CYBA (cytochrome b-245 alpha chain)

Gene

• Entrez ID: 1535
• Gene name: Cytochrome b-245 alpha chain
• Gene symbol: CYBA
• Synonyms: CGD4, p22-PHOX
• Chromosome: 16
• Chromosome location: 16q24.2
• Summary: Cytochrome b is comprised of a light chain (alpha) and a heavy chain (beta). This gene encodes the light, alpha subunit which has been proposed as a primary component of the microbicidal oxidase system of phagocytes. Mutations in this gene are associated

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs4673	A>G,T	Benign, likely-pathogenic	Missense variant, coding sequence variant
rs28941476	C>T	Pathogenic	Missense variant, coding sequence variant
rs104894510	T>C	Pathogenic	Coding sequence variant, missense variant
rs104894511	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894513	C>T	Pathogenic	Coding sequence variant, missense variant
rs104894514	G>A,T	Not-provided, pathogenic	Synonymous variant, coding sequence variant, missense variant
rs104894515	G>T	Pathogenic	Downstream transcript variant, coding sequence variant, genic downstream transcript variant, missense variant
rs114610092	C>A,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Genic downstream transcript variant, downstream transcript variant, coding sequence variant, missense variant, stop gained
rs119103269	C>A,T	Pathogenic	Downstream transcript variant, coding sequence variant, genic downstream transcript variant, missense variant
rs179363890	A>G	Pathogenic	Coding sequence variant, missense variant
rs179363892	G>A,C	Not-provided, pathogenic	Coding sequence variant, missense variant
rs377055239	G>A,C,T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs779809359	G>A,C	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs1352931329	G>-,GG	Pathogenic	Coding sequence variant, frameshift variant
rs1439134665	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1567607736	G>-	Pathogenic	Coding sequence variant, downstream transcript variant, genic downstream transcript variant, frameshift variant
rs1567608830	CACCGAGAGCCTGGGG>-	Likely-pathogenic	Intron variant, coding sequence variant, splice acceptor variant
rs1567608853	G>C	Pathogenic	Intron variant
rs1567609091	C>T	Pathogenic	Splice donor variant
rs1597374562	G>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT046446	hsa-miR-15b-5p	CLASH	23622248
MIRT044553	hsa-miR-320a	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002479	Process	Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	TAS
GO:0005515	Function	Protein binding	IPI	3305576, 11733522, 16326715, 16460309, 17126813, 17803994, 23957209
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005886	Component	Plasma membrane	TAS
GO:0006801	Process	Superoxide metabolic process	IMP	1763037, 2243141
GO:0006954	Process	Inflammatory response	IMP	2243141
GO:0009055	Function	Electron transfer activity	IDA	12042318
GO:0009055	Function	Electron transfer activity	TAS	2243141
GO:0014895	Process	Smooth muscle hypertrophy	ISS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016175	Function	Superoxide-generating NAD(P)H oxidase activity	IMP	1763037
GO:0017004	Process	Cytochrome complex assembly	IDA	7938008
GO:0017124	Function	SH3 domain binding	IPI	7938008
GO:0020037	Function	Heme binding	IEA
GO:0022900	Process	Electron transport chain	IEA
GO:0030141	Component	Secretory granule	TAS	12005167
GO:0030670	Component	Phagocytic vesicle membrane	TAS
GO:0032755	Process	Positive regulation of interleukin-6 production	IDA	22423966
GO:0032760	Process	Positive regulation of tumor necrosis factor production	IDA	22423966
GO:0034137	Process	Positive regulation of toll-like receptor 2 signaling pathway	IDA	22423966
GO:0034599	Process	Cellular response to oxidative stress	TAS
GO:0035579	Component	Specific granule membrane	TAS
GO:0042554	Process	Superoxide anion generation	IBA	21873635
GO:0042554	Process	Superoxide anion generation	IMP	2243141
GO:0043020	Component	NADPH oxidase complex	IBA	21873635
GO:0043020	Component	NADPH oxidase complex	IDA	3305576
GO:0043020	Component	NADPH oxidase complex	IDA	22423966
GO:0043020	Component	NADPH oxidase complex	IMP	1763037
GO:0043312	Process	Neutrophil degranulation	TAS
GO:0045087	Process	Innate immune response	IMP	2243141
GO:0045087	Process	Innate immune response	ISS
GO:0045454	Process	Cell redox homeostasis	TAS
GO:0045730	Process	Respiratory burst	IMP	2243141
GO:0046872	Function	Metal ion binding	IEA
GO:0046982	Function	Protein heterodimerization activity	IPI	12042318
GO:0048010	Process	Vascular endothelial growth factor receptor signaling pathway	TAS
GO:0050665	Process	Hydrogen peroxide biosynthetic process	ISS
GO:0050766	Process	Positive regulation of phagocytosis	IDA	22423966
GO:0070821	Component	Tertiary granule membrane	TAS
GO:1900426	Process	Positive regulation of defense response to bacterium	IDA	22423966
GO:1903428	Process	Positive regulation of reactive oxygen species biosynthetic process	IDA	22423966

Other IDs

• MIM: 608508
• HGNC: 2577
• e!Ensembl: ENSG00000051523

Protein

• UniProt ID: P13498
• Protein name: Cytochrome b-245 light chain (Cytochrome b(558) alpha chain) (Cytochrome b558 subunit alpha) (Neutrophil cytochrome b 22 kDa polypeptide) (Superoxide-generating NADPH oxidase light chain subunit) (p22 phagocyte B-cytochrome) (p22-phox) (p22phox)
• Protein function: Subunit of NADPH oxidase complexes that is required for the NADPH oxidase activity that generates, in various cell types, superoxide from molecular oxygen utilizing NADPH as an electron donor (PubMed:15824103, PubMed:17140397, PubMed:38355798).
• PDB: 1WLP, 7U8G, 7YXW, 8GZ3, 8KEI, 8WEJ, 8X2L
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05038	Cytochrom_B558a	2 → 193	Cytochrome Cytochrome b558 alpha-subunit	Family

• Sequence:

  MGQIEWAMWANEQALASGLILITGGIVATAGRFTQWYFGAYSIVAGVFVCLLEYPRGKRK
  KGSTMERWGQKYMTAVVKLFGPFTRNYYVRAVLHLLLSVPAGFLLATILGTACLAIASGI
  YLLAAVRGEQWTPIEPKPRERPQIGGTIKQPPSNPPPRPPAEARKKPSEEEAAVAAGGPP
  GGPQVNPIPVTDEVV

• Sequence length: 195

Pathways

KEGG:

Phagosome
Osteoclast differentiation
Neutrophil extracellular trap formation
NOD-like receptor signaling pathway
Leukocyte transendothelial migration
Prion disease
Leishmaniasis
Chemical carcinogenesis - reactive oxygen species
Diabetic cardiomyopathy
Lipid and atherosclerosis
Fluid shear stress and atherosclerosis

Reactome:

ROS and RNS production in phagocytes
Cross-presentation of particulate exogenous antigens (phagosomes)
Detoxification of Reactive Oxygen Species
VEGFA-VEGFR2 Pathway
RHO GTPases Activate NADPH Oxidases
Neutrophil degranulation
WNT5:FZD7-mediated leishmania damping

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Granulomatous disease	Autosomal Recessive Chronic Granulomatous Disease, Chronic granulomatous disease, Granulomatous Disease, Chronic, X-Linked, Granulomatous Disease, Chronic, Autosomal Recessive, Cytochrome B-Negative	rs796065030, rs374402066, rs796065031, rs796065032, rs119103276, rs796065033, rs119103274, rs4029402, rs1563003964, rs119103270, rs1307080411, rs119103271, rs119103272, rs119103273, rs104894513, rs104894514, rs104894515, rs1567609091, rs104894511, rs28941476, rs1907271302, rs119103269, rs137854585, rs137854588, rs137854590, rs137854591, rs137854596, rs2146821097, rs137854592, rs1602175016, rs137854593, rs137854594, rs387906485, rs2146810847, rs1569478551, rs387906486, rs151344498, rs151344497, rs876657377, rs387906808, rs193922445, rs193922446, rs193922448, rs193922449, rs179363892, rs179363894, rs151344484, rs151344470, rs151344473, rs151344454, rs151344481, rs151344491, rs151344482, rs151344462, rs151344466, rs151344467, rs137854508, rs193922450, rs869025585, rs886039335, rs886039337, rs886041194, rs886041192, rs990043411, rs1057517730, rs1064794299, rs1453468510, rs28445840, rs145360423, rs1131691828, rs1556473078, rs1556464554, rs1556470775, rs1556464116, rs1556473119, rs1556469197, rs1556471620, rs1558098982, rs1290169467, rs1558092897, rs777621636, rs1569479943, rs1569480333, rs1567608830, rs1567608853, rs1439134665, rs1569480031, rs1569479953, rs766745748, rs782800778, rs1584370623, rs779809359, rs1472146831, rs1572151178, rs1352931329, rs1597374562, rs1602183698, rs200129367, rs1602186299, rs771926427, rs1602173465, rs1200078508, rs1602184316, rs1602183244, rs535897564, rs151344455, rs180899069, rs1929244686, rs1929497736, rs1929531349, rs1352107832, rs1929527785, rs1929245964, rs1939893821, rs763678131	2243141, 20167518, 2243141, 10910929, 19292887, 10914676, 7964505, 10759707, 2243141, 1763037, 27537055, 23910690, 18422995, 1415254, 8168815
Chronic obstructive pulmonary disease	Chronic Obstructive Airway Disease	rs2227956, rs1008438, rs1043618, rs562047, rs1061581, rs2763979, rs6457452, rs13147758, rs1828591, rs13118928
Diabetes mellitus	Diabetes Mellitus, Non-Insulin-Dependent	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs4402960, rs1362648752, rs3745368, rs3792267, rs3842570, rs5030952, rs2975760, rs119489103, rs7903146, rs12255372, rs11196205, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237, rs80356613, rs137852740, rs137852786, rs387906407, rs151344623, rs28938469, rs28936371, rs137852672, rs80356637, rs80356642, rs80356653, rs137852673, rs137852674, rs80356634, rs80356651, rs193929360, rs137853334, rs137853335, rs137853336, rs1600731198, rs137853338, rs121964882, rs121964883, rs387906511, rs121964884, rs121964885, rs2147483647, rs387906512, rs121964887, rs121964888, rs121964889, rs121964890, rs121964891, rs28934878, rs74315383, rs121964893, rs886037620, rs886037621, rs80356663, rs121434593, rs121913150, rs587776825, rs137853236, rs2135842335, rs137853237, rs137853238, rs2135818776, rs1566092470, rs1463923467, rs137853243, rs137853244, rs2135839114, rs137853245, rs2135847417, rs121918407, rs104894005, rs104894006, rs80356655, rs104894008, rs104894009, rs104894010, rs104894011, rs80356654, rs104894016, rs193929376, rs193929374, rs193929375, rs193929373, rs80356666, rs80356669, rs80356664, rs193929366, rs1048095, rs193929355, rs193929356, rs1259467443, rs104893642, rs387906777, rs387906779, rs141804752, rs182349376, rs184917682, rs193922396, rs193922400, rs193922401, rs137852676, rs193922407, rs193922638, rs193922257, rs193922258, rs193922259, rs193922260, rs193922261, rs193922262, rs193922263, rs193922264, rs193922265, rs193922268, rs193921338, rs193922269, rs193922272, rs193922273, rs193922275, rs193922278, rs193922279, rs193922280, rs193922281, rs193922282, rs193922283, rs193922284, rs193922286, rs193922287, rs193922289, rs193922291, rs193922295, rs193922297, rs193922300, rs193922302, rs193922303, rs193922308, rs193922313, rs193922314, rs144723656, rs193922315, rs193922316, rs193922317, rs148311934, rs193922319, rs193922320, rs193922326, rs193922329, rs193922330, rs193922331, rs193922335, rs193922336, rs193922338, rs193922340, rs193922341, rs193922471, rs193922475, rs193922476, rs193922479, rs193922355, rs193922356, rs193922576, rs193922578, rs193922582, rs193922588, rs193922592, rs193922594, rs193922596, rs386134267, rs193922598, rs193922599, rs193922600, rs193922604, rs193922605, rs397514580, rs397515519, rs267601516, rs587780343, rs587780345, rs587780346, rs587780347, rs587780357, rs148954387, rs61736969, rs587783673, rs587783672, rs587783669, rs786204676, rs794727236, rs151344624, rs794727775, rs794727839, rs199946797, rs869320673, rs796065047, rs759072800, rs797045595, rs797045209, rs797045207, rs797045213, rs797045623, rs863225280, rs149703259, rs864321656, rs139964066, rs777870079, rs878853246, rs769268803, rs886039380, rs886041392, rs886041391, rs886042610, rs143064649, rs1057516192, rs746480424, rs1057516281, rs576684889, rs754728827, rs1057520291, rs1057520779, rs893256143, rs1057520504, rs1057524790, rs1057524902, rs1057524904, rs1057524905, rs764232985, rs1064793998, rs1064794268, rs769086289, rs369429452, rs1085307913, rs1131691416, rs765432081, rs1131692182, rs748749585, rs1554335441, rs762263694, rs1312678560, rs767565869, rs1375656631, rs1554335391, rs1360415315, rs1554335616, rs1554335752, rs1554909277, rs769518471, rs757171524, rs768951263, rs762703502, rs1555212248, rs1555212359, rs1555813319, rs1555816654, rs1553638903, rs1553638909, rs948820149, rs371977235, rs1553784995, rs76474829, rs200998587, rs1415041911, rs1554334894, rs1260178539, rs1554335421, rs1555211904, rs779184183, rs1554335564, rs200670692, rs1400535021, rs1554334872, rs1555212749, rs1553876668, rs1553878211, rs954727530, rs1554924035, rs372307320, rs925231098, rs1554913069, rs1554933565, rs766431403, rs746714109, rs751279984, rs770664202, rs1008906426, rs758844607, rs1554924540, rs1566092307, rs753998395, rs1565885935, rs1167124132, rs1376796469, rs556436603, rs1562715657, rs1486280029, rs1564869850, rs755259997, rs769569410, rs1172328722, rs1286294151, rs1375557127, rs1568731279, rs1562715426, rs556581174, rs1564865302, rs1565886545, rs776793516, rs1568724014, rs1392795567, rs781260712, rs1562719705, rs1382448285, rs1564977373, rs750586210, rs1598842892, rs1583592247, rs780612692, rs1593060859, rs1476637197, rs751279776, rs1593060890, rs1191912908, rs1167675604, rs1583601110, rs1593058932, rs778611627, rs753296261	15531508
Hypertension	Hypertensive disease	rs13306026, rs13333226	20505675, 17324946, 16685210
Osteomyelitis	Osteomyelitis	rs11125529, rs10936599, rs7675998, rs398652, rs755017
Renal insufficiency	Renal Insufficiency	rs1596536873	23325087

Unknown
Disease name	Disease term	dbSNP ID	References
Atherosclerosis	Atherosclerosis	rs699947, rs59439148	20720404
Eczema	Eczema
Gingivitis	Gingivitis
Granulomatosis	Granulomatosis
Heart diseases	Heart Diseases		16330681
Immunologic deficiency syndromes	Immunologic Deficiency Syndromes
Inflammatory abnormality of the eye	Inflammatory abnormality of the eye
Kidney failure	Kidney Failure, Chronic, Kidney Failure		19420110, 23325087
Liver cirrhosis	Liver Cirrhosis		25226513
Liver fibrosis	Fibrosis, Liver		25226513
Lupus erythematosus	Lupus Erythematosus, Discoid
Lymphadenitis	Lymphadenitis
Malabsorption syndrome	Malabsorption Syndrome
Mediastinal lymphadenopathy	Mediastinal lymphadenopathy
Otitis media	Otitis Media	rs601338, rs1047781, rs1800028
Sinusitis	Sinusitis