COQ3

gene
On this page

Also known as bA9819.1

Summary

COQ3 (coenzyme Q3, methyltransferase, HGNC:18175) is a protein-coding gene on chromosome 6q16.2, encoding Ubiquinone biosynthesis O-methyltransferase, mitochondrial (Q9NZJ6). O-methyltransferase required for two non-consecutive steps during ubiquinone biosynthesis.

Ubiquinone, also known as coenzyme Q, or Q, is a critical component of the electron transport pathways of both eukaryotes and prokaryotes (Jonassen and Clarke, 2000 [PubMed 10777520]). This lipid consists of a hydrophobic isoprenoid tail and a quinone head group. The tail varies in length depending on the organism, but its purpose is to anchor coenzyme Q to the membrane. The quinone head group is responsible for the activity of coenzyme Q in the respiratory chain. The S. cerevisiae COQ3 gene encodes an O-methyltransferase required for 2 steps in the biosynthetic pathway of coenzyme Q. This enzyme methylates an early coenzyme Q intermediate, 3,4-dihydroxy-5-polyprenylbenzoic acid, as well as the final intermediate in the pathway, converting demethyl-ubiquinone to coenzyme Q. The COQ3 gene product is also capable of methylating the distinct prokaryotic early intermediate 2-hydroxy-6-polyprenyl phenol.

Source: NCBI Gene 51805 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 70 total — 1 likely-pathogenic
  • MANE Select transcript: NM_017421

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18175
Approved symbolCOQ3
Namecoenzyme Q3, methyltransferase
Location6q16.2
Locus typegene with protein product
StatusApproved
AliasesbA9819.1
Ensembl geneENSG00000132423
Ensembl biotypeprotein_coding
OMIM605196
Entrez51805

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000254759, ENST00000369240, ENST00000479163, ENST00000876256, ENST00000876257, ENST00000926084, ENST00000961104

RefSeq mRNA: 1 — MANE Select: NM_017421 NM_017421

CCDS: CCDS5042

Canonical transcript exons

ENST00000254759 — 7 exons

ExonStartEnd
ENSE000009040859936940199369820
ENSE000009040869937142899371587
ENSE000009040879937594099376182
ENSE000034639119939407499394195
ENSE000036124619938369899383824
ENSE000036539909938018999380341
ENSE000037305179937738699377485

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 93.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5894 / max 66.4794, expressed in 1558 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
747934.58941558

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
biceps brachiiUBERON:000150793.19gold quality
heart right ventricleUBERON:000208092.90gold quality
vastus lateralisUBERON:000137992.54gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.13gold quality
quadriceps femorisUBERON:000137791.79gold quality
heart left ventricleUBERON:000208491.47gold quality
cardiac ventricleUBERON:000208291.35gold quality
triceps brachiiUBERON:000150991.31gold quality
deltoidUBERON:000147690.22gold quality
hindlimb stylopod muscleUBERON:000425290.17gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451190.11gold quality
apex of heartUBERON:000209889.73gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.70gold quality
skeletal muscle tissueUBERON:000113489.28gold quality
left ventricle myocardiumUBERON:000656689.12gold quality
muscle organUBERON:000163089.03gold quality
skeletal muscle organUBERON:001489289.03gold quality
diaphragmUBERON:000110389.02silver quality
heartUBERON:000094888.55gold quality
muscle of legUBERON:000138388.20gold quality
muscle tissueUBERON:000238588.12gold quality
gastrocnemiusUBERON:000138887.86gold quality
myocardiumUBERON:000234987.86gold quality
right atrium auricular regionUBERON:000663187.73gold quality
cortical plateUBERON:000534387.70gold quality
gluteal muscleUBERON:000200087.48silver quality
cardiac atriumUBERON:000208187.27gold quality
mucosa of transverse colonUBERON:000499187.24gold quality
middle temporal gyrusUBERON:000277187.04gold quality
cerebellar hemisphereUBERON:000224586.87gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting COQ3, 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-7110-3P100.0073.182486
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-493-5P99.9672.472382
HSA-MIR-570-3P99.9672.414910
HSA-MIR-627-3P99.9071.423316
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-510-3P99.5470.062965
HSA-MIR-129-1-3P98.8668.41779
HSA-MIR-129-2-3P98.8668.41779
HSA-MIR-625-3P97.3266.55554

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocoq3ENSDARG00000069857
mus_musculusCoq3ENSMUSG00000028247
rattus_norvegicusCoq3ENSRNOG00000009974
drosophila_melanogasterCoq3FBGN0032922
caenorhabditis_elegansWBGENE00000763

Protein

Protein identifiers

Ubiquinone biosynthesis O-methyltransferase, mitochondrialQ9NZJ6 (reviewed: Q9NZJ6)

Alternative names: 3-demethylubiquinol 3-O-methyltransferase, 3-demethylubiquinone 3-O-methyltransferase, Polyprenyldihydroxybenzoate methyltransferase

All UniProt accessions (2): Q9NZJ6, F6WGP0

UniProt curated annotations — full annotation on UniProt →

Function. O-methyltransferase required for two non-consecutive steps during ubiquinone biosynthesis. Catalyzes the 2 O-methylation of 3,4-dihydroxy-5-(all-trans-decaprenyl)benzoic acid into 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoic acid. Also catalyzes the last step of ubiquinone biosynthesis by mediating methylation of 3-demethylubiquinone into ubiquinone. Also able to mediate the methylation of 3-demethylubiquinol-10 into ubiquinol-10.

Subunit / interactions. Component of a multi-subunit COQ enzyme complex, composed of at least COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9.

Subcellular location. Mitochondrion inner membrane.

Pathway. Cofactor biosynthesis; ubiquinone biosynthesis.

Similarity. Belongs to the class I-like SAM-binding methyltransferase superfamily. UbiG/COQ3 family.

RefSeq proteins (1): NP_059117* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010233UbiG_MeTrfaseFamily
IPR029063SAM-dependent_MTases_sfHomologous_superfamily

Pfam: PF13489

Enzyme classification (BRENDA):

  • EC 2.1.1.114 — polyprenyldihydroxybenzoate methyltransferase (BRENDA: 6 organisms, 10 substrates, 0 inhibitors, 0 Km, 0 kcat entries)
  • EC 2.1.1.222 — 2-polyprenyl-6-hydroxyphenol methylase (BRENDA: 7 organisms, 12 substrates, 0 inhibitors, 0 Km, 0 kcat entries)
  • EC 2.1.1.64 — 3-demethylubiquinol 3-O-methyltransferase (BRENDA: 5 organisms, 14 substrates, 0 inhibitors, 2 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
S-ADENOSYL-L-METHIONINE0.0221

Catalyzed reactions (Rhea), 3 shown:

  • 3-demethylubiquinol-10 + S-adenosyl-L-methionine = ubiquinol-10 + S-adenosyl-L-homocysteine + H(+) (RHEA:44412)
  • 3,4-dihydroxy-5-(all-trans-decaprenyl)benzoate + S-adenosyl-L-methionine = 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoate + S-adenosyl-L-homocysteine + H(+) (RHEA:44492)
  • a 3-demethylubiquinone + S-adenosyl-L-methionine = a ubiquinone + S-adenosyl-L-homocysteine (RHEA:81215)

UniProt features (19 total): binding site 7, sequence conflict 4, modified residue 3, sequence variant 3, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NZJ6-F171.170.43

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 (7): 124; 154; 175; 222; 223; 226; 227

Post-translational modifications (3): 149, 196, 143

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2142789Ubiquinol biosynthesis

MSigDB gene sets: 151 (showing top): HORIUCHI_WTAP_TARGETS_DN, TGCGCANK_UNKNOWN, GOBP_POLYOL_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_KETONE_METABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOCC_MITOCHONDRIAL_ENVELOPE, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_KETONE_BIOSYNTHETIC_PROCESS, WONG_MITOCHONDRIA_GENE_MODULE, GOBP_METHYLATION, GOBP_QUINONE_METABOLIC_PROCESS

GO Biological Process (3): glycerol metabolic process (GO:0006071), ubiquinone biosynthetic process (GO:0006744), methylation (GO:0032259)

GO Molecular Function (7): O-methyltransferase activity (GO:0008171), polyprenyldihydroxybenzoate methyltransferase activity (GO:0010420), 3-demethylubiquinol 3-O-methyltransferase activity (GO:0061542), 3-demethylubiquinone 3-O-methyltransferase activity (GO:0120537), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), extrinsic component of mitochondrial inner membrane (GO:0031314), ubiquinone biosynthesis complex (GO:0110142), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of cofactors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ubiquinone biosynthetic process3
S-adenosylmethionine-dependent methyltransferase activity3
O-methyltransferase activity2
carbohydrate metabolic process1
polyol metabolic process1
ubiquinone metabolic process1
quinone biosynthetic process1
metabolic process1
methyltransferase activity1
binding1
transferase activity, transferring one-carbon groups1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
mitochondrion1
intracellular organelle lumen1
mitochondrial inner membrane1
extrinsic component of organelle membrane1
catalytic complex1
cellular anatomical structure1

Protein interactions and networks

STRING

2912 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COQ3COQ9O75208984
COQ3COQ5Q5HYK3982
COQ3COQ6Q9Y2Z9976
COQ3COQ7Q99807961
COQ3COQ4Q9Y3A0953
COQ3COQ8AQ8NI60877
COQ3PDSS1Q5T2R2864
COQ3COQ8BQ96D53858
COQ3COQ2Q96H96856
COQ3PDSS2Q86YH6794
COQ3COQ10AQ96MF6728
COQ3NDUFA9Q16795693
COQ3COQ10BQ9H8M1679
COQ3ADCK2Q7Z695638
COQ3ADCK1Q86TW2619

IntAct

49 interactions, top by confidence:

ABTypeScore
COQ8ACOQ9psi-mi:“MI:0914”(association)0.670
COQ3COQ7psi-mi:“MI:0407”(direct interaction)0.590
COQ7COQ3psi-mi:“MI:0407”(direct interaction)0.590
COQ9COQ5psi-mi:“MI:0915”(physical association)0.590
COQ7COQ9psi-mi:“MI:0915”(physical association)0.590
COQ5COQ9psi-mi:“MI:0914”(association)0.590
PTPN9COQ3psi-mi:“MI:0915”(physical association)0.560
SNX1COQ3psi-mi:“MI:0915”(physical association)0.560
TTPACOQ3psi-mi:“MI:0915”(physical association)0.560
COQ3NDRG4psi-mi:“MI:0915”(physical association)0.560
COQ3COQ4psi-mi:“MI:0407”(direct interaction)0.520
COQ3COQ5psi-mi:“MI:0407”(direct interaction)0.520
COQ3COQ6psi-mi:“MI:0407”(direct interaction)0.520
COQ4COQ3psi-mi:“MI:0407”(direct interaction)0.520
COQ5COQ3psi-mi:“MI:0407”(direct interaction)0.520
COQ6COQ3psi-mi:“MI:0407”(direct interaction)0.520
COQ4COQ5psi-mi:“MI:0914”(association)0.520
COQ3NFS1psi-mi:“MI:0915”(physical association)0.500
COQ3COQ9psi-mi:“MI:0914”(association)0.500
COQ4COQ9psi-mi:“MI:0914”(association)0.500
COQ3VPS28psi-mi:“MI:0915”(physical association)0.400
ECE1COQ3psi-mi:“MI:0915”(physical association)0.370
COQ5ACOT7psi-mi:“MI:0914”(association)0.350
COQ9NDUFS8psi-mi:“MI:0914”(association)0.350
COQ3COQ8Bpsi-mi:“MI:0914”(association)0.350

BioGRID (62): VPS28 (Affinity Capture-MS), COQ3 (Co-fractionation), COQ3 (Co-fractionation), NOVA1 (Co-fractionation), COQ6 (Reconstituted Complex), COQ3 (Reconstituted Complex), COQ3 (Affinity Capture-MS), COQ3 (Affinity Capture-MS), COQ3 (Affinity Capture-MS), COQ3 (Affinity Capture-MS), NFS1 (Affinity Capture-MS), COQ9 (Affinity Capture-MS), COQ3 (Affinity Capture-MS), COQ5 (Affinity Capture-MS), COQ6 (Affinity Capture-MS)

ESM2 similar proteins: A0A067XMT3, A0A075D5I4, A0A075D654, A0A075D657, A0A075D6M1, A0A1B4XBK1, A0A1B5L8S2, A0A1D6NER6, A0A1W5SKE9, A0A2I2F2M2, A0A411KUP5, A0A482NB13, A0A8X8M4T9, A0A8X8M4W6, A0A8X8M501, A0A8X8M505, A2XMJ1, C8YTM5, F4J2K2, F4K2A1, H2E7T5, H2E7T6, H2E7T7, H2E7T8, H2E7T9, H2E7U0, O49196, O81027, P74388, P9WEU0, Q03606, Q05763, Q0CXW9, Q0UI02, Q0WVD6, Q1JPN0, Q38932, Q3T131, Q6ZIK0, Q7X7H9

Diamond homologs: A1K8Q1, A1U3K1, A1URT5, A3PNM3, A4JCG7, A4SM99, A4VLX7, A4WW91, A4YKT6, A5VSK3, A5W7G3, A6UCF6, A6V2Q4, A6WXQ0, A7HTX8, A8HVC4, A8LQ43, A9ADW3, A9IQF4, A9M8K8, B0CIC6, B0KTX4, B0SW81, B0U3W1, B0UAV0, B1J5G4, B1Y2L3, B1YV26, B2I705, B2JEZ6, B2S828, B3H0C8, B3PP83, B3QCF3, B5ZRR7, B7V9J5, B8EI29, B8H209, B8IUB0, B9JB78

SIGNOR signaling

1 interactions.

AEffectBMechanism
COQ3“form complex”“CoQ biosynthetic complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 22 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
ubiquinone biosynthetic process7327.7×3e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance49
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1807771GRCh37/hg19 6q16.1-16.2(chr6:97904220-99964434)x1Likely pathogenic

SpliceAI

1532 predictions. Top by Δscore:

VariantEffectΔscore
6:99371426:A:ACdonor_gain1.0000
6:99371427:C:CCdonor_gain1.0000
6:99375938:A:ACdonor_gain1.0000
6:99375939:C:CCdonor_gain1.0000
6:99369817:CCAT:Cacceptor_gain0.9900
6:99369818:CAT:Cacceptor_gain0.9900
6:99369818:CATC:Cacceptor_gain0.9900
6:99371420:ATACT:Adonor_loss0.9900
6:99371421:TACTT:Tdonor_loss0.9900
6:99371422:ACTTA:Adonor_loss0.9900
6:99371423:CTT:Cdonor_loss0.9900
6:99371424:TTAC:Tdonor_loss0.9900
6:99371425:TACTT:Tdonor_loss0.9900
6:99371427:CTTGA:Cdonor_gain0.9900
6:99375941:TTTA:Tdonor_gain0.9900
6:99375983:A:Cdonor_gain0.9900
6:99376001:T:TAdonor_gain0.9900
6:99377384:A:ACdonor_gain0.9900
6:99377385:C:CCdonor_gain0.9900
6:99377485:CCT:Cacceptor_gain0.9900
6:99377491:T:Cacceptor_gain0.9900
6:99377491:T:TCacceptor_gain0.9900
6:99380240:C:CAdonor_gain0.9900
6:99383821:TAAA:Tacceptor_gain0.9900
6:99383825:C:CCacceptor_gain0.9900
6:99369821:C:CAacceptor_loss0.9800
6:99369821:C:CCacceptor_gain0.9800
6:99371427:CTT:Cdonor_gain0.9800
6:99371583:CCGGG:Cacceptor_gain0.9800
6:99371584:CGGGC:Cacceptor_gain0.9800

AlphaMissense

2394 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:99376172:C:GR166P0.989
6:99380203:C:AR124S0.987
6:99380203:C:GR124S0.987
6:99380251:C:AW108C0.987
6:99380251:C:GW108C0.987
6:99376151:C:TG173E0.985
6:99380256:A:GW107R0.984
6:99380256:A:TW107R0.984
6:99369731:C:GA327P0.982
6:99377409:A:GC155R0.982
6:99376013:A:TV219D0.980
6:99376157:A:TV171D0.980
6:99380204:C:GR124T0.980
6:99377407:A:CC155W0.979
6:99380253:A:GW108R0.979
6:99380253:A:TW108R0.979
6:99376110:G:CH187D0.978
6:99376118:G:TA184E0.977
6:99377399:C:TG158E0.977
6:99369730:G:TA327E0.976
6:99380212:A:CN121K0.976
6:99380212:A:TN121K0.976
6:99371448:A:GL290P0.975
6:99377411:C:TG154D0.975
6:99376001:T:AE223V0.974
6:99377420:A:GL151P0.974
6:99380254:C:AW107C0.974
6:99380254:C:GW107C0.974
6:99369764:A:GW316R0.973
6:99369764:A:TW316R0.973

dbSNP variants (sampled 300 via entrez): RS1000078027 (6:99371394 C>T), RS1000131477 (6:99370953 A>C), RS1000228330 (6:99389272 C>A,T), RS1000381799 (6:99395205 T>C,G), RS1000452915 (6:99375721 A>G), RS1000578907 (6:99389559 C>A), RS1000640560 (6:99383270 A>G), RS1000646030 (6:99395448 A>T), RS1000852580 (6:99389411 C>T), RS1000881938 (6:99382240 T>C), RS1000916744 (6:99376927 C>A,T), RS1001089271 (6:99369634 G>C), RS1001141652 (6:99369281 A>C), RS1001245258 (6:99384544 T>C), RS1001253539 (6:99390464 G>T)

Disease associations

OMIM: gene MIM:605196 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006922_14Regular attendance at a religious group2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009592social interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs11548336COQ30.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Cadmium Chlorideincreases expression, decreases expression, increases abundance2
Particulate Matterincreases abundance, affects cotreatment, decreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
quercitrindecreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
Sunitinibdecreases expression1
Zoledronic Aciddecreases expression1
Vorinostatincreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases expression, affects cotreatment, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1
Calcitrioldecreases expression, affects cotreatment1
Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazonedecreases expression1
Cisplatinincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Oxygendecreases expression1
Polycyclic Aromatic Hydrocarbonsincreases abundance, affects cotreatment, decreases expression1
Quercetindecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E1UAHAP1 COQ3 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.