COX7B

gene
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Summary

COX7B (cytochrome c oxidase subunit 7B, HGNC:2291) is a protein-coding gene on chromosome Xq21.1, encoding Cytochrome c oxidase subunit 7B, mitochondrial (P24311). Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. It is a selective cancer dependency (DepMap: 70.8% of cell lines).

Cytochrome c oxidase (COX), the terminal component of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. This component is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in electron transfer, and the nuclear-encoded subunits may function in the regulation and assembly of the complex. This nuclear gene encodes subunit VIIb, which is highly similar to bovine COX VIIb protein and is found in all tissues. This gene may have several pseudogenes on chromosomes 1, 2, 20 and 22.

Source: NCBI Gene 1349 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): linear skin defects with multiple congenital anomalies 2 (Definitive, GenCC) — +2 more curated relationships
  • Clinical variants (ClinVar): 53 total — 4 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 120
  • Cancer dependency (DepMap): dependent in 70.8% of screened cell lines
  • MANE Select transcript: NM_001866

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2291
Approved symbolCOX7B
Namecytochrome c oxidase subunit 7B
LocationXq21.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000131174
Ensembl biotypeprotein_coding
OMIM300885
Entrez1349

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000373335, ENST00000475465, ENST00000647835, ENST00000650309, ENST00000857759, ENST00000912755, ENST00000912756

RefSeq mRNA: 1 — MANE Select: NM_001866 NM_001866

CCDS: CCDS14437

Canonical transcript exons

ENST00000650309 — 3 exons

ExonStartEnd
ENSE000035821337790264377902767
ENSE000038346527789946877899593
ENSE000038501487790518477907376

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 152.1559 / max 1027.8190, expressed in 1826 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
196775152.15591826

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
heart right ventricleUBERON:000208099.85gold quality
apex of heartUBERON:000209899.68gold quality
biceps brachiiUBERON:000150799.62gold quality
body of tongueUBERON:001187699.62gold quality
hindlimb stylopod muscleUBERON:000425299.60gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.56gold quality
diaphragmUBERON:000110399.55gold quality
mucosa of sigmoid colonUBERON:000499399.54gold quality
right atrium auricular regionUBERON:000663199.53gold quality
renal medullaUBERON:000036299.51gold quality
cardiac ventricleUBERON:000208299.51gold quality
heart left ventricleUBERON:000208499.50gold quality
vena cavaUBERON:000408799.47gold quality
triceps brachiiUBERON:000150999.45gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451199.45gold quality
pharyngeal mucosaUBERON:000035599.42gold quality
colonic mucosaUBERON:000031799.41gold quality
tongueUBERON:000172399.40gold quality
mucosa of transverse colonUBERON:000499199.40gold quality
jejunumUBERON:000211599.31gold quality
upper leg skinUBERON:000426299.27gold quality
superior surface of tongueUBERON:000737199.23gold quality
oral cavityUBERON:000016799.22gold quality
jejunal mucosaUBERON:000039999.22gold quality
heartUBERON:000094899.14gold quality
mammalian vulvaUBERON:000099799.13gold quality
gingival epitheliumUBERON:000194999.12gold quality
sigmoid colonUBERON:000115999.11gold quality
gingivaUBERON:000182899.11gold quality
gastrocnemiusUBERON:000138899.08gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-MTAB-7008yes550.23
E-MTAB-8410yes46.35
E-MTAB-7316yes23.73
E-HCAD-10yes12.24
E-MTAB-10042yes10.01
E-MTAB-9388no1566.55
E-MTAB-10596no1324.63
E-MTAB-8271no8.99
E-HCAD-13no3.09
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting COX7B, 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-60799.9773.625593
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-1212999.7267.451311
HSA-MIR-450699.3467.47526
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-556-5P97.7566.17473
HSA-MIR-464297.5267.60916
HSA-MIR-1225-5P96.7666.85417

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 70.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • Novel insights into the assembly and function of human nuclear-encoded cytochrome c oxidase subunits 7b (PMID:20307258)
  • Data indicate that recombinant (r)IL-24 stimulated the mitochondrial apoptotic pathway genes Bax, Bid, Casp8, COX6C, COX7B after 36 h. (PMID:22860893)
  • study analyzed the X-linked COX7B and found deleterious de novo mutations in two simplex cases of microphthalmia with linear skin lesions and a nonsense mutation, which segregates with the disease, in a familial case (PMID:23122588)
  • Our results offer a new transcriptome landscape of platinum-resistance that provides valuable insights into chemosensitivity and drug resistance in cancers, and we identify a novel platinum resistance gene, COX7B, and a surrogate marker, CD63. (PMID:30367559)

Cross-species orthologs

0 orthologs

Paralogs (1): COX7B2 (ENSG00000170516)

Protein

Protein identifiers

Cytochrome c oxidase subunit 7B, mitochondrialP24311 (reviewed: P24311)

Alternative names: Cytochrome c oxidase polypeptide VIIb

All UniProt accessions (4): A0A3B3IRN8, A0A3B3ISY5, A0A3B3ITX0, P24311

UniProt curated annotations — full annotation on UniProt →

Function. Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Plays a role in proper central nervous system (CNS) development in vertebrates.

Subunit / interactions. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I1 (or COX4I2), COX5A, COX5B, COX6A1 (or COX6A2), COX6B1 (or COX6B2), COX6C, COX7A2 (or COX7A1), COX7B, COX7C, COX8A and COXFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)).

Subcellular location. Mitochondrion inner membrane.

Disease relevance. Linear skin defects with multiple congenital anomalies 2 (LSDMCA2) [MIM:300887] A distinct form of aplasia cutis congenita presenting as multiple linear skin defects on the face and neck associated with poor growth, microcephaly, and facial dysmorphism. Additional features include intellectual disability, nail dystrophy, short stature and cardiac abnormalities. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Energy metabolism; oxidative phosphorylation.

Similarity. Belongs to the cytochrome c oxidase VIIb family.

RefSeq proteins (1): NP_001857* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008433Cyt_c_oxidase_suVIIBFamily
IPR023272Cyt_c_oxidase_suVIIB_dom_sfHomologous_superfamily

Pfam: PF05392

UniProt features (6 total): topological domain 2, transit peptide 1, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9I6FELECTRON MICROSCOPY2.95
9I7UELECTRON MICROSCOPY3.15
5Z62ELECTRON MICROSCOPY3.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P24311-F190.150.56

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-5628897TP53 Regulates Metabolic Genes
R-HSA-611105Respiratory electron transport
R-HSA-9707564Cytoprotection by HMOX1
R-HSA-9864848Complex IV assembly

MSigDB gene sets: 432 (showing top): MODULE_93, MODULE_52, HORIUCHI_WTAP_TARGETS_DN, MODULE_151, MORF_RAD21, AACYNNNNTTCCS_UNKNOWN, TGACCTY_ERR1_Q2, MODULE_16, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, PUJANA_CHEK2_PCC_NETWORK, OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, MORF_SKP1A, GOBP_OXIDATIVE_PHOSPHORYLATION

GO Biological Process (5): mitochondrial electron transport, cytochrome c to oxygen (GO:0006123), central nervous system development (GO:0007417), cellular respiration (GO:0045333), oxidative phosphorylation (GO:0006119), proton transmembrane transport (GO:1902600)

GO Molecular Function (2): cytochrome-c oxidase activity (GO:0004129), protein binding (GO:0005515)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial membrane (GO:0031966), respiratory chain complex IV (GO:0045277), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Transcriptional Regulation by TP531
Aerobic respiration and respiratory electron transport1
Cellular response to chemical stress1
Respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
aerobic electron transport chain1
mitochondrial ATP synthesis coupled electron transport1
nervous system development1
system development1
energy derivation by oxidation of organic compounds1
aerobic respiration1
proton motive force-driven ATP synthesis1
monoatomic cation transmembrane transport1
electron transfer activity1
proton transmembrane transporter activity1
oxidoreduction-driven active transmembrane transporter activity1
oxidoreductase activity, acting on a heme group of donors1
active monoatomic ion transmembrane transporter activity1
binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
mitochondrion1
mitochondrial envelope1
organelle membrane1
cytochrome complex1
respiratory chain complex1
transmembrane transporter complex1
oxidoreductase complex1
cellular anatomical structure1

Protein interactions and networks

STRING

1102 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COX7BCOX5BP10606970
COX7BCOX6CP09669961
COX7BCOX7CP15954948
COX7BCOX8AP10176903
COX7BCOX6A1P12074837
COX7BCOX6B1P14854801
COX7BCOX6A2Q02221794
COX7BCOXFA4O00483765
COX7BCOX5AP20674745
COX7BNDUFA1O15239730
COX7BCOX7A1P24310705
COX7BCOX7A2P14406687
COX7BNDUFB9Q9Y6M9683
COX7BUQCR11O14957681
COX7BNDUFA11Q86Y39675

IntAct

8 interactions, top by confidence:

ABTypeScore
COX7BGNMTpsi-mi:“MI:0915”(physical association)0.560
COX7BCOX4I1psi-mi:“MI:0915”(physical association)0.400
HSCBRBP5psi-mi:“MI:0914”(association)0.350
MT-CO2NDUFA4psi-mi:“MI:0914”(association)0.350
GNMTCOX7Bpsi-mi:“MI:0915”(physical association)0.000
MYBCOX7Bpsi-mi:“MI:0915”(physical association)0.000

BioGRID (25): COX7B (Affinity Capture-RNA), COX7B (Synthetic Lethality), BCAP31 (Co-fractionation), NDUFB9 (Co-fractionation), COX7B (Co-fractionation), COX7B (Co-fractionation), COX7B (Co-fractionation), COX7B (Co-fractionation), AUH (Co-fractionation), CTNNB1 (Co-fractionation), CYFIP2 (Co-fractionation), SMDT1 (Co-fractionation), VCP (Co-fractionation), COX7B (Co-fractionation), COX7B (Co-fractionation)

ESM2 similar proteins: A1L2P2, A1XQR7, A8E7D3, A8MTT3, L0R6Q1, O48832, O64497, O82803, P11951, P13183, P14790, P24311, P43883, P46270, P80977, Q148H0, Q1LUK1, Q1MTD4, Q1RMH3, Q21154, Q28EM2, Q2ACH7, Q41112, Q4V8S3, Q5BKW8, Q5CZQ0, Q5R987, Q5XFV8, Q5XKP0, Q63ZZ0, Q68EV8, Q7SGT7, Q7YRK0, Q7YRK1, Q810Q5, Q84K90, Q8BH51, Q8BTE5, Q8R404, Q8VCR3

Diamond homologs: P13183, P24311, P56393, P80431, Q4R648, Q5R9K2, Q8TF08

SIGNOR signaling

1 interactions.

AEffectBMechanism
COX7B“form complex”“Cytochrome c oxidase-Mitochondrial respiratory chain complex IV”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic1
Uncertain significance13
Likely benign18
Benign4

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
39767NM_001866.3(COX7B):c.196del (p.Leu66fs)Pathogenic
39768NM_001866.3(COX7B):c.41-2A>GPathogenic
39769NM_001866.2(COX7B):c.55C>T (p.Gln19Ter)Pathogenic
58660GRCh38/hg38 Xq21.1(chrX:77829855-77902263)x2Pathogenic
449642NM_001866.3(COX7B):c.40+5G>CLikely pathogenic

SpliceAI

550 predictions. Top by Δscore:

VariantEffectΔscore
X:77899591:AAGGT:Adonor_loss1.0000
X:77899593:GGTG:Gdonor_loss1.0000
X:77899595:T:Adonor_loss1.0000
X:77902404:T:Gdonor_gain1.0000
X:77902629:C:Aacceptor_gain1.0000
X:77902637:T:Aacceptor_gain1.0000
X:77902640:A:AGacceptor_gain1.0000
X:77902641:A:Gacceptor_gain1.0000
X:77902642:G:GGacceptor_gain1.0000
X:77899594:G:GGdonor_gain0.9900
X:77902319:A:AGacceptor_gain0.9900
X:77902322:A:AGacceptor_gain0.9900
X:77902766:ATG:Adonor_loss0.9900
X:77902767:TGTA:Tdonor_loss0.9900
X:77902768:G:GGdonor_gain0.9900
X:77902769:T:Adonor_loss0.9900
X:77902770:A:ACdonor_loss0.9900
X:77902771:AG:Adonor_loss0.9900
X:77902772:G:Cdonor_loss0.9900
X:77902320:A:Gacceptor_gain0.9800
X:77902323:C:Gacceptor_gain0.9800
X:77902638:GTAA:Gacceptor_loss0.9800
X:77902640:AAG:Aacceptor_loss0.9800
X:77902642:G:GAacceptor_loss0.9800
X:77902642:GTTC:Gacceptor_gain0.9800
X:77902718:ATGCT:Adonor_loss0.9800
X:77902765:TAT:Tdonor_gain0.9800
X:77905183:GGTA:Gacceptor_gain0.9800
X:77905257:A:AGdonor_gain0.9800
X:77905258:G:GGdonor_gain0.9800

AlphaMissense

522 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:77902699:T:CF33L0.953
X:77902701:T:AF33L0.953
X:77902701:T:GF33L0.953
X:77905249:G:CW77C0.910
X:77905249:G:TW77C0.910
X:77905208:T:AW64R0.904
X:77905208:T:CW64R0.904
X:77905247:T:AW77R0.902
X:77905247:T:CW77R0.902
X:77902747:T:CC49R0.890
X:77905210:G:CW64C0.877
X:77905210:G:TW64C0.877
X:77902759:T:AW53R0.873
X:77902759:T:CW53R0.873
X:77902700:T:CF33S0.827
X:77902700:T:GF33C0.824
X:77902732:A:CS44R0.814
X:77902734:T:AS44R0.814
X:77902734:T:GS44R0.814
X:77902730:C:AA43D0.781
X:77902715:G:TG38V0.778
X:77902744:T:CF48L0.777
X:77902746:C:AF48L0.777
X:77902746:C:GF48L0.777
X:77902724:T:AV41E0.770
X:77902727:T:CL42S0.767
X:77902754:T:AV51D0.758
X:77902736:G:AG45E0.739
X:77902749:T:GC49W0.733
X:77905248:G:CW77S0.733

dbSNP variants (sampled 300 via entrez): RS1000220144 (X:77903384 G>A), RS1000572276 (X:77902913 G>C), RS1001391728 (X:77903792 C>T), RS1002488087 (X:77902244 A>G), RS1002787070 (X:77901778 G>A,T), RS1003057262 (X:77905947 G>A), RS1004328684 (X:77902355 T>G), RS1006021772 (X:77904267 G>T), RS1007192450 (X:77904955 A>G), RS1007655319 (X:77905508 T>G), RS1008001891 (X:77899770 A>T), RS1008034507 (X:77900272 C>G), RS1008914359 (X:77907329 A>C,G), RS1009278157 (X:77906991 G>T), RS1010180957 (X:77903437 G>A,T)

Disease associations

OMIM: gene MIM:300885 | disease phenotypes: MIM:300887, MIM:300853

GenCC curated gene-disease

DiseaseClassificationInheritance
linear skin defects with multiple congenital anomalies 2DefinitiveX-linked
linear skin defects with multiple congenital anomaliesSupportiveX-linked

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
mitochondrial diseaseLimitedXL

Mondo (3): linear skin defects with multiple congenital anomalies 2 (MONDO:0010474), X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia (MONDO:0010455), linear skin defects with multiple congenital anomalies (MONDO:0010672)

Orphanet (2): Microphthalmia with linear skin defects syndrome (Orphanet:2556), XMEN (Orphanet:317476)

HPO phenotypes

120 total (30 of 120 shown, HPO-id order):

HPOTerm
HP:0000013Hypoplasia of the uterus
HP:0000035Abnormal testis morphology
HP:0000036Abnormal penis morphology
HP:0000037Male pseudohermaphroditism
HP:0000039Epispadias
HP:0000041Chordee
HP:0000047Hypospadias
HP:0000054Micropenis
HP:0000062Ambiguous genitalia
HP:0000175Cleft palate
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000278Retrognathia
HP:0000316Hypertelorism
HP:0000331Short chin
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000358Posteriorly rotated ears
HP:0000363Abnormal earlobe morphology
HP:0000365Hearing impairment
HP:0000431Wide nasal bridge
HP:0000445Wide nose
HP:0000492Abnormal eyelid morphology
HP:0000499Abnormal eyelash morphology
HP:0000501Glaucoma
HP:0000505Visual impairment
HP:0000518Cataract
HP:0000528Anophthalmia
HP:0000543Optic disc pallor

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
C537466Microphthalmia, syndromic 7 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsdecreases expression, affects cotreatment, increases abundance, increases oxidation, affects expression5
Valproic Acidaffects cotreatment, increases expression, affects expression4
Particulate Matterdecreases expression, increases abundance4
Acetaminophendecreases expression, increases expression, affects cotreatment3
bisphenol Adecreases expression, affects expression2
sodium arsenitedecreases expression, increases expression2
Atrazinedecreases expression2
Ozoneincreases oxidation, increases abundance, affects expression, affects cotreatment2
Zidovudinedecreases expression, increases expression2
Cyclosporinedecreases expression2
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
cobaltous chloridedecreases expression1
zinc chromateincreases abundance, increases expression1
bleomycetindecreases expression1
potassium chromate(VI)decreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
1-methyl-4-phenyl-2,3-dihydropyridiniumdecreases expression1
beta-methylcholineaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
CD 437decreases expression1
chloropicrinincreases expression1
OSW 1increases expression1
corosolic aciddecreases expression1
K 7174decreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02496676PHASE1/PHASE2COMPLETEDMagnesium Supplementation in People With XMEN Syndrome