NFKB2 (nuclear factor kappa B subunit 2)

Gene

• Entrez ID: 4791
• Gene name: Nuclear factor kappa B subunit 2
• Gene symbol: NFKB2
• Synonyms: CVID10, H2TF1, LYT-10, LYT10, NF-kB2, p100, p49/p100, p52
• Chromosome: 10
• Chromosome location: 10q24.32
• 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 enc

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs748910652	C>T	Pathogenic	Coding sequence variant, stop gained
rs1565207233	C>T	Likely-pathogenic	5 prime UTR variant, stop gained, coding sequence variant
rs1589866171	G>T	Pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016350	hsa-miR-193b-3p	Microarray	20304954
MIRT027644	hsa-miR-98-5p	Microarray	19088304
MIRT038120	hsa-miR-423-5p	CLASH	23622248
MIRT1183464	hsa-miR-203	CLIP-seq
MIRT1183465	hsa-miR-3144-5p	CLIP-seq
MIRT1183466	hsa-miR-3179	CLIP-seq
MIRT1183467	hsa-miR-3191	CLIP-seq
MIRT1183468	hsa-miR-3202	CLIP-seq
MIRT1183469	hsa-miR-342-5p	CLIP-seq
MIRT1183470	hsa-miR-4497	CLIP-seq
MIRT1183471	hsa-miR-4651	CLIP-seq
MIRT1183472	hsa-miR-4652-5p	CLIP-seq
MIRT1183473	hsa-miR-4664-5p	CLIP-seq
MIRT1183474	hsa-miR-4694-5p	CLIP-seq
MIRT1183475	hsa-miR-4718	CLIP-seq
MIRT1183476	hsa-miR-4747-5p	CLIP-seq
MIRT1183477	hsa-miR-491-5p	CLIP-seq
MIRT1183478	hsa-miR-608	CLIP-seq
MIRT1183479	hsa-miR-609	CLIP-seq
MIRT1183480	hsa-miR-615-5p	CLIP-seq
MIRT2282468	hsa-miR-3151	CLIP-seq
MIRT2282469	hsa-miR-3184	CLIP-seq
MIRT1183469	hsa-miR-342-5p	CLIP-seq
MIRT2282470	hsa-miR-4447	CLIP-seq
MIRT2282471	hsa-miR-4455	CLIP-seq
MIRT2282472	hsa-miR-4472	CLIP-seq
MIRT1183471	hsa-miR-4651	CLIP-seq
MIRT1183473	hsa-miR-4664-5p	CLIP-seq
MIRT1183474	hsa-miR-4694-5p	CLIP-seq
MIRT1183477	hsa-miR-491-5p	CLIP-seq
MIRT1183478	hsa-miR-608	CLIP-seq
MIRT1183479	hsa-miR-609	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
AIP	Repression	21984905
JUN	Unknown	7541912
SP1	Unknown	7541912

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
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	12835724
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:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	12835724
GO:0002268	Process	Follicular dendritic cell differentiation	IEA
GO:0002467	Process	Germinal center formation	IEA
GO:0003700	Function	DNA-binding transcription factor activity	TAS	1760839, 1876189
GO:0005515	Function	Protein binding	IPI	8441377, 11239468, 11526476, 14743216, 16108830, 18617892, 21988832, 25609649, 25852190, 28514442
GO:0005634	Component	Nucleus	IDA	15677444
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	15677444
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006355	Process	Regulation of transcription, DNA-templated	IDA	8360178
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007568	Process	Aging	IEA
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0032481	Process	Positive regulation of type I interferon production	TAS
GO:0032496	Process	Response to lipopolysaccharide	IEA
GO:0033257	Component	Bcl3/NF-kappaB2 complex	IDA	9407099
GO:0034097	Process	Response to cytokine	IEA
GO:0038061	Process	NIK/NF-kappaB signaling	TAS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	12835724
GO:0048511	Process	Rhythmic process	IEA
GO:0048536	Process	Spleen development	IEA
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	TAS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 164012
• HGNC: 7795
• e!Ensembl: ENSG00000077150

Protein

• UniProt ID: Q00653
• Protein name: Nuclear factor NF-kappa-B p100 subunit (DNA-binding factor KBF2) (H2TF1) (Lymphocyte translocation chromosome 10 protein) (Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2) (Oncogene Lyt-10) (Lyt10) [Cleaved into: Nuclear factor NF-kap
• 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 inflammati
• PDB: 1A3Q, 2D96, 3DO7, 4OT9, 5ZMC, 7CLI, 7VUP, 7VUQ, 7W7L, 8G8Q, 8G8S
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00554	RHD_DNA_bind	40 → 220	Rel homology DNA-binding domain	Domain
  PF16179	RHD_dimer	229 → 329	Rel homology dimerisation domain	Domain
  PF00023	Ank	527 → 558	Ankyrin repeat	Repeat
  PF00023	Ank	667 → 699	Ankyrin repeat	Repeat
  PF00531	Death	775 → 850	Death domain	Domain

• Sequence:

  MESCYNPGLDGIIEYDDFKLNSSIVEPKEPAPETADGPYLVIVEQPKQRGFRFRYGCEGP
  SHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGIC
  AVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKE
  LKKVMDLSIVRLRFSAFLRASDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSV
  RGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIE
  RPVTVFLQLKRKRGGDVSDSKQFTYYPLVEDKEEVQRKRRKALPTFSQPFGGGSHMGGGS
  GGAAGGYGGAGGGGSLGFFPSSLAYSPYQSGAGPMGCYPGGGGGAQMAATVPSRDSGEEA
  AEPSAPSRTPQCEPQAPEMLQRAREYNARLFGLAQRSARALLDYGVTADARALLAGQRHL
  LTAQDENGDTPLHLAIIHGQTSVIEQIVYVIHHAQDLGVVNLTNHLHQTPLHLAVITGQT
  SVVSFLLRVGADPALLDRHGDSAMHLALRAGAGAPELLRALLQSGAPAVPQLLHMPDFEG
  LYPVHLAVRARSPECLDLLVDSGAEVEATERQGGRTALHLATEMEELGLVTHLVTKLRAN
  VNARTFAGNTPLHLAAGLGYPTLTRLLLKAGADIHAENEEPLCPLPSPPTSDSDSDSEGP
  EKDTRSSFRGHTPLDLTCSTKVKTLLLNAAQNTMEPPLTPPSPAGPGLSLGDTALQNLEQ
  LLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDMGL
  EEGVRLLRGPETRDKLPSTAEVKEDSAYGSQSVEQEAEKLGPPPEPPGGLCHGHPQPQVH
  

• Sequence length: 900

Pathways

KEGG:

MAPK signaling pathway
NF-kappa B signaling pathway
Osteoclast differentiation
C-type lectin receptor signaling pathway
Legionellosis
Human T-cell leukemia virus 1 infection
Epstein-Barr virus infection
Pathways in cancer
Viral carcinogenesis
Breast cancer

Reactome:

RIP-mediated NFkB activation via ZBP1
DEx/H-box helicases activate type I IFN and inflammatory cytokines production
PKMTs methylate histone lysines
TAK1 activates NFkB by phosphorylation and activation of IKKs complex
Interleukin-1 processing
SUMOylation of immune response proteins
IkBA variant leads to EDA-ID
Dectin-1 mediated noncanonical NF-kB signaling
NIK-->noncanonical NF-kB signaling
The NLRP3 inflammasome
TRAF6 mediated NF-kB activation
Purinergic signaling in leishmaniasis infection

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Anemia	Anemia, Hemolytic	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Asthma	Asthma	rs324981, rs121912630, rs150116809, rs4950928, rs708494, rs1581842283
Bronchiectasis	Bronchiectasis	rs121908758, rs121908811, rs76649725, rs267606722, rs121909008, rs387906360, rs387906361, rs80034486, rs74767530, rs121908776, rs121909012, rs77646904, rs121908754, rs121909015, rs121909016, rs387906365, rs80055610, rs75528968, rs121908748, rs77932196, rs121909026, rs121908751, rs121908750, rs746418935, rs79282516, rs77409459, rs121909031, rs76554633, rs75115087, rs79633941, rs387906375, rs75389940, rs121909043, rs387906379, rs121908784, rs121909047, rs137852709, rs1596894031, rs137852710, rs61759860, rs121908805, rs193922501, rs193922503, rs193922504, rs1554389296, rs121908812, rs74467662, rs193922510, rs193922514, rs121908797, rs193922515, rs76151804, rs78984783, rs77035409, rs193922532, rs121908767, rs77188391, rs121908789, rs121908779, rs36210737, rs121908763, rs121908794, rs121908796, rs121908772, rs79031340, rs397508137, rs397508139, rs121908774, rs397508150, rs397508152, rs397508158, rs397508165, rs397508168, rs397508173, rs397508192, rs397508196, rs397508200, rs397508205, rs397508208, rs397508211, rs397508222, rs397508225, rs397508231, rs397508243, rs397508251, rs397508261, rs397508272, rs397508273, rs397508276, rs397508295, rs397508296, rs397508298, rs397508300, rs77284892, rs397508310, rs201978662, rs201124247, rs121908780, rs397508331, rs397508333, rs397508339, rs397508341, rs121908760, rs397508350, rs397508353, rs121908810, rs397508360, rs374946172, rs145449046, rs397508377, rs397508379, rs397508380, rs397508386, rs397508387, rs397508393, rs397508399, rs397508400, rs397508412, rs397508413, rs121909034, rs149790377, rs121908792, rs397508426, rs397508431, rs397508441, rs397508451, rs397508461, rs397508479, rs397508482, rs397508496, rs397508498, rs397508506, rs397508510, rs142394380, rs121909036, rs139304906, rs121908798, rs397508532, rs397508535, rs146521846, rs139729994, rs397508570, rs397508572, rs77834169, rs78655421, rs121908765, rs397508595, rs397508596, rs397508600, rs397508604, rs397508609, rs397508616, rs397508620, rs397508624, rs121908808, rs397508635, rs397508636, rs397508637, rs397508658, rs397508673, rs397508680, rs397508686, rs76371115, rs397508702, rs397508706, rs397508712, rs397508715, rs397508721, rs397508732, rs397508734, rs397508740, rs121908771, rs397508761, rs78440224, rs121908793, rs397508767, rs121908803, rs397508777, rs397508784, rs397508791, rs397508796, rs397508799, rs397508805, rs397508808, rs397508809, rs397508824, rs786204693, rs755416052, rs397508263, rs1057516619, rs397508176, rs1057516415, rs1057516970, rs754392413, rs1057516457, rs397508709, rs1060503164, rs775663783, rs397508294, rs1554380497, rs397508163, rs121908785, rs1235397597, rs397508405, rs1554392800, rs375661578, rs397508693, rs766063304, rs141482808, rs1290078234, rs756219310, rs1554390958, rs1555112332, rs750559671, rs533959068, rs1554389062, rs1554389486, rs1330431481, rs193922730, rs779177972, rs1562928997, rs1562908997, rs1562876459, rs1584785196, rs1584786454, rs1299250440, rs1584837090, rs1584764596, rs1584812425	26279205
Common variable immunodeficiency	Common Variable Immunodeficiency, Acquired Hypogammaglobulinemia, IMMUNODEFICIENCY, COMMON VARIABLE, 1, IMMUNODEFICIENCY, COMMON VARIABLE, 10	rs72553883, rs121908379, rs104894650, rs587776775, rs398122863, rs398122864, rs397514332, rs397514331, rs727502786, rs727502787, rs72553882, rs869320688, rs869320689, rs869320754, rs773694113, rs1553319504, rs201017642, rs1555550717, rs1558192723, rs1030733127, rs749636258, rs185689791, rs1559035937, rs1565214594, rs1560679469, rs1560711146, rs1569376229, rs1578790573, rs939459600, rs1572952530, rs1572950925, rs772481080, rs369363360, rs72553885, rs72553879, rs1265262160, rs1303637368, rs757598952, rs1016142312, rs1578771120, rs1578771197, rs1578793298, rs1578793312, rs1578809101, rs1578811073, rs1590715754, rs144718007, rs759649059, rs1723945421, rs2061279365	24888602, 25237204, 24702956, 24140114, 25524009, 25605273, 16303288, 26279205
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Gastrointestinal stromal tumor	Gastrointestinal Stromal Tumors	rs587776653, rs74315368, rs74315369, rs587776793, rs587776794, rs587776795, rs606231209, rs121908589, rs121913685, rs121913680, rs794726675, rs587776804, rs121913517, rs121913234, rs121913512, rs267607032, rs387906780, rs201286421, rs587778661, rs587781270, rs587782243, rs74315370, rs587782703, rs786203457, rs764575966, rs786203251, rs587782604, rs200245469, rs397516836, rs786202732, rs786201161, rs786201063, rs751000085, rs869025568, rs876660642, rs876658713, rs151170408, rs878854632, rs752360961, rs121913235, rs121913521, rs121913513, rs1057519708, rs1057519710, rs121913514, rs1057519713, rs778582853, rs1060503757, rs1060502521, rs1060502543, rs898854295, rs981049067, rs916516745, rs1553887262, rs1057520032, rs1553887960, rs775143272, rs1560395607, rs1560418178, rs751904543, rs1560420761, rs1560417385, rs1560417396, rs1560417427, rs1560417438, rs1560417535, rs1560417642, rs1560417666, rs1560417673, rs1577992594, rs1577995761, rs1578003055, rs1301704156, rs1734957331
Isolated somatotropin deficiency	Isolated somatotropin deficiency	rs797044450, rs71640277, rs863223306, rs2144738731, rs863223307, rs2144739370, rs863223309, rs863223310, rs137853223, rs2144739380, rs2144739391
Lymphoma	Lymphoma, Lymphoma, T-Cell, Cutaneous	rs11540652, rs1592119138, rs1592123162, rs1599367044	26192916
Adrenal insufficiency	Secondary Adrenal Insufficiency	rs104894118, rs104894119	25524009
Vasculitis	Vasculitis	rs376785840, rs587777240, rs200930463, rs587777241, rs77563738, rs202134424, rs148936893, rs587777242, rs775440641, rs770689762, rs45511697, rs139750129, rs756881285, rs747774101, rs1568966771, rs766602945, rs1601419986, rs1489114116, rs754904956, rs755007390, rs368615054

Unknown
Disease name	Disease term	dbSNP ID	References
Adrenocorticotropin deficient adrenal insufficiency	Adrenocorticotropin deficient adrenal insufficiency
Alopecia	Alopecia totalis
Brachycephaly	Brachycephaly
Bronchitis	Recurrent bronchitis
David syndrome	Deficiency in anterior pituitary function-variable immunodeficiency syndrome
Granulomatous slack skin	Granulomatous Slack Skin		26192916
Hypoglycemia	Hypoglycemia
Hypoglycemic coma	Hypoglycemic coma
Immune thrombocytopenic purpura	Immune thrombocytopenic purpura
Immunoglobulin deficiency	Immunoglobulin Deficiency, Late-Onset
Immunologic deficiency syndromes	Immunologic Deficiency Syndromes
Imperforate anus	Anus, Imperforate
Lymphopenia	Lymphopenia
Nail dystrophy	Dystrophia unguium
Otitis media	Chronic otitis media, Recurrent otitis media	rs601338, rs1047781, rs1800028
Psoriasiform eczema	Psoriasiform eczema
Sinusitis	Recurrent sinusitis
Somatotropin deficiency	Somatotropin deficiency