CYB5R3

gene
On this page

Also known as B5R

Summary

CYB5R3 (cytochrome b5 reductase 3, HGNC:2873) is a protein-coding gene on chromosome 22q13.2, encoding NADH-cytochrome b5 reductase 3 (P00387). Catalyzes the reduction of two molecules of cytochrome b5 using NADH as the electron donor.

This gene encodes cytochrome b5 reductase, which includes a membrane-bound form in somatic cells (anchored in the endoplasmic reticulum, mitochondrial and other membranes) and a soluble form in erythrocytes. The membrane-bound form exists mainly on the cytoplasmic side of the endoplasmic reticulum and functions in desaturation and elongation of fatty acids, in cholesterol biosynthesis, and in drug metabolism. The erythrocyte form is located in a soluble fraction of circulating erythrocytes and is involved in methemoglobin reduction. The membrane-bound form has both membrane-binding and catalytic domains, while the soluble form has only the catalytic domain. Alternate splicing results in multiple transcript variants. Mutations in this gene cause methemoglobinemias.

Source: NCBI Gene 1727 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): methemoglobinemia due to deficiency of methemoglobin reductase (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 1
  • Clinical variants (ClinVar): 297 total — 23 pathogenic, 10 likely-pathogenic
  • Phenotypes (HPO): 36
  • Druggable target: yes
  • MANE Select transcript: NM_000398

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2873
Approved symbolCYB5R3
Namecytochrome b5 reductase 3
Location22q13.2
Locus typegene with protein product
StatusApproved
AliasesB5R
Ensembl geneENSG00000100243
Ensembl biotypeprotein_coding
OMIM613213
Entrez1727

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 21 protein_coding, 11 retained_intron, 7 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000352397, ENST00000361740, ENST00000402438, ENST00000407332, ENST00000407623, ENST00000438270, ENST00000466276, ENST00000470741, ENST00000684963, ENST00000685184, ENST00000686129, ENST00000686523, ENST00000687183, ENST00000687198, ENST00000688004, ENST00000688117, ENST00000688244, ENST00000689001, ENST00000689195, ENST00000689239, ENST00000689795, ENST00000690835, ENST00000690993, ENST00000691295, ENST00000691918, ENST00000692152, ENST00000692344, ENST00000693157, ENST00000693363, ENST00000693367, ENST00000693639, ENST00000693646, ENST00000693716, ENST00000897014, ENST00000897015, ENST00000897016, ENST00000897017, ENST00000897018, ENST00000897019, ENST00000966833

RefSeq mRNA: 5 — MANE Select: NM_000398 NM_000398, NM_001129819, NM_001171660, NM_001171661, NM_007326

CCDS: CCDS14040, CCDS33658, CCDS54535

Canonical transcript exons

ENST00000352397 — 9 exons

ExonStartEnd
ENSE000006566324263137842631450
ENSE000018927904264929542649392
ENSE000023079314261784042619945
ENSE000031994774263088242630988
ENSE000034679534262815242628281
ENSE000034890644263671542636846
ENSE000035948464262760542627688
ENSE000036115934262378942623888
ENSE000036354804262730442627389

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 99.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 124.6718 / max 728.0471, expressed in 1824 samples.

FANTOM5 promoters (20 alternative TSS)

Promoter IDTPM avgSamples expressed
194465102.88641822
1944493.57431364
1944473.42351369
1944612.4182327
1944552.12301189
1944582.10081176
1944541.69221013
1944661.0598749
1944641.0084193
1944530.8175476

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right coronary arteryUBERON:000162599.54gold quality
descending thoracic aortaUBERON:000234599.54gold quality
thoracic aortaUBERON:000151599.50gold quality
ascending aortaUBERON:000149699.49gold quality
saphenous veinUBERON:000731899.48gold quality
urethraUBERON:000005799.46gold quality
aortaUBERON:000094799.44gold quality
olfactory bulbUBERON:000226499.44gold quality
popliteal arteryUBERON:000225099.40gold quality
tibial arteryUBERON:000761099.40gold quality
skin of hipUBERON:000155499.37gold quality
coronary arteryUBERON:000162199.35gold quality
left coronary arteryUBERON:000162699.33gold quality
synovial jointUBERON:000221799.33gold quality
vena cavaUBERON:000408799.30gold quality
stromal cell of endometriumCL:000225599.22gold quality
dorsal root ganglionUBERON:000004499.21gold quality
subcutaneous adipose tissueUBERON:000219099.21gold quality
pancreatic ductal cellCL:000207999.19gold quality
adipose tissueUBERON:000101399.19gold quality
layer of synovial tissueUBERON:000761699.18gold quality
right adrenal glandUBERON:000123399.17gold quality
apex of heartUBERON:000209899.17gold quality
nippleUBERON:000203099.16gold quality
seminal vesicleUBERON:000099899.14gold quality
cardia of stomachUBERON:000116299.13gold quality
right adrenal gland cortexUBERON:003582799.13gold quality
connective tissueUBERON:000238499.11gold quality
right atrium auricular regionUBERON:000663199.11gold quality
adrenal cortexUBERON:000123599.10gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-GEOD-135922yes37.28
E-HCAD-1yes32.21
E-MTAB-8410yes11.82
E-MTAB-10042yes7.76
E-CURD-88yes7.38
E-MTAB-6678yes7.37
E-MTAB-7249yes4.82
E-MTAB-10137no4.54
E-CURD-112no3.52
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting CYB5R3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4455100.0065.481587
HSA-MIR-4283100.0066.422097
HSA-MIR-4533100.0069.482758
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-449299.8768.253611
HSA-MIR-444799.8567.812900
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-182799.6368.573265
HSA-MIR-397599.6265.97697
HSA-MIR-6752-5P99.5967.321243
HSA-MIR-76299.5866.611994
HSA-MIR-447299.5666.081478
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-449899.4767.422360
HSA-MIR-6837-5P99.2565.471632

Literature-anchored findings (GeneRIF, showing 31)

  • It was shown that Yakut patients have none of three missence mutations, Arg57Gln, Leu72Pro, and Val105Met, described in case of this disease in the neighboring populations, Chinese and Japanese, inhabiting the territories south of Yakutia (PMID:12884529)
  • A decrease of the activity of membrane-bound NADH-methemoglobin reductase and a change of physical state of the lipid bilayer of membranes under oxidative stress were found in erythrocytes in vivo and in vitro. (PMID:15039026)
  • Amino acid substitution results in congsenital methemoglobinemia. (PMID:15297856)
  • crystal structure of cytochrome b(5) reductase (PMID:15502298)
  • Recessive congenital methaemoglobinaemia observed in a Lebanese subject with a novel mutation in NADH-cytochrome b5 reductase gene. (PMID:15813912)
  • A novel intronic mutation at 22163 caused markedly reduced mRNA (7% of normal) resulting in type II methemoglobinemia. (PMID:15921385)
  • Dia1 is required for the formation of the actin coat around endosomes downstream of RhoB, connecting membrane trafficking with the regulation of actin dynamics. (PMID:15944396)
  • DIA1 and IQGAP1 interact in cell migration and phagocytic cup formation. (PMID:17620407)
  • report of the clinical and molecular characteristics of 6 new patients with recessive hereditary methemoglobinemia due to cytochrome b5 reductase deficiency; two new mutations of DIA1, c. 82 C>T(Gln27STOP) and c. 136 C>T(Arg45Trp), were found (PMID:18343696)
  • The decline in the activities of G6PD and b5Rm would indicate a decrease in the antioxidant response associated with RBC aging. (PMID:19811411)
  • novel cSNPs associated with significantly altered protein expression and/or hydroxylamine reduction activities, but only minimally impact overall observed phenotypic variability (PMID:19997042)
  • Dia1 is localized to the perinuclear endoplasmic reticulum in an RNA-zipcode-independent manner in fibroblasts. (PMID:21266463)
  • novel allelic mutation identified at codon 235 is in helix 5; first report of mental retardation because of the novel mutation, along with a second mutation in the NADH-b5R gene in an Indian family with recessive congenital methemoglobinemia Type II (PMID:21328435)
  • CYB5R3 gene of three probands with type I methemoglobinemia and their relatives were sequenced revealing several putative causative mutations; in one subject multiple mutations were present (PMID:21349748)
  • Dapsone-associated methemoglobinemia in a patient with slow NAT2*5B haplotype and impaired cytochrome b5 reductase activity (PMID:21422237)
  • We conclude that Cytochrome b(5)and cytochrome b(5) reductase catalyze the reduction of arylhydroxylamines in breast tissue. (PMID:21447608)
  • A comprehensive overview of the study of structure and function of human cytochrome b5 reductase. (PMID:23113554)
  • Novel large deletion c.22-1320_633+1224del in the CYB5R3 gene from patients with hereditary methemoglobinemia (PMID:23297489)
  • Data indicate that mitochondrial amidoxime reducing components 1 and 2 together with the electron transport proteins NADH-cytochrome b5 reductase (CYB5R) and cytochrome b5 (CYB5) catalyze the reduction of N-hydroxylated compounds such as amidoximes. (PMID:23703616)
  • Population frequency and age of c.806C > T mutation in CYB5R3 gene as cause of recessive congenital methemoglobinemia in Yakutia. (PMID:23866629)
  • NADH-CYB5R deficiency causes two forms of recessive congenital methemoglobinemia with cyanosis. (PMID:24266649)
  • The results unveil a potential mechanism of action by which CYB5R3 deficiency contributes to the pathophysiological underpinnings of neurological disorders in RHM patients. (PMID:24450884)
  • Variants in CYB5A and CYB5R3 should be considered in the evaluation of breast cancer risk in African American women. (PMID:25225034)
  • Genetic variation in CYB5R3 is associated with methemoglobin levels in preterm infants receiving nitric oxide therapy. (PMID:25521918)
  • CYB5R3 promotes colonization and metastasis formation and is a prognostic marker of disease-free and overall survival in estrogen receptor-negative breast cancer. (PMID:26351264)
  • Data suggest that cytochrome b5 (CYB5) and cytochrome b5 reductase 3 (CYB5R3) can reduce human cytoglobin (CYGB) and zebrafish cytoglobins at rates up to 250-fold higher than those reported for the known physiological substrates, hemoglobin and myoglobin; the three proteins (CYB5+CYB5R3+CYGB) appear to constitute a metabolon involved in generation of nitric oxide. (PMID:28671819)
  • study indicated that novel homozygous mutation p.Arg192Cys in CYB5R3 gene present in eight cases and the possibility of high prevalence of heterozygous in Indian population causing Type I recessive congenital methemoglobinemia. (PMID:29482478)
  • Mutation update: Variants of the CYB5R3 gene in recessive congenital methemoglobinemia. (PMID:31898843)
  • The CYB5R3(c) (.350C>G) and G6PD A alleles modify severity of anemia in malaria and sickle cell disease. (PMID:32697331)
  • Three novel mutations in CYB5R3 gene causing NADH-cytochrome b5 reductase enzyme deficiency leads to recessive congenital methaemoglobinemia. (PMID:35064402)
  • CYB5R3 T117S Genetic Mutation Is Associated With Major Adverse Cardiovascular and Cerebrovascular Events in Black Adults. (PMID:38353123)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriocyb5r3ENSDARG00000005891
mus_musculusCyb5r3ENSMUSG00000018042
rattus_norvegicusCyb5r3ENSRNOG00000009592
drosophila_melanogasterCG5946FBGN0036211
caenorhabditis_elegansWBGENE00020267
caenorhabditis_elegansWBGENE00020268

Paralogs (5): CYB5R4 (ENSG00000065615), OXNAD1 (ENSG00000154814), CYB5R1 (ENSG00000159348), CYB5R2 (ENSG00000166394), CYB5RL (ENSG00000215883)

Protein

Protein identifiers

NADH-cytochrome b5 reductase 3P00387 (reviewed: P00387)

Alternative names: Diaphorase-1

All UniProt accessions (16): P00387, A0A8I5KNV1, A0A8I5KPU0, A0A8I5KR71, A0A8I5KTF9, A0A8I5KUA5, A0A8I5KVD2, A0A8I5KW26, A0A8I5KXI5, A0A8I5KYU1, A0A8I5QKL2, A0A8I5QKT9, A0A8I5QKX1, A0A8J8YWN6, A0A8J8Z3C6, B1AHF3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the reduction of two molecules of cytochrome b5 using NADH as the electron donor.

Subunit / interactions. Component of a complex composed of cytochrome b5, NADH-cytochrome b5 reductase (CYB5R3) and MTARC2. Interacts with MTLN; the interaction is required to maintain cellular lipid composition and leads to stimulation of mitochondrial respiratory complex I activity.

Subcellular location. Endoplasmic reticulum membrane. Mitochondrion outer membrane Cytoplasm.

Tissue specificity. Expressed at late stages of erythroid maturation.

Disease relevance. Methemoglobinemia CYB5R3-related (METHB-CYB5R3) [MIM:250800] A form of methemoglobinemia, a hematologic disease characterized by the presence of excessive amounts of methemoglobin in blood cells, resulting in decreased oxygen carrying capacity of the blood, cyanosis and hypoxia. There are two types of methemoglobinemia CYB5R3-related. In type 1, the defect affects the soluble form of the enzyme, is restricted to red blood cells, and causes well-tolerated methemoglobinemia. In type 2, the defect affects both the soluble and microsomal forms of the enzyme and is thus generalized, affecting red cells, leukocytes and all body tissues. Type 2 methemoglobinemia is associated with mental deficiency and other neurologic symptoms. The disease is caused by variants affecting the gene represented in this entry.

Polymorphism. Ser-117 seems to only be found in persons of African origin. The allele frequency is 0.23 in African Americans. It was not found in Caucasians, Asians, Indo-Aryans, or Arabs. There seems to be no effect on the enzyme activity.

Similarity. Belongs to the flavoprotein pyridine nucleotide cytochrome reductase family.

Isoforms (3)

UniProt IDNamesCanonical?
P00387-11, Myes
P00387-22, S
P00387-33

RefSeq proteins (5): NP_000389, NP_001123291, NP_001165131, NP_001165132, NP_015565 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001433OxRdtase_FAD/NAD-bdDomain
IPR001709Flavoprot_Pyr_Nucl_cyt_RdtaseDomain
IPR001834CBR-likeFamily
IPR008333Cbr1-like_FAD-bd_domDomain
IPR017927FAD-bd_FR_typeDomain
IPR017938Riboflavin_synthase-like_b-brlHomologous_superfamily
IPR039261FNR_nucleotide-bdHomologous_superfamily

Pfam: PF00175, PF00970

Enzyme classification (BRENDA):

  • EC 1.6.2.2 — cytochrome-b5 reductase (BRENDA: 34 organisms, 101 substrates, 111 inhibitors, 300 Km, 221 kcat entries)

Substrate kinetics (BRENDA)

23 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
NADH0.0002–3.3294
FERRICYANIDE0.0006–4.3572
FERRICYTOCHROME B566
CYTOCHROME B50.0011–0.04219
NADPH0.001–7.6917
FERROCYTOCHROME B50.001–0.1076
FERRICYTOCHOME B50.01–0.0134
FERRICYTOCHROME C0.0003–0.0073
OXIDIZED 2,6-DICHLOROPHENOLINDOPHENOL0.328–0.832
1,4-NAPHTHOQUINONE0.00981
2-HYDROXYESTRADIOL0.00261
2-METHYL-1,4-NAPHTHOQUINONE0.0771
9,10-PHENANTHRENEQUINONE0.00571
AQUACOBALAMIN0.04191
BENZAMIDOXIME0.631

Catalyzed reactions (Rhea), 1 shown:

  • 2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD(+) + H(+) (RHEA:46680)

UniProt features (83 total): strand 18, sequence variant 14, mutagenesis site 12, binding site 10, helix 10, sequence conflict 9, modified residue 3, splice variant 2, initiator methionine 1, chain 1, lipid moiety-binding region 1, domain 1, turn 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
1UMKX-RAY DIFFRACTION1.75
7TNVX-RAY DIFFRACTION1.93
7TSWX-RAY DIFFRACTION2.4
7W3OX-RAY DIFFRACTION2.46
7THGX-RAY DIFFRACTION2.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P00387-F193.900.89

Functional residue map

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

Ligand- & substrate-binding residues (10): 127; 128; 185; 92; 93; 94; 109; 111; 114; 126

Post-translational modifications (4): 42, 43, 120, 2

Mutagenesis-validated functional residues (12):

PositionPhenotype
128decreased nadh-cytochrome b5 reductase activity, highly increases km for nadh and decreases kcat.
204no effect on nadh-cytochrome b5 reductase activity.
274loss of 30% of nadh-cytochrome b5 reductase activity.
274loss of 80% of nadh-cytochrome b5 reductase activity.
274no effect on nadh-cytochrome b5 reductase activity.
284no effect on nadh-cytochrome b5 reductase activity.
298no effect on nadh-cytochrome b5 reductase activity.
299–301no effect on protein stability and nadh-cytochrome b5 reductase activity.
299decreases protein stability and slightly decreases nadh-cytochrome b5 reductase activity.
299no effect on protein stability and nadh-cytochrome b5 reductase activity.
301decreases protein stability and slightly decreases nadh-cytochrome b5 reductase activity.
301no effect on protein stability and nadh-cytochrome b5 reductase activity.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

IDPathway
R-HSA-196836Vitamin C (ascorbate) metabolism
R-HSA-211945Phase I - Functionalization of compounds
R-HSA-6798695Neutrophil degranulation
R-HSA-1430728Metabolism
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-196849Metabolism of water-soluble vitamins and cofactors
R-HSA-196854Metabolism of vitamins and cofactors
R-HSA-211859Biological oxidations

MSigDB gene sets: 268 (showing top): MODULE_93, REACTOME_BIOLOGICAL_OXIDATIONS, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOCC_SECRETORY_GRANULE, HSIAO_HOUSEKEEPING_GENES, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_REACTIVE_NITROGEN_SPECIES_METABOLIC_PROCESS, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, GOBP_STEROID_BIOSYNTHETIC_PROCESS, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_LIPID_METABOLIC_PROCESS, SANSOM_APC_TARGETS_DN

GO Biological Process (8): cholesterol biosynthetic process (GO:0006695), nitric oxide biosynthetic process (GO:0006809), blood circulation (GO:0008015), lipid metabolic process (GO:0006629), steroid biosynthetic process (GO:0006694), steroid metabolic process (GO:0008202), cholesterol metabolic process (GO:0008203), sterol biosynthetic process (GO:0016126)

GO Molecular Function (6): cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128), FAD binding (GO:0071949), cytochrome-b5 reductase activity, acting on NADH (GO:0090524), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), nitrite reductase (NO-forming) activity (GO:0050421)

GO Cellular Component (18): extracellular region (GO:0005576), cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), lipid droplet (GO:0005811), cytosol (GO:0005829), hemoglobin complex (GO:0005833), membrane (GO:0016020), mitochondrial membrane (GO:0031966), perinuclear theca (GO:0033011), azurophil granule lumen (GO:0035578), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), sperm head-tail coupling apparatus (GO:0120212), sperm glycocalyx (GO:0120238), nitric-oxide synthase complex (GO:1903958)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Metabolism2
Metabolism of water-soluble vitamins and cofactors1
Biological oxidations1
Innate Immune System1
Immune System1
Metabolism of vitamins and cofactors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure7
cytoplasm3
sterol metabolic process2
intracellular membrane-bounded organelle2
organelle membrane2
sperm flagellum2
cholesterol metabolic process1
sterol biosynthetic process1
secondary alcohol biosynthetic process1
biosynthetic process1
nitric oxide metabolic process1
circulatory system process1
primary metabolic process1
steroid metabolic process1
lipid biosynthetic process1
lipid metabolic process1
secondary alcohol metabolic process1
steroid biosynthetic process1
oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor1
flavin adenine dinucleotide binding1
cytochrome-b5 reductase activity, acting on NAD(P)H1
binding1
catalytic activity1
oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor1
nitrite reductase activity1
intracellular anatomical structure1
mitochondrial membrane1
organelle outer membrane1
endomembrane system1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular membraneless organelle1
cytosol1
protein-containing complex1
mitochondrion1
mitochondrial envelope1
cytoskeleton1
perinuclear region of cytoplasm1
vacuolar lumen1
secretory granule lumen1

Protein interactions and networks

STRING

2012 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYB5R3CYB5AP00167999
CYB5R3CYB5BO43169993
CYB5R3SCDO00767810
CYB5R3CYP51A1Q16850777
CYB5R3ARSAP15289774
CYB5R3PORP16435663
CYB5R3ACKR5O15218652
CYB5R3HBA1P01922641
CYB5R3NOS3P29474530
CYB5R3SUOXP51687504
CYB5R3HBBP02023476
CYB5R3TK2O00142465
CYB5R3DHODHQ02127462
CYB5R3MCATQ8IVS2452
CYB5R3CYCSP00001452

IntAct

288 interactions, top by confidence:

ABTypeScore
CYB5R3STOMpsi-mi:“MI:0915”(physical association)0.670
CYB5R3FUNDC2psi-mi:“MI:0915”(physical association)0.670
CANXCYB5R3psi-mi:“MI:0915”(physical association)0.560
TMEM14CCYB5R3psi-mi:“MI:0915”(physical association)0.560
CYB5R3AQP6psi-mi:“MI:0915”(physical association)0.560
CYB5R3ELOVL4psi-mi:“MI:0915”(physical association)0.560
ADAM33CYB5R3psi-mi:“MI:0915”(physical association)0.560
CDIPTCYB5R3psi-mi:“MI:0915”(physical association)0.560
CYB5R3SLC10A6psi-mi:“MI:0915”(physical association)0.560
VAMP1CYB5R3psi-mi:“MI:0915”(physical association)0.560
CYB5R3TMEM51psi-mi:“MI:0915”(physical association)0.560
CYB5R3HSD17B13psi-mi:“MI:0915”(physical association)0.560
ZDHHC15CYB5R3psi-mi:“MI:0915”(physical association)0.560
CYB5R3psi-mi:“MI:0915”(physical association)0.560
CYB5R3CERS4psi-mi:“MI:0915”(physical association)0.560
CYB5R3FAM210Bpsi-mi:“MI:0915”(physical association)0.560
CYB5R3AIG1psi-mi:“MI:0915”(physical association)0.560
CYB5R3LAPTM5psi-mi:“MI:0915”(physical association)0.560
CYB5R3TMEM115psi-mi:“MI:0915”(physical association)0.560
CYB5R3CSGALNACT2psi-mi:“MI:0915”(physical association)0.560

BioGRID (415): CYB5R3 (Affinity Capture-RNA), CYB5R3 (Affinity Capture-RNA), CYB5R3 (Affinity Capture-RNA), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), ATP5F1 (Co-fractionation), CYB5R3 (Co-fractionation), CYB5R3 (Synthetic Growth Defect), CYB5R3 (Proximity Label-MS), CYB5R3 (Proximity Label-MS)

ESM2 similar proteins: A1C7E9, A1DHW1, A2QCV4, A3GF86, A4QR21, A4R935, A5DQ25, A5DQE4, A5E7U2, A6R2K7, A6ZVM6, A7THS1, A7TNL7, B0CQN7, O74557, P00387, P07514, P0CP14, P0CP15, P20070, P37040, P38626, P83291, Q0CY37, Q0P487, Q0UEY4, Q0X0E5, Q1DWN4, Q27597, Q2UFN3, Q4PGW7, Q4X0B5, Q54NC1, Q59P03, Q5AZB4, Q5BJ68, Q5PQA4, Q6BQ54, Q6BUX2, Q6CA86

Diamond homologs: A0A286R227, A1C7E9, A1DHW1, A2QCV4, A3GF86, A3LT66, A4QR21, A4R935, A5DQ25, A5E7U2, A6R2K7, A6ZVM6, A7TNL7, B0CQN7, O74557, P00387, P07514, P07850, P08509, P08619, P0CP14, P0CP15, P11035, P11605, P11832, P16081, P17569, P17570, P17571, P20070, P22945, P23312, P27783, P27967, P27968, P27969, P36841, P36842, P36858, P36859

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 102 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.

GO biological processes:

GO termPartnersFoldFDR
mitochondrial electron transport, NADH to ubiquinone519.7×3e-03
proton motive force-driven mitochondrial ATP synthesis514.5×8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic23
Likely pathogenic10
Uncertain significance115
Likely benign68
Benign46

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1458058NM_000398.7(CYB5R3):c.706del (p.Trp236fs)Pathogenic
1694454NM_000398.7(CYB5R3):c.708G>A (p.Trp236Ter)Pathogenic
234NM_000398.7(CYB5R3):c.382T>C (p.Ser128Pro)Pathogenic
236NM_000398.7(CYB5R3):c.446T>C (p.Leu149Pro)Pathogenic
238NM_000398.7(CYB5R3):c.734-1G>TPathogenic
239NM_000398.7(CYB5R3):c.463+8G>CPathogenic
240NM_000398.7(CYB5R3):c.655C>T (p.Arg219Ter)Pathogenic
241NM_000398.7(CYB5R3):c.610T>C (p.Cys204Arg)Pathogenic
242NM_000398.7(CYB5R3):c.817_819del (p.Met273del)Pathogenic
2423026NC_000022.10:g.(?43015779)(43015971_?)delPathogenic
2423027NC_000022.10:g.(?43015779)(43024307_?)delPathogenic
243NM_000398.7(CYB5R3):c.895_897del (p.Phe299del)Pathogenic
247NM_000398.7(CYB5R3):c.229C>T (p.Gln77Ter)Pathogenic
248NM_000398.7(CYB5R3):c.478C>T (p.Arg160Ter)Pathogenic
249NM_000398.7(CYB5R3):c.611G>A (p.Cys204Tyr)Pathogenic
3624442NM_000398.7(CYB5R3):c.403C>T (p.Gln135Ter)Pathogenic
4291975NM_000398.7(CYB5R3):c.244_245del (p.Ser82fs)Pathogenic
431812NM_000398.7(CYB5R3):c.250C>T (p.Arg84Ter)Pathogenic
4531856NM_000398.7(CYB5R3):c.226G>A (p.Gly76Ser)Pathogenic
4531857NM_000398.7(CYB5R3):c.173G>C (p.Arg58Pro)Pathogenic
801428NM_000398.7(CYB5R3):c.226+2T>CPathogenic
827632NM_000398.7(CYB5R3):c.103A>C (p.Thr35Pro)Pathogenic
827633NM_000398.7(CYB5R3):c.190C>G (p.Leu64Val)Pathogenic
1174130NM_000398.7(CYB5R3):c.830dup (p.Pro278fs)Likely pathogenic
1502415NM_000398.7(CYB5R3):c.547+1G>ALikely pathogenic
235NM_000398.7(CYB5R3):c.173G>A (p.Arg58Gln)Likely pathogenic
2430191NM_000398.7(CYB5R3):c.274C>T (p.Arg92Trp)Likely pathogenic
251NM_000398.7(CYB5R3):c.763GAG[1] (p.Glu256del)Likely pathogenic
2664646NM_000398.7(CYB5R3):c.508A>G (p.Arg170Gly)Likely pathogenic
3906148NC_000022.11:g.42631838_42638363delins[GTAATCCCAGCAA;42592521_42635366inv;AAGAGTGGGTGGATCACCTGAGGTCAGGAGTGCTAAAC]Likely pathogenic

SpliceAI

2089 predictions. Top by Δscore:

VariantEffectΔscore
22:42619941:CCAGG:Cacceptor_gain1.0000
22:42619942:CAGG:Cacceptor_gain1.0000
22:42619942:CAGGC:Cacceptor_gain1.0000
22:42619944:GGC:Gacceptor_loss1.0000
22:42619945:GC:Gacceptor_loss1.0000
22:42619946:C:CCacceptor_gain1.0000
22:42619946:C:Tacceptor_loss1.0000
22:42623785:TCACC:Tdonor_loss1.0000
22:42623786:CACCT:Cdonor_loss1.0000
22:42623787:A:ACdonor_gain1.0000
22:42623788:C:CCdonor_gain1.0000
22:42623788:CCTT:Cdonor_gain1.0000
22:42623885:CGGT:Cacceptor_gain1.0000
22:42623886:GGT:Gacceptor_gain1.0000
22:42623889:C:CCacceptor_gain1.0000
22:42623890:T:Aacceptor_loss1.0000
22:42628195:A:ACdonor_gain1.0000
22:42628283:T:Gacceptor_loss1.0000
22:42630878:T:TAdonor_gain1.0000
22:42630878:TCACC:Tdonor_loss1.0000
22:42630879:CACCT:Cdonor_loss1.0000
22:42630880:ACCT:Adonor_loss1.0000
22:42630881:CCTT:Cdonor_loss1.0000
22:42630884:TGATG:Tdonor_gain1.0000
22:42630984:CTGGC:Cacceptor_gain1.0000
22:42630985:TGGC:Tacceptor_gain1.0000
22:42630987:GC:Gacceptor_gain1.0000
22:42630987:GCCT:Gacceptor_loss1.0000
22:42630988:CC:Cacceptor_gain1.0000
22:42630988:CCT:Cacceptor_loss1.0000

AlphaMissense

1980 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:42628232:G:AS128F0.996
22:42630892:A:GL108P0.995
22:42628185:C:GG144R0.994
22:42628187:C:GR143P0.994
22:42628252:A:CF121L0.994
22:42628252:A:TF121L0.994
22:42628254:A:GF121L0.994
22:42630882:C:AK111N0.994
22:42630882:C:GK111N0.994
22:42619776:G:CF301L0.993
22:42619776:G:TF301L0.993
22:42619778:A:GF301L0.993
22:42631419:A:GF62S0.993
22:42631422:C:GR61P0.993
22:42628184:C:TG144D0.992
22:42630928:G:TP96H0.992
22:42627320:A:GL206P0.991
22:42631425:A:GF60S0.991
22:42631431:C:GR58P0.991
22:42619859:A:GC274R0.990
22:42627311:G:TA209D0.990
22:42627389:C:TG183D0.990
22:42627616:G:TA179E0.990
22:42628175:C:TG147E0.990
22:42631386:A:GL73P0.990
22:42628232:G:TS128Y0.989
22:42630935:A:GY94H0.989
22:42630973:A:GL81P0.989
22:42630988:C:TG76D0.989
22:42619827:G:CC284W0.988

dbSNP variants (sampled 300 via entrez): RS1000045604 (22:42644305 G>A,T), RS1000182000 (22:42622199 C>A,T), RS1000267007 (22:42629168 T>C), RS1000331267 (22:42634613 A>C,G), RS1000376010 (22:42635958 T>A), RS1000388107 (22:42650737 C>A,G,T), RS1000458762 (22:42650562 G>T), RS1000476358 (22:42626497 T>A), RS1000506509 (22:42645520 G>A,C), RS1000720378 (22:42640095 A>G), RS1000722480 (22:42635023 G>A), RS1000743071 (22:42649401 G>A,T), RS1000773019 (22:42640348 C>A,T), RS1000862138 (22:42617638 G>A,C), RS1000869830 (22:42622247 A>G)

Disease associations

OMIM: gene MIM:613213 | disease phenotypes: MIM:250800, MIM:117000

GenCC curated gene-disease

DiseaseClassificationInheritance
methemoglobinemiaDefinitiveAutosomal recessive
methemoglobinemia due to deficiency of methemoglobin reductaseStrongAutosomal recessive
hereditary methemoglobinemiaSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
methemoglobinemia due to deficiency of methemoglobin reductaseDefinitiveAR

Mondo (5): methemoglobinemia due to deficiency of methemoglobin reductase (MONDO:0009606), central core myopathy (MONDO:0007294), hereditary methemoglobinemia (MONDO:0018963), intellectual disability (MONDO:0001071), methemoglobinemia (MONDO:0001117)

Orphanet (3): Autosomal recessive methemoglobinemia (Orphanet:621), Central core disease (Orphanet:597), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

36 total (30 of 36 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000252Microcephaly
HP:0000486Strabismus
HP:0000565Esotropia
HP:0000592Blue sclerae
HP:0000707Abnormality of the nervous system
HP:0000961Cyanosis
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001272Cerebellar atrophy
HP:0001276Hypertonia
HP:0001337Tremor
HP:0001510Growth delay
HP:0001518Small for gestational age
HP:0001597Abnormal nail morphology
HP:0001901Polycythemia
HP:0002179Opisthotonus
HP:0002283Global brain atrophy
HP:0002305Athetosis
HP:0002315Headache
HP:0002451Limb dystonia
HP:0002510Spastic tetraplegia
HP:0002875Exertional dyspnea
HP:0006808Cerebral hypomyelination
HP:0006913Frontal cortical atrophy
HP:0007112Temporal cortical atrophy
HP:0010864Severe intellectual disability
HP:0011344Severe global developmental delay

GWAS associations

1 associations (top):

StudyTraitp-value
GCST005023_31Initial pursuit acceleration8.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008434initial pursuit acceleration

MeSH disease descriptors (4)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D008708MethemoglobinemiaC15.378.619
D020512Myopathy, Central CoreC05.651.575.300; C10.668.491.550.300
C580280Congenital Methemoglobinemia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2146 (SINGLE PROTEIN)

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

PharmGKB variants

4 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7284807CYB5R30.000
rs8190370CYB5R30.000
rs76458556CYB5R30.000
rs77499608CYB5R30.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression3
sodium arseniteaffects expression, increases expression3
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation3
Benzo(a)pyreneaffects methylation, increases methylation2
NADaffects binding, affects cotreatment, increases reduction2
Tetrachlorodibenzodioxinincreases expression2
Particulate Matteraffects cotreatment, increases abundance, increases expression, decreases expression2
aristolochic acid Idecreases expression1
bisphenol Faffects cotreatment, increases expression1
2,4,6-tribromophenoldecreases expression1
N(4)-hydroxycytidineaffects cotreatment, increases reduction1
decabromobiphenyl etherdecreases expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
N(4)-hydroxycytosineincreases reduction, affects cotreatment1
ochratoxin Adecreases expression1
ciglitazoneaffects binding, increases expression1
benzamidoximeaffects cotreatment, increases reduction1
sulfamethoxazole hydroxylamineaffects cotreatment, increases reduction1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
ICG 001increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1

ChEMBL screening assays

18 unique, capped per target: 18 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4482745BindingInhibition of N-terminal His6-tagged human Cyb5R3 expressed in Escherichia coli SoluBL21 assessed as reduction in NADH-ferricyanide reductase activity at 500 uM pre-incubated for 15 mins before addition of NADH and potassium ferricyanide byTargeting cyb5r3

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D1M6Abcam K-562 CYB5R3 KOCancer cell lineFemale
CVCL_D2IRAbcam Raji CYB5R3 KOCancer cell lineMale
CVCL_UQ38Abcam Jurkat CYB5R3 KOCancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT02478281PHASE1COMPLETEDSafety, Tolerability, and Pharmacokinetic Study of Methylene Blue Following a 1 mg/kg Intravenous Dose in Healthy Adults
NCT02493283PHASE1COMPLETEDPharmacokinetics and Distribution of Dapsone in Leucocytes After Single-dose and Multiple-dose Administration
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00993694Not specifiedCOMPLETEDMethemoglobinemia in Young Patients With Hematologic Cancer or Aplastic Anemia Treated With Dapsone
NCT01402869Not specifiedCOMPLETEDMethemoglobin Levels in Generally Anesthetized Pediatric Dental Patients Receiving Local Anesthetics
NCT01766999Not specifiedCOMPLETEDMethemoglobinemia After Liposuction - Diagnostic by Pulse Oximetry and Blood Gas Analysis.
NCT03542760Not specifiedCOMPLETEDAcquired Methemoglobinemia Observational Registry
NCT06309641Not specifiedCOMPLETEDMethemoglobinemia Following Intravenous Iron Treatment
NCT06958822Not specifiedCOMPLETEDFerric Carboxymaltose Methemoglobinemia Study
NCT00272883Not specifiedRECRUITINGMolecular and Genetic Studies of Congenital Myopathies
NCT06157268Not specifiedRECRUITINGThe Natural History and Muscle Fatigability of Patients With Congenital Myopathies.
NCT06791369Not specifiedNOT_YET_RECRUITINGThe Prevalence of RYR1-related Disease
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability