COA7

gene
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Also known as FLJ12439RESA1

Summary

COA7 (cytochrome c oxidase assembly factor 7, HGNC:25716) is a protein-coding gene on chromosome 1p32.3, encoding Cytochrome c oxidase assembly factor 7 (Q96BR5). Required for assembly of mitochondrial respiratory chain complex I and complex IV. It is a selective cancer dependency (DepMap: 42.1% of cell lines).

Enables protein-disulfide reductase activity. Involved in respiratory chain complex IV assembly. Located in mitochondrion and nucleoplasm. Is active in mitochondrial intermembrane space. Implicated in spinocerebellar ataxia with axonal neuropathy type 3.

Source: NCBI Gene 65260 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +1 more curated relationship
  • Clinical variants (ClinVar): 80 total — 4 pathogenic, 6 likely-pathogenic
  • Phenotypes (HPO): 23
  • Cancer dependency (DepMap): dependent in 42.1% of screened cell lines
  • MANE Select transcript: NM_023077

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25716
Approved symbolCOA7
Namecytochrome c oxidase assembly factor 7
Location1p32.3
Locus typegene with protein product
StatusApproved
AliasesFLJ12439, RESA1
Ensembl geneENSG00000162377
Ensembl biotypeprotein_coding
OMIM615623
Entrez65260

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000371538, ENST00000486918, ENST00000939652

RefSeq mRNA: 1 — MANE Select: NM_023077 NM_023077

CCDS: CCDS570

Canonical transcript exons

ENST00000371538 — 3 exons

ExonStartEnd
ENSE000014554755268444952688168
ENSE000014554765269822152698347
ENSE000036570865269272752692867

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 91.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1649 / max 177.2784, expressed in 1770 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1237311.16491770

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
type B pancreatic cellCL:000016991.27gold quality
olfactory bulbUBERON:000226491.13gold quality
secondary oocyteCL:000065589.76gold quality
cortical plateUBERON:000534388.76gold quality
vastus lateralisUBERON:000137988.15silver quality
quadriceps femorisUBERON:000137787.27silver quality
skeletal muscle tissue of biceps brachiiUBERON:000450287.19gold quality
mucosa of sigmoid colonUBERON:000499386.88gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451186.87gold quality
gastrocnemiusUBERON:000138886.41gold quality
colonic mucosaUBERON:000031786.20gold quality
muscle organUBERON:000163086.03gold quality
biceps brachiiUBERON:000150785.89gold quality
muscle of legUBERON:000138385.76gold quality
skeletal muscle tissueUBERON:000113485.72gold quality
gingival epitheliumUBERON:000194985.38silver quality
hindlimb stylopod muscleUBERON:000425285.02gold quality
gingivaUBERON:000182884.95gold quality
islet of LangerhansUBERON:000000684.88gold quality
heart right ventricleUBERON:000208084.34gold quality
muscle tissueUBERON:000238584.03gold quality
cervix squamous epitheliumUBERON:000692283.64gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.58gold quality
prefrontal cortexUBERON:000045183.29gold quality
diaphragmUBERON:000110383.07silver quality
Brodmann (1909) area 23UBERON:001355482.89gold quality
body of tongueUBERON:001187682.87gold quality
ponsUBERON:000098882.56gold quality
stromal cell of endometriumCL:000225582.44gold quality
smooth muscle tissueUBERON:000113582.11gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting COA7, 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-513A-5P100.0069.772465
HSA-MIR-5692A100.0074.406850
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548AN99.9770.912817
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-22-3P99.9368.13917
HSA-MIR-335-3P99.9373.364958
HSA-MIR-130599.9171.433443
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-129-5P99.8870.263273
HSA-LET-7A-2-3P99.8770.531921
HSA-LET-7G-3P99.8570.431929
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-498-5P99.7669.641807
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-453099.6966.471509
HSA-MIR-6757-3P99.6366.881089
HSA-MIR-508-5P99.4164.251248
HSA-MIR-584-3P99.3567.691082
HSA-MIR-542-3P99.3467.581270
HSA-MIR-127299.3468.79878
HSA-MIR-2116-5P99.3269.341273
HSA-MIR-488-5P99.2868.12821
HSA-MIR-5584-3P99.2368.791351
HSA-MIR-66199.0965.942062
HSA-MIR-3619-5P99.0068.872308

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 42.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • C1orf163 is a novel factor important for the assembly of respiratory chain complexes in human mitochondria. (PMID:24333015)
  • The first patient carrying pathogenic mutations of COA7, causative of isolated COX deficiency and progressive neurological impairment is reported. It is also shown that COA7 is a soluble protein localized to the matrix, rather than in the intermembrane space as previously suggested. (PMID:27683825)
  • The results of this study suggest that loss-of-function COA7 mutation is responsible for the phenotype of the presented patients, and this new entity of disease would be referred to as spinocerebellar ataxia with axonal neuropathy type 3. (PMID:29718187)
  • pathogenic mutant versions of COA7 are imported slower than the wild-type protein, and mislocalized proteins are degraded in the cytosol by the proteasome. (PMID:30885959)
  • Mitochondrial COA7 is a heme-binding protein with disulfide reductase activity, which acts in the early stages of complex IV assembly. (PMID:35210360)
  • Dystonia and Parkinsonism in COA7-related disorders: expanding the phenotypic spectrum. (PMID:37750949)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocoa7ENSDARG00000019355
mus_musculusCoa7ENSMUSG00000048351
rattus_norvegicusCoa7ENSRNOG00000010636
drosophila_melanogasterCoa7FBGN0039965
caenorhabditis_elegansWBGENE00013925

Protein

Protein identifiers

Cytochrome c oxidase assembly factor 7Q96BR5 (reviewed: Q96BR5)

Alternative names: Beta-lactamase hcp-like protein, Respiratory chain assembly factor 1, Sel1 repeat-containing protein 1

All UniProt accessions (1): Q96BR5

UniProt curated annotations — full annotation on UniProt →

Function. Required for assembly of mitochondrial respiratory chain complex I and complex IV.

Subunit / interactions. Interacts with CHCHD4/MIA40 through transient intermolecular disulfide bonds.

Subcellular location. Mitochondrion intermembrane space.

Disease relevance. Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 (SCAN3) [MIM:618387] A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAN3 is an autosomal recessive disorder characterized by onset in the first decade of slowly progressive distal muscle weakness and atrophy and distal sensory impairment due to an axonal peripheral neuropathy. Affected individuals have gait disturbances and sometimes manual dexterity difficulties, as well as cerebellar ataxia associated with cerebellar atrophy on brain imaging. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the hcp beta-lactamase family.

RefSeq proteins (1): NP_075565* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006597Sel1-likeRepeat
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR040239HcpB-likeFamily

Pfam: PF08238

UniProt features (28 total): helix 12, sequence variant 5, repeat 5, initiator methionine 1, chain 1, sequence conflict 1, turn 1, strand 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
7MQZX-RAY DIFFRACTION2.39

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96BR5-F195.470.93

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

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_RESPIRATORY_CHAIN_COMPLEX_IV_ASSEMBLY, MAZ_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, GOBP_CYTOCHROME_COMPLEX_ASSEMBLY, MODULE_301, GOCC_MITOCHONDRIAL_ENVELOPE, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MODULE_188, HAMAI_APOPTOSIS_VIA_TRAIL_DN, SHEN_SMARCA2_TARGETS_DN, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_ORGANELLE_ENVELOPE_LUMEN

GO Biological Process (1): respiratory chain complex IV assembly (GO:0008535)

GO Molecular Function (2): protein-disulfide reductase activity (GO:0015035), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytochrome complex assembly1
disulfide oxidoreductase activity1
catalytic activity, acting on a protein1
binding1
nuclear lumen1
cellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrial envelope1
organelle envelope lumen1

Protein interactions and networks

STRING

1118 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COA7COA6Q5JTJ3603
COA7COA5Q86WW8602
COA7COX17Q14061598
COA7COA4Q9NYJ1598
COA7SETXQ7Z333581
COA7SAMM50Q9Y512573
COA7COX8AP10176557
COA7SYVN1Q86TM6551
COA7CHCHD4Q8N4Q1549
COA7COX6B1P14854536
COA7ATP23Q9Y6H3531
COA7TIMM9Q9Y5J7525
COA7TIMM8AO60220522
COA7SEL1LQ9UBV2498
COA7TIMM10P62072494

IntAct

141 interactions, top by confidence:

ABTypeScore
RIN1NRASpsi-mi:“MI:0914”(association)0.840
B3GNT3PGRMC1psi-mi:“MI:0914”(association)0.670
HSPB2BAG3psi-mi:“MI:0914”(association)0.670
CRHBPCCNB2psi-mi:“MI:0914”(association)0.640
CHCHD4SSNA1psi-mi:“MI:0914”(association)0.640
CRIPTOAIPpsi-mi:“MI:0914”(association)0.640
MPPED1CLUHpsi-mi:“MI:0914”(association)0.640
PDK4PDK2psi-mi:“MI:0914”(association)0.640
SNRPBCOA7psi-mi:“MI:0915”(physical association)0.560
SUOXCOA7psi-mi:“MI:0915”(physical association)0.560
COA7GPSM3psi-mi:“MI:0915”(physical association)0.560
TLE5COA7psi-mi:“MI:0915”(physical association)0.560
COA7ENKD1psi-mi:“MI:0915”(physical association)0.560
COA7CASP6psi-mi:“MI:0915”(physical association)0.560
COA7DMWDpsi-mi:“MI:0915”(physical association)0.560
COA7psi-mi:“MI:0915”(physical association)0.560
COA7FGFR3psi-mi:“MI:0915”(physical association)0.560
COA7GSNpsi-mi:“MI:0915”(physical association)0.560
COA7HMOX2psi-mi:“MI:0915”(physical association)0.560
COA7LAMP2psi-mi:“MI:0915”(physical association)0.560
COA7PMP22psi-mi:“MI:0915”(physical association)0.560
COA7RANpsi-mi:“MI:0915”(physical association)0.560
COA7CYCSpsi-mi:“MI:0915”(physical association)0.560
COA7PRPF40Apsi-mi:“MI:0915”(physical association)0.560
COA7SPRED1psi-mi:“MI:0915”(physical association)0.560

BioGRID (141): COA7 (Affinity Capture-MS), COA7 (Co-fractionation), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Affinity Capture-MS), COA7 (Proximity Label-MS), COA7 (Proximity Label-MS), COA7 (Proximity Label-MS), COA7 (Proximity Label-MS), COA7 (Proximity Label-MS)

ESM2 similar proteins: A1CP31, A1D1Y5, A2QAQ3, A2QQE8, G5EEN4, J9VSG5, O42632, P0CQ16, P0CQ17, P17885, P23231, P36583, P46822, P87253, Q00078, Q01317, Q0D0A1, Q0UXL8, Q20168, Q2U0M4, Q2URJ0, Q338B9, Q4IQC1, Q4QR29, Q4WKB2, Q4WVF4, Q4WVG0, Q4X0I8, Q52DF3, Q5AZT7, Q5BD89, Q5BFB1, Q5BGN7, Q5BH69, Q5M7J9, Q5TYQ3, Q5ZIK9, Q62018, Q6DEU9, Q6INS3

Diamond homologs: Q0V9D9, Q23450, Q5FWY3, Q5TYQ3, Q66KY0, Q921H9, Q96BR5, Q9W5N0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 130 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
Complex IV assembly717.8×4e-05
Cytoprotection by HMOX1510.2×8e-03
Mitochondrial protein degradation78.9×2e-03
Respiratory electron transport88.5×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic6
Uncertain significance34
Likely benign29
Benign7

Top pathogenic / likely-pathogenic (10)

Variant IDHGVSClassification
438350NM_023077.3(COA7):c.410A>G (p.Tyr137Cys)Pathogenic
438351NM_023077.3(COA7):c.247+1G>TPathogenic
625459NM_023077.3(COA7):c.446G>T (p.Ser149Ile)Pathogenic
625461NM_023077.3(COA7):c.431del (p.Gly144fs)Pathogenic
1335810NM_023077.3(COA7):c.107-2A>GLikely pathogenic
2585171NM_023077.3(COA7):c.97del (p.Asp33fs)Likely pathogenic
4819770NM_023077.3(COA7):c.106+2T>GLikely pathogenic
625460NM_023077.3(COA7):c.17A>G (p.Asp6Gly)Likely pathogenic
806136NM_023077.3(COA7):c.574C>T (p.Arg192Cys)Likely pathogenic
806137NM_023077.3(COA7):c.540_550dup (p.Ile184fs)Likely pathogenic

SpliceAI

380 predictions. Top by Δscore:

VariantEffectΔscore
1:52692721:CCTTA:Cdonor_loss1.0000
1:52692722:CTTA:Cdonor_loss1.0000
1:52692723:TTACC:Tdonor_loss1.0000
1:52692724:TA:Tdonor_loss1.0000
1:52692725:A:ACdonor_gain1.0000
1:52692725:A:Cdonor_loss1.0000
1:52692726:C:CCdonor_gain1.0000
1:52692863:GCAAC:Gacceptor_gain1.0000
1:52692864:CAAC:Cacceptor_gain1.0000
1:52692864:CAACC:Cacceptor_gain1.0000
1:52692865:AAC:Aacceptor_gain1.0000
1:52692866:ACCT:Aacceptor_loss1.0000
1:52692868:C:CCacceptor_gain1.0000
1:52692868:CTG:Cacceptor_loss1.0000
1:52692869:T:Cacceptor_loss1.0000
1:52698180:C:Adonor_gain1.0000
1:52692725:AC:Adonor_gain0.9900
1:52692726:CC:Cdonor_gain0.9900
1:52692726:CCTT:Cdonor_gain0.9900
1:52692799:TCAAC:Tdonor_gain0.9900
1:52692866:AC:Aacceptor_gain0.9900
1:52692867:CC:Cacceptor_gain0.9900
1:52692872:G:Tacceptor_gain0.9900
1:52698131:T:TAdonor_gain0.9900
1:52698216:CTCA:Cdonor_loss0.9900
1:52698217:TCA:Tdonor_loss0.9900
1:52698218:CA:Cdonor_loss0.9900
1:52698219:A:ACdonor_gain0.9900
1:52698219:A:Cdonor_loss0.9900
1:52698219:ACCGT:Adonor_gain0.9900

AlphaMissense

1547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:52687969:A:CS149R0.998
1:52687969:A:TS149R0.998
1:52687971:T:GS149R0.998
1:52687954:A:CS154R0.997
1:52687954:A:TS154R0.997
1:52687956:T:GS154R0.997
1:52692764:G:CS70R0.995
1:52692764:G:TS70R0.995
1:52692766:T:GS70R0.995
1:52692751:C:AG75W0.993
1:52687958:A:GL153P0.992
1:52687841:C:GR192P0.991
1:52688072:C:TG115D0.991
1:52687848:C:GA190P0.990
1:52692750:C:TG75E0.989
1:52687880:C:TC179Y0.988
1:52687963:G:CF151L0.988
1:52687963:G:TF151L0.988
1:52687965:A:GF151L0.988
1:52687843:A:CS191R0.987
1:52687843:A:TS191R0.987
1:52687845:T:GS191R0.987
1:52687991:C:TC142Y0.987
1:52688073:C:GG115R0.987
1:52692751:C:GG75R0.987
1:52692751:C:TG75R0.987
1:52687797:C:GA207P0.985
1:52687893:A:GS175P0.984
1:52692791:G:CN61K0.984
1:52692791:G:TN61K0.984

dbSNP variants (sampled 300 via entrez): RS1000003548 (1:52693686 C>G,T), RS1000030772 (1:52684441 C>T), RS1000054882 (1:52694180 T>C,G), RS1000241546 (1:52687410 C>G), RS1000593398 (1:52687826 C>T), RS1000981086 (1:52689195 G>A), RS1001045285 (1:52692747 GC>G), RS1001090274 (1:52686282 C>G), RS1001192141 (1:52686621 G>C), RS1001574947 (1:52697586 T>A), RS1001852248 (1:52685244 TAA>T), RS1001893439 (1:52689208 T>G), RS1002286907 (1:52699186 G>T), RS1002577204 (1:52698920 A>G), RS1003023052 (1:52689927 T>A)

Disease associations

OMIM: gene MIM:615623 | disease phenotypes: MIM:618387

GenCC curated gene-disease

DiseaseClassificationInheritance
spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3StrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
mitochondrial diseaseDefinitiveAR

Mondo (1): spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 (MONDO:0020770)

Orphanet (0):

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0001251Ataxia
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001265Hyporeflexia
HP:0001272Cerebellar atrophy
HP:0001310Dysmetria
HP:0001337Tremor
HP:0001761Pes cavus
HP:0001765Hammertoe
HP:0002066Gait ataxia
HP:0002352Leukoencephalopathy
HP:0002460Distal muscle weakness
HP:0002936Distal sensory impairment
HP:0003236Elevated circulating creatine kinase concentration
HP:0003376Steppage gait
HP:0003477Peripheral axonal neuropathy
HP:0003677Slowly progressive
HP:0003690Limb muscle weakness
HP:0003693Distal amyotrophy
HP:0009027Foot dorsiflexor weakness
HP:0011402Demyelinating sensory neuropathy
HP:0011463Childhood onset

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression2
(+)-JQ1 compounddecreases expression2
Estradiolincreases expression2
Ethyl Methanesulfonatedecreases expression2
Methyl Methanesulfonatedecreases expression2
Oxygendecreases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
ginger extractdecreases reaction, increases abundance, increases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression, decreases reaction, increases abundance1
salinomycindecreases expression1
trichostatin Aaffects expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
nivalenolincreases expression1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
corosolic aciddecreases expression1
abrinedecreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Adeninedecreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Cisplatindecreases expression1
Colchicinedecreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dimethyl Sulfoxideincreases expression1

Clinical trials (associated diseases)

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