20102618
MIRT003193	hsa-miR-9-5p	GFP reporter assay, Western blot, EGFP reporter assay, qRT-PCR	22131135
MIRT003193	hsa-miR-9-5p	Reporter assay;Western blot	19289835
MIRT003193	hsa-miR-9-5p	GFP reporter assay, qRT-PCR, Western blot	22825752
MIRT003193	hsa-miR-9-5p	Luciferase reporter assay, qRT-PCR, Western blot	27603333
MIRT003193	hsa-miR-9-5p	Luciferase reporter assay, qRT-PCR, Western blot	26248136
MIRT004459	hsa-miR-146a-5p	Luciferase reporter assay	18504431
MIRT004459	hsa-miR-146a-5p	qRT-PCR, Western blot	20124483
MIRT004459	hsa-miR-146a-5p	Microarray	18660546
MIRT004459	hsa-miR-146a-5p	Luciferase reporter assay, qRT-PCR, Western blot, Flow	23706078
MIRT004459	hsa-miR-146a-5p	ELISA, Immunoblot, Luciferase reporter assay, qRT-PCR, Western blot	25052989
MIRT004530	hsa-miR-146b-5p	Luciferase reporter assay	18504431
MIRT004829	hsa-miR-15a-5p	Microarray, qRT-PCR	17260024
MIRT004830	hsa-let-7a-5p	Microarray, qRT-PCR	17260024
MIRT006528	hsa-miR-16-5p	ChIP-seq	21081469
MIRT006529	hsa-miR-21-5p	ChIP-seq	21081469
MIRT021048	hsa-miR-155-5p	Proteomics	21030878
MIRT021048	hsa-miR-155-5p	Immunofluorescence, Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	26934326
MIRT030242	hsa-miR-26b-5p	Microarray	19088304
MIRT049105	hsa-miR-92a-3p	CLASH	23622248
MIRT210911	hsa-miR-508-3p	Luciferase reporter assay, Western blot, ChIP-seq, Immunohistochemistry, qRT-PCR	26801246
MIRT438174	hsa-miR-199a-5p	Luciferase reporter assay, qRT-PCR, Western blot	24299514
MIRT438493	hsa-miR-139-5p	Luciferase reporter assay	24158791
MIRT732565	hsa-miR-138-5p	Western blot	26823826
MIRT733775	hsa-miR-9-3p	Luciferase reporter assay	26354749
MIRT733784	hsa-miR-339-3p	Western blot	25695055
MIRT734015	hsa-miR-34a-5p	PCR array	28097098

Transcription factors

Transcription factor	Regulation	Reference
APEX1	Activation	17045925
AR	Repression	18386814
BCL3	Repression	11387332
BCL3	Unknown	14573596;7896265
BCL6	Repression	15611242
BTF3	Repression	17312387
EGR1	Unknown	10671503
EP300	Unknown	9560267
ETV3	Repression	18025162
FHL2	Unknown	18752053
FOS	Repression	20188076
GATA3	Unknown	19686049
HDAC1	Unknown	24448807
HDAC9	Repression	15964798
HOXA9	Repression	18068911
HSF1	Unknown	18689673
LYL1	Repression	10023675
NFKB1	Unknown	19469019
NFKBIA	Activation	9500973
NFKBIA	Repression	11278471;18606063;20173029
NFKBIA	Unknown	15713458;17148610
NR1H4	Activation	21364590
NR1I2	Repression	22248096
NR3C1	Repression	17016446
PARP1	Unknown	16026317
PIR	Unknown	14573596
RBPJ	Unknown	14570916
RELA	Activation	20596645
RELA	Unknown	19469019
RUNX1	Unknown	19686049
SP1	Activation	20538607;9151857
SP3	Activation	20538607
SP4	Activation	20538607
SRSF1	Repression	19183244
TAL1	Repression	16778171
TNFAIP3	Repression	19124729
TNFAIP3	Unknown	24039598
TP53	Unknown	15988033
TRIM22	Unknown	21651891
USF1	Unknown	19686049
ZNF382	Repression	20682794

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IC	16938301
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IGI	24434150
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IMP	19881551
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription regulatory region sequence-specific DNA binding	IDA	16938301, 17426251, 18718911
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	7959007
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA	21873635
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	1406630
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	24434510
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	1406630
GO:0002223	Process	Stimulatory C-type lectin receptor signaling pathway	TAS
GO:0003682	Function	Chromatin binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IDA	17426251
GO:0005515	Function	Protein binding	IPI	8196632, 8441377, 9865693, 10023675, 10498867, 11297557, 11526476, 11931769, 12482991, 12832462, 14624448, 14743216, 15799966, 16108830, 16306601, 16319921, 17003112, 18045535, 18212740, 19358846, 20195357, 20237821, 20547752, 21483817, 21988832, 23636254, 25241761, 25609649, 258521
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	IDA	11819787, 16938301, 25411248
GO:0005634	Component	Nucleus	IGI	23729669
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	11819787
GO:0005737	Component	Cytoplasm	IGI	23729669
GO:0005739	Component	Mitochondrion	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0006366	Process	Transcription by RNA polymerase II	TAS	1992489
GO:0006915	Process	Apoptotic process	IEA
GO:0006954	Process	Inflammatory response	TAS	1992489
GO:0008134	Function	Transcription factor binding	IDA	18270204
GO:0010629	Process	Negative regulation of gene expression	IDA	26687115
GO:0010744	Process	Positive regulation of macrophage derived foam cell differentiation	IC	16938301
GO:0010884	Process	Positive regulation of lipid storage	IC	16938301
GO:0010956	Process	Negative regulation of calcidiol 1-monooxygenase activity	IDA	15243130
GO:0010957	Process	Negative regulation of vitamin D biosynthetic process	IC	15243130
GO:0031293	Process	Membrane protein intracellular domain proteolysis	TAS
GO:0032269	Process	Negative regulation of cellular protein metabolic process	IC	16938301
GO:0032375	Process	Negative regulation of cholesterol transport	IC	16938301
GO:0032481	Process	Positive regulation of type I interferon production	TAS
GO:0032695	Process	Negative regulation of interleukin-12 production	IEA
GO:0033256	Component	I-kappaB/NF-kappaB complex	TAS	16938301
GO:0034774	Component	Secretory granule lumen	TAS
GO:0035580	Component	Specific granule lumen	TAS
GO:0035994	Process	Response to muscle stretch	IEA
GO:0038095	Process	Fc-epsilon receptor signaling pathway	TAS
GO:0042802	Function	Identical protein binding	IPI	12482991, 12832462, 21988832, 25609649
GO:0042805	Function	Actinin binding	IPI	25411248
GO:0043066	Process	Negative regulation of apoptotic process	TAS	10811897
GO:0043312	Process	Neutrophil degranulation	TAS
GO:0045893	Process	Positive regulation of transcription, DNA-templated	IDA	17426251
GO:0045893	Process	Positive regulation of transcription, DNA-templated	IMP	20018240
GO:0045893	Process	Positive regulation of transcription, DNA-templated	NAS	8096091
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	1406630
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	19955433
GO:0050728	Process	Negative regulation of inflammatory response	IEA
GO:0050852	Process	T cell receptor signaling pathway	TAS
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	TAS
GO:0051403	Process	Stress-activated MAPK cascade	TAS
GO:0070498	Process	Interleukin-1-mediated signaling pathway	TAS
GO:0071222	Process	Cellular response to lipopolysaccharide	IMP	23776175
GO:0071260	Process	Cellular response to mechanical stimulus	IEP	19593445
GO:0071316	Process	Cellular response to nicotine	IMP	22357537
GO:0071347	Process	Cellular response to interleukin-1	IEP	12958148
GO:0071354	Process	Cellular response to interleukin-6	IMP	22357537
GO:0071356	Process	Cellular response to tumor necrosis factor	IEA
GO:0071359	Process	Cellular response to dsRNA	IEA
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IMP	20018240
GO:1900127	Process	Positive regulation of hyaluronan biosynthetic process	IDA	17324121
GO:1904385	Process	Cellular response to angiotensin	IMP	22357537
GO:2000630	Process	Positive regulation of miRNA metabolic process	IMP	22357537

Other IDs

• MIM: 164011
• HGNC: 7794
• e!Ensembl: ENSG00000109320

Protein

• UniProt ID: P19838
• Protein name: Nuclear factor NF-kappa-B p105 subunit (DNA-binding factor KBF1) (EBP-1) (Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1) [Cleaved into: Nuclear factor NF-kappa-B p50 subunit]
• Protein function: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. NF-kappa-B heterodimeric p65-p50 and RelB-p50 complexes are transcriptional activators. The NF-kappa-B p50-p50 homodimer is a transcriptional repressor, but can act as a transcriptional activator when associated with BCL3. NFKB1 appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins by p105 and generation of p50 by a cotranslational processing. The proteasome-mediated process ensures the production of both p50 and p105 and preserves their independent function, although processing of NFKB1/p105 also appears to occur post-translationally. p50 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. In a complex with MAP3K8, NFKB1/p105 represses MAP3K8-induced MAPK signaling; active MAP3K8 is released by proteasome-dependent degradation of NFKB1/p105.
• PDB: 1MDI, 1MDJ, 1MDK, 1NFI, 1SVC, 2DBF, 2O61, 3GUT
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00554	RHD_DNA_bind	44 → 242	Rel homology DNA-binding domain	Domain
  PF16179	RHD_dimer	251 → 353	Rel homology dimerisation domain	Domain
  PF00023	Ank	583 → 613	Ankyrin repeat	Repeat
  PF12796	Ank_2	679 → 749	Ankyrin repeats (3 copies)	Repeat
  PF00531	Death	816 → 892	Death domain	Domain

• Sequence:

  MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTDGPYLQILEQPKQRGFRFRYV
  CEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCED
  GICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQA
  EGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIY
  DSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDF
  SPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQ
  RKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFH
  PGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGE
  VTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQD
  ENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVED
  LLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMM
  SNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGT
  TPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMAT
  SWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLG
  LGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQ
  AHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQ
  EGPLEGKI

• Sequence length: 968