COA6

gene
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Summary

COA6 (cytochrome c oxidase assembly factor 6, HGNC:18025) is a protein-coding gene on chromosome 1q42.2, encoding Cytochrome c oxidase assembly factor 6 homolog (Q5JTJ3). Involved in the maturation of the mitochondrial respiratory chain complex IV subunit MT-CO2/COX2. It is a selective cancer dependency (DepMap: 28.1% of cell lines).

This gene encodes a member of the cytochrome c oxidase subunit 6B family. The encoded protein associates with cytochrome c oxidase may act has an cytochrome c oxidase mitochondrial respiratory complex VI assembly factor. Mutations in this gene may be associated with fatal infantile cardiomyopathy. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 388753 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 2
  • Clinical variants (ClinVar): 87 total — 2 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 16
  • Cancer dependency (DepMap): dependent in 28.1% of screened cell lines
  • MANE Select transcript: NM_001206641

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18025
Approved symbolCOA6
Namecytochrome c oxidase assembly factor 6
Location1q42.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000168275
Ensembl biotypeprotein_coding
OMIM614772
Entrez388753

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000366612, ENST00000366613, ENST00000366615, ENST00000619305

RefSeq mRNA: 3 — MANE Select: NM_001206641 NM_001012985, NM_001206641, NM_001301733

CCDS: CCDS31059, CCDS55690, CCDS76275

Canonical transcript exons

ENST00000366615 — 3 exons

ExonStartEnd
ENSE00001831497234383723234385080
ENSE00001873248234373456234373678
ENSE00002222990234374230234374389

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 97.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.7034 / max 360.2284, expressed in 1826 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
911123.66701818
91105.59551707
91141.90111143
91131.3465879
91150.6700379
91120.2763126
91160.2470118

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656697.52gold quality
tibialis anteriorUBERON:000138596.16silver quality
gastrocnemiusUBERON:000138895.56gold quality
putamenUBERON:000187495.50gold quality
deltoidUBERON:000147695.13silver quality
muscle of legUBERON:000138395.12gold quality
caudate nucleusUBERON:000187394.95gold quality
kidney epitheliumUBERON:000481994.94silver quality
quadriceps femorisUBERON:000137794.89gold quality
vastus lateralisUBERON:000137994.72gold quality
nucleus accumbensUBERON:000188294.59gold quality
myocardiumUBERON:000234994.22silver quality
Brodmann (1909) area 9UBERON:001354094.04gold quality
mucosa of transverse colonUBERON:000499193.97gold quality
skeletal muscle tissueUBERON:000113493.91gold quality
anterior cingulate cortexUBERON:000983593.72gold quality
upper arm skinUBERON:000426393.64silver quality
nasal cavity epitheliumUBERON:000538493.53silver quality
hindlimb stylopod muscleUBERON:000425293.48gold quality
muscle tissueUBERON:000238593.43gold quality
cardiac muscle of right atriumUBERON:000337993.37silver quality
prefrontal cortexUBERON:000045193.27gold quality
monocyteCL:000057693.26gold quality
gingival epitheliumUBERON:000194993.21gold quality
amygdalaUBERON:000187693.18gold quality
leukocyteCL:000073893.08gold quality
dorsolateral prefrontal cortexUBERON:000983492.74gold quality
body of tongueUBERON:001187692.63silver quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.59gold quality
biceps brachiiUBERON:000150792.48gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.90
E-MTAB-6524no187.33
E-MTAB-7606no161.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting COA6, 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-6513-3P99.5969.771102
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-1213299.4768.901341
HSA-MIR-19898.7067.32920
HSA-MIR-950098.6266.541845
HSA-MIR-1022698.2566.50811
HSA-MIR-489-5P94.6963.0553
HSA-MIR-135A-3P94.1966.09495
HSA-MIR-6750-5P93.9466.68797
HSA-MIR-6822-5P93.9466.34812

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 28.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 11)

  • Strong candidate gene for mitochondrial disease, based on recessive mutations detected in infantile patients (PMID:22277967)
  • COX assembly candidate, ortholog of fungal YMR244C-A (PMID:22356826)
  • Co-purified with C7orf44 (the human ortholog of fungal COX assembly protein) (PMID:22356826)
  • Cooperation between COA6 and SCO2 in COX2 maturation during cytochrome c oxidase assembly links two mitochondrial cardiomyopathies. (PMID:25959673)
  • Results find that COA6 associates with COX2 and is crucial for its maturation and complex IV biogenesis. Also, COA6 interacts with the copper chaperone SCO1 which indicates that COA6 is intrinsically involved in the copper delivery process for COX2. (PMID:26160915)
  • Data present the crystal structures of human Coa6 and the pathogenic (W59C)Coa6-mutant protein. These structures show that Coa6 has a 3-helical bundle structure, with the first 2 helices tethered by disulfide bonds, one of which likely provides the copper-binding site. Disulfide-mediated oligomerization of the (W59C)Coa6 protein provides a structural explanation for the loss-of-function mutation. (PMID:31515291)
  • COA6 Is Structurally Tuned to Function as a Thiol-Disulfide Oxidoreductase in Copper Delivery to Mitochondrial Cytochrome c Oxidase. (PMID:31851937)
  • COA6 Facilitates Cytochrome c Oxidase Biogenesis as Thiol-reductase for Copper Metallochaperones in Mitochondria. (PMID:32061935)
  • What Role Does COA6 Play in Cytochrome C Oxidase Biogenesis: A Metallochaperone or Thiol Oxidoreductase, or Both? (PMID:32977416)
  • High Expression of COA6 Is Related to Unfavorable Prognosis and Enhanced Oxidative Phosphorylation in Lung Adenocarcinoma. (PMID:36982777)
  • Pan-cancer analysis reveals potential immunological and prognostic roles of COA6 in human cancers and preliminary exploration of COA6 in bladder cancer. (PMID:38395184)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocoa6ENSDARG00000092677
mus_musculusCoa6ENSMUSG00000051671
rattus_norvegicusCoa6ENSRNOG00000062808
drosophila_melanogasterCG42376FBGN0259722

Protein

Protein identifiers

Cytochrome c oxidase assembly factor 6 homologQ5JTJ3 (reviewed: Q5JTJ3)

All UniProt accessions (1): Q5JTJ3

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the maturation of the mitochondrial respiratory chain complex IV subunit MT-CO2/COX2. Thereby, may regulate early steps of complex IV assembly. Mitochondrial respiratory chain complex IV or cytochrome c oxidase is the component of the respiratory chain that catalyzes the transfer of electrons from intermembrane space cytochrome c to molecular oxygen in the matrix and as a consequence contributes to the proton gradient involved in mitochondrial ATP synthesis. May also be required for efficient formation of respiratory supercomplexes comprised of complexes III and IV.

Subunit / interactions. Interacts with COA1. Found in a complex with TMEM177, COX20, MT-CO2/COX2, COX18, SCO1 and SCO2. Interacts with MT-CO2/COX2 and SCO2. Interacts with SCO1. Interacts with COX20 in a MT-CO2/COX2- and COX18-dependent manner. Interacts with COX16.

Subcellular location. Mitochondrion intermembrane space.

Disease relevance. Mitochondrial complex IV deficiency, nuclear type 13 (MC4DN13) [MIM:616501] An autosomal recessive, infantile disorder with a fatal course in the first weeks of life, characterized by hypertrophic cardiomyopathy, left ventricular non-compaction, lactic acidosis, metabolic hypotonia, and mitochondrial complex IV deficiency. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the cytochrome c oxidase subunit 6B family.

Isoforms (3)

UniProt IDNamesCanonical?
Q5JTJ3-11yes
Q5JTJ3-22
Q5JTJ3-33

RefSeq proteins (3): NP_001013003, NP_001193570, NP_001288662 (=MANE)

Domains & families (InterPro)

IDNameType
IPR036549CX6/COA6-like_sfHomologous_superfamily
IPR042289COA6Family
IPR048280COX6B-likeFamily

Pfam: PF02297

UniProt features (18 total): helix 5, short sequence motif 2, disulfide bond 2, splice variant 2, sequence variant 2, chain 1, domain 1, turn 1, initiator methionine 1, modified residue 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6PCEX-RAY DIFFRACTION1.65
6PCFX-RAY DIFFRACTION2.2
6NL3SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5JTJ3-F178.740.51

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 (1): 2

Disulfide bonds (2): 58–90, 68–79

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1268020Mitochondrial protein import

MSigDB gene sets: 161 (showing top): GOBP_RESPIRATORY_CHAIN_COMPLEX_IV_ASSEMBLY, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, GOBP_CYTOCHROME_COMPLEX_ASSEMBLY, GOCC_MITOCHONDRIAL_ENVELOPE, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GRYDER_PAX3FOXO1_TOP_ENHANCERS, GOCC_ORGANELLE_ENVELOPE_LUMEN, GOMF_DISULFIDE_OXIDOREDUCTASE_ACTIVITY, GOMF_COPPER_ION_BINDING, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, GOCC_ORGANELLE_ENVELOPE, FEVR_CTNNB1_TARGETS_DN, REACTOME_PROTEIN_LOCALIZATION, CAHOY_ASTROGLIAL

GO Biological Process (2): respiratory chain complex IV assembly (GO:0008535), mitochondrial respiratory chain complex IV assembly (GO:0033617)

GO Molecular Function (3): RNA binding (GO:0003723), copper ion binding (GO:0005507), protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial intermembrane space (GO:0005758)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Protein localization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytochrome complex assembly1
mitochondrion1
respiratory chain complex IV assembly1
mitochondrial respiratory chain complex assembly1
nucleic acid binding1
transition metal ion binding1
binding1
nuclear lumen1
cellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrial envelope1
organelle envelope lumen1

Protein interactions and networks

STRING

1432 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COA6SCO1O75880905
COA6SCO2O43819832
COA6COA3Q9Y2R0807
COA6COX11Q9Y6N1800
COA6COX17Q14061760
COA6COA5Q86WW8751
COA6COX16Q9P0S2750
COA6COX19Q49B96729
COA6COA4Q9NYJ1714
COA6COX7CP15954704
COA6COX20Q5RI15697
COA6COX18Q8N8Q8697
COA6PET117Q6UWS5686
COA6PET100P0DJ07658
COA6COX5BP10606657

IntAct

23 interactions, top by confidence:

ABTypeScore
NAP1L5IQGAP1psi-mi:“MI:0914”(association)0.640
CABP2COA6psi-mi:“MI:0915”(physical association)0.560
COA6CABP2psi-mi:“MI:0915”(physical association)0.560
COA6DTX2psi-mi:“MI:0915”(physical association)0.560
COA6TTC19psi-mi:“MI:0915”(physical association)0.560
CD81HIP1Rpsi-mi:“MI:0914”(association)0.350
PRNPCARNS1psi-mi:“MI:0914”(association)0.350
STYXBANF1psi-mi:“MI:0914”(association)0.350
GABARAPpsi-mi:“MI:0914”(association)0.350
MFSD5ILVBLpsi-mi:“MI:0914”(association)0.350
AIFM1NUDT19psi-mi:“MI:2364”(proximity)0.270
COX14NUDT19psi-mi:“MI:2364”(proximity)0.270
COX4I1HAX1psi-mi:“MI:2364”(proximity)0.270
PLGRKTHAX1psi-mi:“MI:2364”(proximity)0.270
SCO1HAX1psi-mi:“MI:2364”(proximity)0.270
SFXN1HAX1psi-mi:“MI:2364”(proximity)0.270
DTX2COA6psi-mi:“MI:0915”(physical association)0.000
TTC19COA6psi-mi:“MI:0915”(physical association)0.000
adgACOA6psi-mi:“MI:0915”(physical association)0.000

BioGRID (31): COA6 (Affinity Capture-MS), SCO2 (Affinity Capture-Western), COX2 (Affinity Capture-Western), COA6 (Proximity Label-MS), COA6 (Proximity Label-MS), COA6 (Proximity Label-MS), COA6 (Proximity Label-MS), COA6 (Proximity Label-MS), COA6 (Proximity Label-MS), MSRB2 (Co-fractionation), ISOC2 (Co-fractionation), COA6 (Co-fractionation), COA6 (Co-fractionation), COA6 (Two-hybrid), COA6 (Two-hybrid)

ESM2 similar proteins: A2VE78, A5WUL3, A6QR44, B9F4I8, E9Q6D6, F4KIA8, O75916, O82238, O93279, O94763, O94988, P35922, P55265, Q05809, Q06787, Q13233, Q28C33, Q2R2B1, Q3B7M7, Q3T136, Q3ULM0, Q3ZBR0, Q5B4S6, Q5E9J6, Q5JTJ3, Q5R6E1, Q5RGA4, Q5XIX8, Q63505, Q69Z66, Q6GL38, Q6GQ95, Q7TN31, Q7TP65, Q86XL3, Q8C2S5, Q8K284, Q8N302, Q8WYQ5, Q93ZS1

Diamond homologs: G2TRP6, Q2M2S5, Q3E846, Q5JTJ3, Q8BGD8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic3
Uncertain significance28
Likely benign26
Benign16

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
144036NM_001206641.3(COA6):c.267G>C (p.Trp89Cys)Pathogenic
204622NM_001206641.3(COA6):c.286T>C (p.Trp96Arg)Pathogenic
1690932NM_001206641.3(COA6):c.274del (p.Arg92fs)Likely pathogenic
1690965NM_001206641.3(COA6):c.212+163G>ALikely pathogenic
3767189NM_001206641.3(COA6):c.415_418dup (p.Lys140fs)Likely pathogenic

SpliceAI

487 predictions. Top by Δscore:

VariantEffectΔscore
1:234373653:G:GTdonor_gain1.0000
1:234373660:G:GTdonor_gain1.0000
1:234374386:GTGG:Gdonor_gain1.0000
1:234373653:G:Tdonor_gain0.9900
1:234373654:A:Tdonor_gain0.9900
1:234374228:A:AGacceptor_gain0.9900
1:234374229:G:GGacceptor_gain0.9900
1:234374229:GCTTC:Gacceptor_gain0.9900
1:234374388:GG:Gdonor_gain0.9900
1:234374389:GG:Gdonor_gain0.9900
1:234374389:GGT:Gdonor_loss0.9900
1:234374390:G:GGdonor_gain0.9900
1:234374390:GTAAG:Gdonor_loss0.9900
1:234374391:T:Gdonor_loss0.9900
1:234373660:G:Tdonor_gain0.9800
1:234374351:T:Gdonor_gain0.9800
1:234383717:CAACA:Cacceptor_loss0.9800
1:234383718:AACAG:Aacceptor_loss0.9800
1:234383719:ACAGA:Aacceptor_loss0.9800
1:234383720:CAGA:Cacceptor_loss0.9800
1:234383721:A:AGacceptor_gain0.9800
1:234383721:A:Cacceptor_loss0.9800
1:234383722:G:Aacceptor_loss0.9800
1:234383722:G:GGacceptor_gain0.9800
1:234383722:GAT:Gacceptor_gain0.9800
1:234383722:GATA:Gacceptor_gain0.9800
1:234383722:GATAA:Gacceptor_gain0.9800
1:234373504:GCCGC:Gdonor_gain0.9700
1:234373507:GC:Gdonor_gain0.9700
1:234373509:G:GGdonor_gain0.9700

AlphaMissense

996 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:234374389:G:CW94C0.998
1:234374389:G:TW94C0.998
1:234383732:T:CF98L0.998
1:234383734:T:AF98L0.998
1:234383734:T:GF98L0.998
1:234374387:T:AW94R0.997
1:234374387:T:CW94R0.997
1:234383764:A:CK108N0.997
1:234383764:A:TK108N0.997
1:234374305:G:CW66C0.994
1:234374305:G:TW66C0.994
1:234383745:G:CR102T0.994
1:234383746:A:CR102S0.994
1:234383746:A:TR102S0.994
1:234374272:A:CR55S0.993
1:234374272:A:TR55S0.993
1:234374292:G:CR62P0.993
1:234383733:T:CF98S0.993
1:234383733:T:GF98C0.993
1:234374279:T:AC58S0.991
1:234374280:G:CC58S0.991
1:234383729:T:GY97D0.991
1:234383743:A:CR101S0.991
1:234383743:A:TR101S0.991
1:234374284:G:CW59C0.990
1:234374284:G:TW59C0.990
1:234374375:T:AC90S0.990
1:234374376:G:AC90Y0.990
1:234374376:G:CC90S0.990
1:234374271:G:CR55T0.989

dbSNP variants (sampled 300 via entrez): RS1000530178 (1:234375640 A>G), RS1000591904 (1:234376810 C>T), RS1000972208 (1:234381100 C>A), RS1001023221 (1:234380872 C>A,T), RS1001214246 (1:234374949 T>C), RS1001487136 (1:234371842 T>C), RS1001635249 (1:234382026 C>CT), RS1002045080 (1:234379038 A>C), RS1002253883 (1:234381692 A>G), RS1002361988 (1:234375948 C>T), RS1002485171 (1:234373256 C>T), RS1002636717 (1:234383280 G>A), RS1002926712 (1:234385014 G>T), RS1002969016 (1:234384719 C>G), RS1003022818 (1:234378334 C>T)

Disease associations

OMIM: gene MIM:614772 | disease phenotypes: MIM:616501

GenCC curated gene-disease

DiseaseClassificationInheritance
cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 4StrongUnknown

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
mitochondrial diseaseDefinitiveAR

Mondo (1): cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 4 (MONDO:0014668)

Orphanet (1): Fatal infantile cytochrome C oxidase deficiency (Orphanet:1561)

HPO phenotypes

16 total (16 of 16 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000331Short chin
HP:0001252Hypotonia
HP:0001319Neonatal hypotonia
HP:0001639Hypertrophic cardiomyopathy
HP:0001643Patent ductus arteriosus
HP:0001659Aortic regurgitation
HP:0001942Metabolic acidosis
HP:0002045Hypothermia
HP:0002789Tachypnea
HP:0003128Lactic acidosis
HP:0003577Congenital onset
HP:0005180Tricuspid regurgitation
HP:0008347Decreased activity of mitochondrial complex IV
HP:0012664Reduced left ventricular ejection fraction
HP:0030682Left ventricular noncompaction

GWAS associations

2 associations (top):

StudyTraitp-value
GCST009391_2134Metabolite levels7.000000e-06
GCST009391_964Metabolite levels9.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010383phosphatidylcholine 36:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression3
beauvericinaffects cotreatment, decreases expression1
lead acetateincreases expression1
tetrahydropalmatinedecreases expression1
sulforaphaneincreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
perfluorooctanoic acidincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
potassium chromate(VI)affects cotreatment, decreases expression1
cupric chlorideincreases expression1
epigallocatechin gallatedecreases expression, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
azoxystrobinincreases expression1
enniatinsaffects cotreatment, decreases expression1
deguelinincreases expression1
K 7174decreases expression1
fenpyroximateincreases expression1
pyrachlostrobinincreases expression1
picoxystrobinincreases expression1
Resveratrolaffects cotreatment, increases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Antimycin Aincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Cisplatindecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Plant Extractsaffects cotreatment, increases expression1
Rotenoneincreases expression1
Smokedecreases expression1

Clinical trials (associated diseases)

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