CYBA

gene
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Also known as p22-PHOXp22phox

Summary

CYBA (cytochrome b-245 alpha chain, HGNC:2577) is a protein-coding gene on chromosome 16q24.2, encoding Cytochrome b-245 light chain (P13498). 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.

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 with autosomal recessive chronic granulomatous disease (CGD), that is characterized by the failure of activated phagocytes to generate superoxide, which is important for the microbicidal activity of these cells.

Source: NCBI Gene 1535 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): granulomatous disease, chronic, autosomal recessive, cytochrome b-negative (Definitive, GenCC) — +1 more curated relationship
  • GWAS associations: 2
  • Clinical variants (ClinVar): 531 total — 42 pathogenic, 26 likely-pathogenic
  • Phenotypes (HPO): 44
  • Druggable target: yes
  • MANE Select transcript: NM_000101

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2577
Approved symbolCYBA
Namecytochrome b-245 alpha chain
Location16q24.2
Locus typegene with protein product
StatusApproved
Aliasesp22-PHOX, p22phox
Ensembl geneENSG00000051523
Ensembl biotypeprotein_coding
OMIM608508
Entrez1535

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 3 retained_intron

ENST00000261623, ENST00000562209, ENST00000563526, ENST00000565588, ENST00000566229, ENST00000566534, ENST00000567174, ENST00000568278, ENST00000569359, ENST00000696156, ENST00000696157, ENST00000696158, ENST00000696159, ENST00000696160, ENST00000696161, ENST00000696162, ENST00000696163, ENST00000967612, ENST00000967613

RefSeq mRNA: 1 — MANE Select: NM_000101 NM_000101

CCDS: CCDS32504

Canonical transcript exons

ENST00000261623 — 6 exons

ExonStartEnd
ENSE000035059808864710188647175
ENSE000036516778864675588646838
ENSE000036625038864611688646197
ENSE000036702748864804588648114
ENSE000039662468864328988643571
ENSE000039662478865095688651053

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 99.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 298.9461 / max 4697.4355, expressed in 1735 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
158554297.89621735
1585510.9692482
1585530.080623

Top tissues by expression

291 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.73gold quality
monocyteCL:000057699.72gold quality
leukocyteCL:000073899.67gold quality
mononuclear cellCL:000084299.67gold quality
mucosa of transverse colonUBERON:000499199.49gold quality
spleenUBERON:000210699.48gold quality
bone marrowUBERON:000237199.06gold quality
right lungUBERON:000216798.97gold quality
right uterine tubeUBERON:000130298.91gold quality
upper lobe of left lungUBERON:000895298.82gold quality
bone marrow cellCL:000209298.81gold quality
upper lobe of lungUBERON:000894898.58gold quality
olfactory segment of nasal mucosaUBERON:000538698.57gold quality
small intestine Peyer’s patchUBERON:000345498.56gold quality
right lobe of thyroid glandUBERON:000111998.48gold quality
bloodUBERON:000017898.33gold quality
lymph nodeUBERON:000002998.32gold quality
endometrium epitheliumUBERON:000481198.32gold quality
gall bladderUBERON:000211098.31gold quality
transverse colonUBERON:000115798.30gold quality
left lobe of thyroid glandUBERON:000112098.24gold quality
periodontal ligamentUBERON:000826698.21gold quality
metanephros cortexUBERON:001053398.08gold quality
omental fat padUBERON:001041498.07gold quality
peritoneumUBERON:000235897.98gold quality
minor salivary glandUBERON:000183097.77gold quality
right coronary arteryUBERON:000162597.75gold quality
vermiform appendixUBERON:000115497.72gold quality
thoracic aortaUBERON:000151597.65gold quality
ascending aortaUBERON:000149697.64gold quality

Single-cell (SCXA)

Detected in 45 experiment(s), a significant marker in 36.

ExperimentMarker?Max mean expression
E-MTAB-8207yes4568.64
E-MTAB-8495yes3329.40
E-MTAB-6701yes2139.28
E-MTAB-10855yes1801.12
E-HCAD-6yes1795.76
E-GEOD-134144yes1637.49
E-HCAD-8yes1636.81
E-HCAD-11yes1634.96
E-MTAB-9841yes1633.84
E-MTAB-10042yes1457.84
E-GEOD-124263yes1451.78
E-GEOD-114530yes1156.61
E-MTAB-8205yes499.52
E-MTAB-8381yes455.18
E-GEOD-111727yes434.61

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOS, JUN, PPARA, PPARG, RELA, SPI1

Literature-anchored findings (GeneRIF, showing 40)

  • Anaplasma phagocytophila causes a change in p22phox. (PMID:11854221)
  • p22(phox), gp91(phox), p47(phox), p67(phox), and p40(phox) existed as a functional complex in the cytoskeletal fraction. (PMID:11893732)
  • Increased free radical production in hypertension due to increased expression of the NADPH oxidase subunit p22(phox) in lymphoblast cell lines. (PMID:11910303)
  • Tumor necrosis factor-alpha increases airway smooth muscle oxidants production through a NADPH oxidase-like system to enhance myosin light chain phosphorylation and contractility. (PMID:11940577)
  • mutagenesis of histidine 94 is not required for flavocytochrome b558 function (PMID:12042318)
  • A novel and unusual case of chronic granulomatous disease in a child with a homozygous 36-bp deletion in the CYBA gene (A22(0)) leading to the activation of a cryptic splice site in intron 4. (PMID:12073015)
  • no association between a genetic variant and the incidence and progression of IgA nephropathy (PMID:12147803)
  • Data show that the A640G and the C242T polymorphisms of p22(phox)-based NAD(P)H oxidase were not associated with severity of coronary artery disease and endothelial function. (PMID:12230880)
  • In nonatherosclerotic aortic intima, the expression of p22phox by intimal smooth muscle cells is low; aortic fatty streaks contain higher levels of p22phox peptides, mostly localized in macrophages. (PMID:12482831)
  • C242T mutation in p22 phox gene is associated with progression of asymptomatic atherosclerosis in type 2 diabetes and is also associated with insulin resistance in nondiabetic subjects. (PMID:12547880)
  • decompensated type 2 diabetes is associated with increased NADPH oxidase subunit p22(phox) and hemeoxygenase-1 gene expressions in circulating monocytes (PMID:12679469)
  • Identification of a new p22(phox)polymorphism associated with hypertension. (PMID:12729892)
  • adenosine pretreatment of fMLF-stimulated neutrophils results in decreased plasma membrane/secretory granule content of the flavocytochrome b components p22phox and gp91phox of the NADPH oxidase, which correlates with inhibition of ROS production (PMID:12772776)
  • results suggest that the CYBA C242T polymorphism is involved in NAD(P)H oxidase activity and affects oxidation of lipoproteins by altering the redox state in the vasculature (PMID:12927691)
  • highly significant increase in the frequency of the T/T242 genotype in patients with nephropathy compared with those with retinopathy alone or no microvascular disease after 20 years’ diabetes duration (PMID:14578247)
  • findings demonstrate that activator protein-1 activation in human smooth muscle cells in response to angiotensin II and platelet-derived growth factor-AA is mediated via generation of p22phox-dependent reactive oxygen species (PMID:14652666)
  • NADPH p22phox C242T polymorphisms may be useful in identifying the risk for developing diabetic nephropathy in type 2 diabetic patients. (PMID:14747204)
  • Superoxide production was significantly reduced by the C242T , but not the A640G or the -930A/G, polymorphism. Since p22phox exists in both the neutrophil & vessel wall, vascular oxidative stress is likely diminished in individuals with this polymorphism. (PMID:15078863)
  • Binding of FAD to cytochrome b558 is facilitated during activation of the phagocyte NADPH oxidase (PMID:15102859)
  • No assosication between p22-phox polymorphism and coronary disease in a low-risk Spanish population (PMID:15193812)
  • Human p22phox (CYBA) -930A/G polymorphism associates with increased p22phox expression and NADPH oxidase activity in phagocytes of hypertensive patients. (PMID:15210651)
  • Hypertensive subjects carrying the GG genotype of the p22phox -930A/G polymorphism are highly exposed to NADPH oxidase-mediated oxidative stress. (PMID:15210651)
  • NAD(P)H oxidase activity is associated with increased protein levels of p22phox, p47phox, and p67phox, and increased p22phox and nox2 (gp91phox) mRNA expression. (PMID:15256399)
  • significantly reduced at the Anaplasma phagocytophilum phagosome (PMID:15322037)
  • p22phox directly interacts with Nox1 and Nox4, to form an superoxide-generating NADPH oxidase. (PMID:15322091)
  • The significance of the G(-930)A polymorphism of CYBA in the pathogenesis of hypertension was confirmed; significant effects of the genotype on BP status were observed in the male, but not the female, population (PMID:15671602)
  • These findings suggest a positive feedback mechanism whereby reactive oxygen species (ROS), possibly generated by the NADPH oxidase, lead to elevated levels of p22phox and, thus, sustained ROS generation as is observed in endothelial dysfunction. (PMID:15683718)
  • Nox3 functions together with p22(phox) as an enzyme constitutively producing superoxide (PMID:15824103)
  • The Nox4 requires p22phox for ROS generation and mutational analysis revealed structural requirements affecting expression of the p22phox protein and Nox activity. (PMID:15927447)
  • Both regulatory subunit binding-dependent and -independent functions of p22(phox) are implicated in regulating reactive oxygen species production by NADPH oxidase (Nox) subunits (PMID:15994299)
  • p22phox polymorphisms, especially A640G, were associated with differential changes in systemic oxidative stress with aerobic exercise training (PMID:16002772)
  • the p22(phox) gene has a role in hypertension [review] (PMID:16115038)
  • We identified a risk haplotype for nondiabetic end-stage renal disease in the CYBA gene using haplotype analysis. (PMID:16215641)
  • Increased expression and activity of NAD(P)H oxidase subunits and xanthine oxidase, in part mediated through angiotensin II and PKC-dependent pathways, are important mechanisms underlying increased oxidative stress in human coronary artery disease (PMID:16293794)
  • the C-terminal alpha-helical region of the p22phox peptide increases the binding affinity for the tandem SH3 domains of p47phox more than 10-fold (PMID:16326715)
  • the CT+TT genotypes were independently associated with a higher risk of having overt nephropathy among smokers [odds ratio (OR)=6.76, 95% confidence interval (95% CI) 1.83-25.02]. (PMID:16358232)
  • Pro152, Pro156 & Arg158 in the p22phox PRR are indispensable for interaction with p47phox. A region C-terminal to the PRR of p22phox (AA161-164), in an a-helical conformation, aids in full oxidase activation via the association with p47phox SH3. (PMID:16460309)
  • In EH p22(phox) and PAI-1 mRNA and protein level was increased compared with C. In EH + D, doxazosin reduced p22(phox) and PAI-1 gene and protein expression, which was similar to that of C. (PMID:16546843)
  • The results from this study reveal that cannabidiol, acting through CB2 and regulation of Nox4 and p22(phox) expression, may be a novel and highly selective treatment for leukemia. (PMID:16754784)
  • These results support the increased risk of developing early coronary artery disease and of having rapid progression of coronary stenosis in subjects carrying the C242T nucleotide transition among the Italian population. (PMID:16788250)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocybaENSDARG00000018283
mus_musculusCybaENSMUSG00000006519
rattus_norvegicusCybaENSRNOG00000013014

Protein

Protein identifiers

Cytochrome b-245 light chainP13498 (reviewed: P13498)

Alternative names: 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

All UniProt accessions (14): A0A8Q3SIH4, A0A8Q3SIJ9, A0A8Q3SJ80, A0A8Q3WL14, A0A8Q3WL20, A0A8Q3WL26, A0A8Q3WL27, A0A8Q3WLM1, P13498, H3BNP7, H3BPX1, H3BPZ7, H3BR52, H3BT77

UniProt curated annotations — full annotation on UniProt →

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. Subunit of the phagocyte NADPH oxidase complex that mediates the transfer of electrons from cytosolic NADPH to O2 to produce the superoxide anion (O2(-)). In the activated complex, electrons are first transferred from NADPH to flavin adenine dinucleotide (FAD) and subsequently transferred via two heme molecules to molecular oxygen, producing superoxide through an outer-sphere reaction. Activation of the NADPH oxidase complex is initiated by the assembly of cytosolic subunits of the NADPH oxidase complex with the core NADPH oxidase complex to form a complex at the plasma membrane or phagosomal membrane. This activation process is initiated by phosphorylation dependent binding of the cytosolic NCF1/p47-phox subunit to the C-terminus of CYBA/p22-phox. Aassociates with NOX3 to form a functional NADPH oxidase constitutively generating superoxide.

Subunit / interactions. Component of the phagocyte NADPH oxidase core complex/cytochrome b558 complex, composed of CYBB (heavy chain (beta)) and CYBA (light chain (alpha)). Component of the phagocyte NADPH oxidase complex composed of an obligatory core heterodimer formed by the membrane proteins CYBA and CYBB and the cytosolic regulatory subunits NCF1/p47-phox, NCF2/p67-phox, NCF4/p40-phox and the small GTPase RAC1 or RAC2. Interacts with NCF1 (via SH3 domain). Interacts with SH3PXD2A. Interacts with DUOX1, DUOX2 and TPO. Interacts with NOX4; this interaction mediates superoxide generation. Interacts with calprotectin (S100A8/9). Interacts with GBP7. Interacts with NOXO1. Forms a heterodimer with NOX3 and is essential for activity and cell membrane localization of NOX3. Interacts with NOX1.

Subcellular location. Cell membrane.

Post-translational modifications. Phosphorylation at Thr-147 enhances NADPH oxidase activity by promoting NCF1/p47-phox binding. Ubiquitinated at Lys-149 likely by RNF145.

Disease relevance. Granulomatous disease, chronic, autosomal recessive, 4 (CGD4) [MIM:233690] A form of chronic granulomatous disease, a primary immunodeficiency characterized by severe recurrent bacterial and fungal infections, along with manifestations of chronic granulomatous inflammation. It results from an impaired ability of phagocytes to mount a burst of reactive oxygen species in response to pathogens. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the p22phox family.

RefSeq proteins (1): NP_000092* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007732Cyt_b558_asuFamily

Pfam: PF05038

UniProt features (43 total): sequence variant 16, helix 8, topological domain 6, transmembrane region 4, modified residue 2, initiator methionine 1, chain 1, region of interest 1, cross-link 1, mutagenesis site 1, strand 1, intramembrane region 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
7YXWX-RAY DIFFRACTION2.5
8WEJELECTRON MICROSCOPY2.79
8X2LELECTRON MICROSCOPY2.99
7U8GELECTRON MICROSCOPY3.2
8GZ3ELECTRON MICROSCOPY3.3
8KEIELECTRON MICROSCOPY3.56
1WLPSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P13498-F177.280.40

Antibody-complex structures (SAbDab): 57U8G, 8GZ3, 8KEI, 8WEJ, 8X2L

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 147, 168, 149

Mutagenesis-validated functional residues (1):

PositionPhenotype
157loss of interaction with noxo1.

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

IDPathway
R-HSA-1222556ROS and RNS production in phagocytes
R-HSA-1236973Cross-presentation of particulate exogenous antigens (phagosomes)
R-HSA-3299685Detoxification of Reactive Oxygen Species
R-HSA-4420097VEGFA-VEGFR2 Pathway
R-HSA-5668599RHO GTPases Activate NADPH Oxidases
R-HSA-6798695Neutrophil degranulation
R-HSA-9013149RAC1 GTPase cycle
R-HSA-9013404RAC2 GTPase cycle
R-HSA-9013423RAC3 GTPase cycle
R-HSA-9673324WNT5:FZD7-mediated leishmania damping

MSigDB gene sets: 555 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, MODULE_93, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_IONIZING_RADIATION, REACTOME_INNATE_IMMUNE_SYSTEM, GRUETZMANN_PANCREATIC_CANCER_DN, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, MCLACHLAN_DENTAL_CARIES_UP, GOBP_REGULATION_OF_BLOOD_PRESSURE, GOBP_CIRCULATORY_SYSTEM_PROCESS, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, GOBP_CELLULAR_RESPONSE_TO_LIPID

GO Biological Process (38): response to hypoxia (GO:0001666), positive regulation of endothelial cell proliferation (GO:0001938), negative regulation of glomerular filtration by angiotensin (GO:0003106), superoxide metabolic process (GO:0006801), inflammatory response (GO:0006954), response to xenobiotic stimulus (GO:0009410), response to activity (GO:0014823), smooth muscle hypertrophy (GO:0014895), cytochrome complex assembly (GO:0017004), positive regulation of cell growth (GO:0030307), response to nutrient levels (GO:0031667), positive regulation of interleukin-6 production (GO:0032755), positive regulation of tumor necrosis factor production (GO:0032760), positive regulation of superoxide anion generation (GO:0032930), positive regulation of toll-like receptor 2 signaling pathway (GO:0034137), superoxide anion generation (GO:0042554), innate immune response (GO:0045087), respiratory burst (GO:0045730), positive regulation of smooth muscle cell proliferation (GO:0048661), hydrogen peroxide biosynthetic process (GO:0050665), positive regulation of phagocytosis (GO:0050766), regulation of release of sequestered calcium ion into cytosol (GO:0051279), establishment of localization in cell (GO:0051649), mucus secretion (GO:0070254), positive regulation of mucus secretion (GO:0070257), response to interleukin-1 (GO:0070555), cellular response to mechanical stimulus (GO:0071260), cellular response to glucose stimulus (GO:0071333), cellular response to tumor necrosis factor (GO:0071356), cellular response to gamma radiation (GO:0071480), positive regulation of defense response to bacterium (GO:1900426), positive regulation of reactive oxygen species biosynthetic process (GO:1903428), response to aldosterone (GO:1904044), cellular response to angiotensin (GO:1904385), cellular response to phorbol 13-acetate 12-myristate (GO:1904628), cellular response to L-glutamine (GO:1904845), positive regulation of blood pressure (GO:0045777), reactive oxygen species metabolic process (GO:0072593)

GO Molecular Function (8): electron transfer activity (GO:0009055), superoxide-generating NAD(P)H oxidase activity (GO:0016175), SH3 domain binding (GO:0017124), heme binding (GO:0020037), metal ion binding (GO:0046872), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (16): stress fiber (GO:0001725), endosome (GO:0005768), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), focal adhesion (GO:0005925), membrane (GO:0016020), apical plasma membrane (GO:0016324), secretory granule (GO:0030141), dendrite (GO:0030425), phagocytic vesicle membrane (GO:0030670), specific granule membrane (GO:0035579), NADPH oxidase complex (GO:0043020), neuronal cell body (GO:0043025), tertiary granule membrane (GO:0070821), perinuclear endoplasmic reticulum (GO:0097038), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-7 pathways:

CategoryPathways
RHO GTPase cycle3
Innate Immune System2
Antigen processing-Cross presentation1
Cellular response to chemical stress1
Signaling by VEGF1
RHO GTPase Effectors1
Killing mechanisms1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
response to stimulus2
endomembrane system2
secretory granule membrane2
response to stress1
response to decreased oxygen levels1
endothelial cell proliferation1
regulation of endothelial cell proliferation1
positive regulation of epithelial cell proliferation1
negative regulation of renal output by angiotensin1
negative regulation of glomerular filtration1
reactive oxygen species metabolic process1
defense response1
response to chemical1
smooth muscle adaptation1
muscle hypertrophy1
protein-containing complex assembly1
regulation of cell growth1
cell growth1
positive regulation of growth1
positive regulation of cellular process1
positive regulation of cytokine production1
interleukin-6 production1
regulation of interleukin-6 production1
tumor necrosis factor production1
regulation of tumor necrosis factor production1
positive regulation of tumor necrosis factor superfamily cytokine production1
regulation of superoxide anion generation1
superoxide anion generation1
positive regulation of reactive oxygen species metabolic process1
toll-like receptor 2 signaling pathway1
regulation of toll-like receptor 2 signaling pathway1
positive regulation of pattern recognition receptor signaling pathway1
superoxide metabolic process1
immune response1
defense response to symbiont1
metabolic process1
positive regulation of cell population proliferation1
smooth muscle cell proliferation1
regulation of smooth muscle cell proliferation1

Protein interactions and networks

STRING

1550 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYBACYBBP04839999
CYBANCF1P14598999
CYBANCF2P19878999
CYBANCF4Q15080999
CYBANOXA1Q86UR1999
CYBANOX1Q9Y5S8999
CYBANOXO1Q8NFA2998
CYBANOX4Q9NPH5998
CYBANOX3Q9HBY0996
CYBARAC2P15153996
CYBAPOLDIP2Q9Y2S7994
CYBAAKT1P31749992
CYBANOX5Q96PH1989
CYBADUOX1Q9NRD9956
CYBARAP1AP10113947

IntAct

67 interactions, top by confidence:

ABTypeScore
NCF1CYBApsi-mi:“MI:0407”(direct interaction)0.740
CYBANCF1psi-mi:“MI:0407”(direct interaction)0.740
CYBANOXO1psi-mi:“MI:0407”(direct interaction)0.710
NOXO1CYBApsi-mi:“MI:0407”(direct interaction)0.710
SLC12A2CLGNpsi-mi:“MI:0914”(association)0.640
SLC2A12METTL15psi-mi:“MI:0914”(association)0.530
TMEM184ASLC33A1psi-mi:“MI:0914”(association)0.530
EVA1CSTK25psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
MDFICYBApsi-mi:“MI:0915”(physical association)0.490
RFKCYBApsi-mi:“MI:0914”(association)0.460
NCF4CYBApsi-mi:“MI:0407”(direct interaction)0.440
CYBANCF4psi-mi:“MI:0407”(direct interaction)0.440
NOXO1CYBApsi-mi:“MI:0407”(direct interaction)0.440
CYBANOXO1psi-mi:“MI:0407”(direct interaction)0.440
CYBACPT1Apsi-mi:“MI:0915”(physical association)0.370
RCHY1CYBApsi-mi:“MI:0915”(physical association)0.370
TNFRSF1ACYBBpsi-mi:“MI:0914”(association)0.350
CYBATNFRSF1Apsi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
MYCpsi-mi:“MI:0914”(association)0.350

BioGRID (82): PSMA3 (Two-hybrid), RBPMS (Two-hybrid), CYBA (Affinity Capture-MS), APPBP2 (Two-hybrid), APPBP2 (Reconstituted Complex), APPBP2 (Far Western), APPBP2 (Affinity Capture-Western), CYBA (Affinity Capture-MS), CYBA (Affinity Capture-Western), CYBA (Affinity Capture-Western), CYBA (Co-fractionation), BCAP31 (Co-fractionation), CYBA (Co-fractionation), CYBA (Reconstituted Complex), CYBA (Proximity Label-MS)

ESM2 similar proteins: A1CKG4, A1D708, A2XSY1, A4R2N5, A6QRX6, A6RRF7, A7EMV1, B0XXU1, B2AR67, O46521, O95214, O95807, P13498, P52650, Q0CNZ5, Q0JDK9, Q0V0G4, Q17QF8, Q1E1E0, Q28F21, Q2GSS4, Q32PD8, Q39080, Q3ZBX1, Q4WXT2, Q566G2, Q5PQQ4, Q5R5Z8, Q5RDE9, Q61462, Q62737, Q6CC06, Q6GM42, Q6GPA8, Q6P0C7, Q6PDU4, Q7S693, Q8K3C0, Q8TAC9, Q92535

Diamond homologs: O46521, P13498, P52650, Q61462, Q62737, Q95L73, Q95MN4, Q9N2H0, Q867X6

SIGNOR signaling

4 interactions.

AEffectBMechanism
NCF1“up-regulates activity”CYBAbinding
CYBA“form complex”“Phagocyte NADPH oxidase complex”binding
PRKCAup-regulatesCYBAphosphorylation
PRKCDup-regulatesCYBAphosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
RAC3 GTPase cycle511.2×7e-03

GO biological processes:

GO termPartnersFoldFDR
superoxide anion generation545.5×4e-05
response to xenobiotic stimulus76.5×1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

531 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic42
Likely pathogenic26
Uncertain significance146
Likely benign245
Benign26

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1032885NM_000101.4(CYBA):c.393G>A (p.Trp131Ter)Pathogenic
1071345NM_000101.4(CYBA):c.111C>G (p.Tyr37Ter)Pathogenic
1072119NM_000101.4(CYBA):c.166dup (p.Arg56fs)Pathogenic
1074797NC_000016.9:g.(?88713499)(88714532_?)delPathogenic
1371434NM_000101.4(CYBA):c.399del (p.Ile134fs)Pathogenic
1429693NC_000016.9:g.(?88713499)(88718353_?)delPathogenic
1458360NC_000016.9:g.(?88717354)(88718353_?)delPathogenic
1458496NM_000101.4(CYBA):c.17G>A (p.Trp6Ter)Pathogenic
1458628NC_000016.9:g.(?88712514)(88718096_?)delPathogenic
1489230NM_000101.4(CYBA):c.59-2A>TPathogenic
1967713NM_000101.4(CYBA):c.68_76del (p.Thr23_Gly25del)Pathogenic
2256NC_000016.10:g.(?_88638115)(88648115_88650955)delPathogenic
2262NM_000101.4(CYBA):c.287+1G>APathogenic
2264NM_000101.4(CYBA):c.7C>T (p.Gln3Ter)Pathogenic
2266NM_000101.4(CYBA):c.288-13_310delPathogenic
2267NM_000101.4(CYBA):c.373G>A (p.Ala125Thr)Pathogenic
2736377NM_000101.4(CYBA):c.107G>A (p.Trp36Ter)Pathogenic
2755870NM_000101.4(CYBA):c.109dup (p.Tyr37fs)Pathogenic
2817163NM_000101.4(CYBA):c.18G>A (p.Trp6Ter)Pathogenic
2907500NM_000101.4(CYBA):c.246_273del (p.Phe83fs)Pathogenic
2968090NM_000101.4(CYBA):c.467del (p.Pro156fs)Pathogenic
3008362NM_000101.4(CYBA):c.103C>T (p.Gln35Ter)Pathogenic
3065668NM_000101.4(CYBA):c.369+1G>TPathogenic
3243439NC_000016.9:g.(?88709761)(88717421_?)delPathogenic
3243440NC_000016.9:g.(?88713143)(88717421_?)delPathogenic
3640816NM_000101.4(CYBA):c.433G>T (p.Gly145Ter)Pathogenic
3725589NM_000101.4(CYBA):c.288-2A>GPathogenic
4535536NC_000016.9:g.(?88709696)(88717462_?)delPathogenic
4817432NM_000101.4(CYBA):c.58+2T>GPathogenic
596212NM_000101.4(CYBA):c.415del (p.Arg139fs)Pathogenic

SpliceAI

1427 predictions. Top by Δscore:

VariantEffectΔscore
16:88646111:CTCA:Cdonor_loss1.0000
16:88646112:TCA:Tdonor_loss1.0000
16:88646113:CACCA:Cdonor_loss1.0000
16:88646115:C:CAdonor_loss1.0000
16:88646753:A:ACdonor_gain1.0000
16:88646754:C:CCdonor_gain1.0000
16:88650954:A:ACdonor_gain1.0000
16:88650955:C:CCdonor_gain1.0000
16:88650955:CT:Cdonor_gain1.0000
16:88646110:ACTCA:Adonor_loss0.9900
16:88646114:A:ACdonor_gain0.9900
16:88646115:C:CCdonor_gain0.9900
16:88646194:GAGC:Gacceptor_gain0.9900
16:88646195:AGCCT:Aacceptor_loss0.9900
16:88646196:GC:Gacceptor_gain0.9900
16:88646196:GCCTG:Gacceptor_loss0.9900
16:88646197:CC:Cacceptor_gain0.9900
16:88646198:C:CCacceptor_gain0.9900
16:88646198:CT:Cacceptor_loss0.9900
16:88646199:T:Cacceptor_loss0.9900
16:88646209:CGGG:Cacceptor_gain0.9900
16:88646210:G:Tacceptor_gain0.9900
16:88646836:CCC:Cacceptor_gain0.9900
16:88646837:CC:Cacceptor_gain0.9900
16:88646837:CCC:Cacceptor_gain0.9900
16:88646838:CC:Cacceptor_gain0.9900
16:88647182:CCA:Cacceptor_gain0.9900
16:88647183:C:CTacceptor_gain0.9900
16:88647184:A:Cacceptor_gain0.9900
16:88648115:C:CCacceptor_gain0.9900

AlphaMissense

1231 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:88643548:C:AW131C0.999
16:88643548:C:GW131C0.999
16:88643550:A:GW131R0.999
16:88643550:A:TW131R0.999
16:88646131:G:CS118R0.999
16:88646131:G:TS118R0.999
16:88646133:T:GS118R0.999
16:88646157:C:AG110W0.999
16:88646157:C:GG110R0.999
16:88646157:C:TG110R0.999
16:88650987:C:AW9C0.999
16:88650987:C:GW9C0.999
16:88650989:A:GW9R0.999
16:88650989:A:TW9R0.999
16:88650998:A:GW6R0.999
16:88650998:A:TW6R0.999
16:88646156:C:TG110E0.998
16:88647168:C:GG46R0.998
16:88648100:C:GG25R0.998
16:88650962:C:GG18R0.998
16:88650996:C:AW6C0.998
16:88650996:C:GW6C0.998
16:88646144:A:GL114P0.997
16:88647144:A:CY54D0.997
16:88647167:C:TG46D0.997
16:88648074:G:CF33L0.997
16:88648074:G:TF33L0.997
16:88648076:A:GF33L0.997
16:88650961:C:TG18D0.997
16:88650980:C:TE12K0.997

dbSNP variants (sampled 300 via entrez): RS1000166971 (16:88645769 C>T), RS1000370025 (16:88648463 C>A,T), RS1000510917 (16:88652000 A>C,G), RS1000603799 (16:88644512 G>A,C,T), RS1000667256 (16:88652372 A>T), RS1001429506 (16:88652603 C>T), RS1001520966 (16:88652743 T>C), RS1001664999 (16:88646162 A>G,T), RS1001706757 (16:88653021 G>A), RS1001725744 (16:88649145 G>A,C,T), RS1001727646 (16:88644772 C>T), RS1001762932 (16:88649655 G>A), RS1001791471 (16:88643302 G>A,C,T), RS1001843742 (16:88643161 G>A), RS1002098279 (16:88650417 G>A)

Disease associations

OMIM: gene MIM:608508 | disease phenotypes: MIM:233690, MIM:306400, MIM:240300, MIM:138990

GenCC curated gene-disease

DiseaseClassificationInheritance
granulomatous disease, chronic, autosomal recessive, cytochrome b-negativeDefinitiveAutosomal recessive
chronic granulomatous diseaseSupportiveAutosomal recessive

Mondo (4): granulomatous disease, chronic, autosomal recessive, cytochrome b-negative (MONDO:0009308), chronic granulomatous disease (MONDO:0018305), autoimmune polyendocrine syndrome type 1 (MONDO:0009411), granulomatous disease, chronic, X-linked (MONDO:0010600)

Orphanet (2): Chronic granulomatous disease (Orphanet:379), Autoimmune polyendocrinopathy type 1 (Orphanet:3453)

HPO phenotypes

44 total (30 of 44 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000230Gingivitis
HP:0000246Sinusitis
HP:0000388Otitis media
HP:0000964Eczematoid dermatitis
HP:0000992Cutaneous photosensitivity
HP:0001034Hypermelanotic macule
HP:0001287Meningitis
HP:0001744Splenomegaly
HP:0001874Abnormality of neutrophils
HP:0001945Fever
HP:0002021Pyloric stenosis
HP:0002024Malabsorption
HP:0002205Recurrent respiratory infections
HP:0002240Hepatomegaly
HP:0002575Tracheoesophageal fistula
HP:0002716Lymphadenopathy
HP:0002721Immunodeficiency
HP:0002723Absence of bactericidal oxidative respiratory burst in phagocytes
HP:0002724Recurrent Aspergillus infections
HP:0002726Recurrent Staphylococcus aureus infections
HP:0002740Recurrent E. coli infections
HP:0002741Recurrent Serratia marcescens infections
HP:0002742Recurrent Klebsiella infections
HP:0002754Osteomyelitis
HP:0002840Lymphadenitis
HP:0002842Recurrent Burkholderia cepacia infections
HP:0002955Granulomatosis
HP:0003203Decreased neutrophil oxidative burst
HP:0003206Decreased activity of NADPH oxidase

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002390_5Glycated hemoglobin levels1.000000e-08
GCST003479_9Hair color1.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004541HbA1c measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D006105Granulomatous Disease, ChronicC15.378.553.774.535; C16.320.322.233; C20.673.774.535; C23.550.291.500.423
C564210Granulomatous Disease, Chronic, Autosomal Dominant Type (supp.)
C565533Granulomatous Disease, Chronic, Autosomal Recessive, Cytochrome B-Negative (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL1613744 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

4 annotations.

VariantTypeLevelDrugsPhenotypes
rs4673Other3simvastatinHypercholesterolemia
rs4673Toxicity3doxorubicin;idarubicinNeoplasms
rs4673Efficacy,Toxicity3doxorubicin;idarubicinNeoplasms
rs4673Toxicity3cisplatin;doxorubicinAnemia;Mucositis;Osteosarcoma

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs4673CYBA35.254doxorubicin;idarubicin;simvastatin;cisplatin;doxorubicin

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.14Kd7281nMCHEMBL5653589
5.14ED507281nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148186: Binding affinity to human CYBA incubated for 45 mins by Kinobead based pull down assaykd7.2815uM

CTD chemical–gene interactions

101 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tretinoinincreases expression4
sodium arseniteaffects cotreatment, decreases expression, increases expression3
Acetaminophenaffects cotreatment, increases expression, decreases expression3
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation3
Glucoseincreases expression, decreases expression, decreases reaction3
Tetrachlorodibenzodioxinincreases expression3
Tetradecanoylphorbol Acetatedecreases reaction, increases expression, affects reaction, decreases expression, increases reaction (+1 more)3
Aflatoxin B1decreases expression, increases expression3
lasiocarpinedecreases expression2
methyleugenoldecreases expression2
ochratoxin Aincreases acetylation, increases expression2
chloropicrinaffects expression, decreases expression2
Arsenic Trioxideincreases expression2
Arsenicaffects response to substance2
Estradiolincreases expression2
Hydrogen Peroxidedecreases reaction, increases expression2
Lipopolysaccharidesincreases secretion, affects cotreatment, increases expression, affects reaction2
N-Nitrosopyrrolidinedecreases expression2
Plant Extractsdecreases reaction, increases expression, increases reaction2
Quercetindecreases reaction, increases expression2
Superoxidesincreases abundance, increases reaction2
Tobacco Smoke Pollutionincreases expression, increases reaction2
Valproic Acidincreases expression, increases methylation2
Cyclosporinedecreases reaction, decreases expression, increases expression2
aristolochic acid Idecreases expression1
testosterone enanthateaffects expression1
methylmercuric chlorideincreases expression1
naringindecreases reaction, increases expression1
triphenyl phosphateaffects expression1
2,2’-methylenebis(4-methyl-6-tert-butylphenol)affects expression, affects response to substance1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651228BindingBinding affinity to human CYBA incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

4 cell lines: 3 spontaneously immortalized cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2VHAbcam HEK293T CYBA KOTransformed cell lineFemale
CVCL_V326CHO-22Spontaneously immortalized cell lineFemale
CVCL_V328CHO-91-22Spontaneously immortalized cell lineFemale
CVCL_V329CHO-91-22-47-67Spontaneously immortalized cell lineFemale

Clinical trials (associated diseases)

69 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00001317PHASE4COMPLETEDA Phase IV Study of Recombinant Human Gamma Interferon in Patients With Chronic Granulomatous Diseases of Childhood
NCT00023192PHASE3COMPLETEDTreatment of Chronic Granulomatous Disease With Allogeneic Stem Cell Transplantation Versus Standard of Care
NCT00033982PHASE3COMPLETEDPosaconazole to Treat Invasive Fungal Infections
NCT00006417PHASE2COMPLETEDModified Stem Cell Transplantation Procedure for Treating Chronic Granulomatous Disease
NCT00578643PHASE2COMPLETEDMatched Unrelated or Non-Genotype Identical Related Donor Transplantation For Chronic Granulomatous Disease
NCT00799071PHASE2COMPLETEDPharmacokinetics of Posaconazole in Children With Chronic Granulomatous Disease (CGD)
NCT01821781PHASE2ACTIVE_NOT_RECRUITINGImmune Disorder HSCT Protocol
NCT01998633PHASE2COMPLETEDReduced Intensity Conditioning for Hemophagocytic Syndromes or Selected Primary Immune Deficiencies (BMT CTN 1204)
NCT02512679PHASE2TERMINATEDRelated Hematopoietic Stem Cell Transplantation (HSCT) for Genetic Diseases of Blood Cells
NCT03333486PHASE2TERMINATEDFludarabine Phosphate, Cyclophosphamide, Total Body Irradiation, and Donor Stem Cell Transplant in Treating Patients With Blood Cancer
NCT03547830PHASE2UNKNOWNPlerixafor/G-CSF as Additional Agents for Conditioning Before HSCT in CGD Patients
NCT03983837PHASE2COMPLETEDElemental Diet for Treatment of Inflammatory Bowel Disease in Patients With Chronic Granulomatous Disease
NCT07284641PHASE2RECRUITINGHematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT00743782PHASE2COMPLETEDComparing Pump With Subcutaneous Injection Delivery of PTH 1-34 in the Management of Chronic Hypoparathyroidism
NCT05398809PHASE2RECRUITINGEvaluate the Efficacy and Safety of Ruxolitinib on Hair Regrowth in Patients With Autoimmune Polyendocrinopathy Candidiasis Ectodermal Dystrophy (APECED)-Associated Alopecia Areata
NCT00001476PHASE1COMPLETEDGene Therapy for Chronic Granulomatous Diseases - Long-term Follow-up
NCT00001515PHASE1COMPLETEDDiagnostic Effectiveness of Virtual Bronchoscopy
NCT00001765PHASE1COMPLETEDStem Cell Transplant Following Low-Intensity Chemotherapy to Treat Chronic Granulomatous Disease
NCT01917708PHASE1COMPLETEDBone Marrow Transplant With Abatacept for Non-Malignant Diseases
NCT02609932PHASE1COMPLETEDEffect of IFN-γ on Innate Immune Cells
NCT05189925PHASE1RECRUITINGNADPH Oxidase Correction in mRNA-transfected Granulocyte-enriched Cells in Chronic Granulomatous Disease (CGD)
NCT03984890PHASE2/PHASE3COMPLETEDVitamin D3 For CGD Patients With BCGosis/Itis
NCT00325078PHASE1/PHASE2TERMINATEDInfliximab to Treat Crohn’S-like Inflammatory Bowel Disease in Chronic Granulomatous Disease
NCT00564759PHASE1/PHASE2UNKNOWNGene Therapy for Chronic Granulomatous Disease
NCT00778882PHASE1/PHASE2WITHDRAWNGene Therapy for Chronic Granulomatous Disease in Korea
NCT00927134PHASE1/PHASE2COMPLETEDGene Therapy for X-linked Chronic Granulomatous Disease (CGD) in Children
NCT01338675PHASE1/PHASE2UNKNOWNTargeted Busulfan, Fludarabine Conditioning Regimen for Hematopoietic Stem Cell Transplantation in Chronic Granulomatous Disease(CGD)
NCT01852370PHASE1/PHASE2ENROLLING_BY_INVITATIONSequential Cadaveric Lung and Bone Marrow Transplant for Immune Deficiency Diseases
NCT02282904PHASE1/PHASE2TERMINATEDHaploidentical Transplant for People With Chronic Granulomatous Disease Using Post Transplant Cyclophosphamide
NCT03080480PHASE1/PHASE2TERMINATEDPioglitazone Therapy for Chronic Granulomatous Disease
NCT03513328PHASE1/PHASE2COMPLETEDConditioning Regimen for Allogeneic Hematopoietic Stem-Cell Transplantation
NCT05104723PHASE1/PHASE2COMPLETEDSafety and Efficacy of Tofacitinib for Chronic Granulomatous Disease With Inflammatory Complications
NCT05463133PHASE1/PHASE2RECRUITINGAllogeneic Hematopoietic Stem Cell Transplantation for Chronic Granulomatous Disease (CGD) With an Alemtuzumab, Busulfan and TBI-based Conditioning Regimen Combined With Cytokine (IL-6, +/- IFN-gamma) Antagonists
NCT06253507PHASE1/PHASE2ENROLLING_BY_INVITATIONpCCLCHIM-p47 (Lentiviral Vector Transduced CD34 Plus Cells) in Patients With p47 Autosomal Recessive Chronic Granulomatous Disease (AR-CGD)
NCT06325709PHASE1/PHASE2RECRUITINGBase Editing for Mutation Repair in Hematopoietic Stem & Progenitor Cells for X-Linked Chronic Granulomatous Disease
NCT06559176PHASE1/PHASE2ENROLLING_BY_INVITATIONA Study of the Safety and Efficacy of Prime Editing (PM359) in Participants With p47phox Autosomal Recessive Chronic Granulomatous Disease (CGD )
NCT07113743PHASE1/PHASE2ENROLLING_BY_INVITATIONPart B- G1X-CGD (Lentiviral Vector Transduced CD34+ Cells) in Patients With X-Linked Chronic Granulomatous Disease
NCT00394316EARLY_PHASE1TERMINATEDGene Therapy for Chronic Granulomatous Disease
NCT03910452EARLY_PHASE1ACTIVE_NOT_RECRUITINGHaploidentical Transplant for People With Chronic Granulomatous Disease (CGD) Using Alemtuzumab, Busulfan and TBI With Post-Transplant Cyclophosphamide
NCT03921515EARLY_PHASE1WITHDRAWNSkin Immunity Sample Collection Involving Blisters and Biopsies