{"gene":"COQ6","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2003,"finding":"COQ6 encodes a flavin-dependent monooxygenase that localizes to mitochondria; the Coq6 polypeptide is imported into mitochondria in a membrane potential-dependent manner and functions as a peripheral membrane protein on the matrix side of the inner mitochondrial membrane. coq6 mutants accumulate the Q biosynthetic intermediate 3-hexaprenyl-4-hydroxybenzoic acid, establishing COQ6 as required for a step after that intermediate in the CoQ biosynthesis pathway.","method":"Functional complementation cloning, mitochondrial import assay, submitochondrial fractionation, metabolic intermediate accumulation analysis in yeast","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (complementation, fractionation, import assay, metabolite profiling) in a single focused study establishing subcellular localization and pathway position","pmids":["12721307"],"is_preprint":false},{"year":2011,"finding":"Coq6 is required exclusively for the C5-hydroxylation reaction in CoQ biosynthesis. The ferredoxin Yah1 and ferredoxin reductase Arh1 serve as the in vivo electron donors for Coq6. Hydroxylated analogs of 4-hydroxybenzoic acid (vanillic acid or 3,4-dihydroxybenzoic acid) can bypass Coq6 deficiency and restore Q biosynthesis and respiration in coq6 yeast mutants.","method":"Yeast genetic complementation, metabolic labeling, bypass assay with substrate analogs, in vivo functional assay with electron donor mutants","journal":"Chemistry & biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — biochemical reaction assignment with genetic epistasis through electron donor mutants and bypass rescue, replicated across multiple experimental approaches","pmids":["21944752"],"is_preprint":false},{"year":2011,"finding":"COQ6 is a monooxygenase responsible for the C5-hydroxylation step of CoQ biosynthesis; human COQ6 mutations fail to complement coq6-deficient yeast, demonstrating loss of function. In podocytes, COQ6 localizes to cell processes and the Golgi apparatus; in the inner ear it localizes to stria vascularis cells. Knockdown of Coq6 in podocyte cell lines and zebrafish causes apoptosis partially reversed by CoQ10 treatment.","method":"Yeast complementation assay, siRNA knockdown in podocyte cell lines, zebrafish morpholino knockdown, immunolocalization in rat tissue, CoQ10 rescue experiment","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (yeast complementation, cell line KD, zebrafish KD, tissue localization, pharmacological rescue) across vertebrate models","pmids":["21540551"],"is_preprint":false},{"year":2013,"finding":"Human COQ6 isoform a can partially complement coq6-deficient yeast, while isoform b (lacking part of the FAD-binding domain) is enzymatically inactive but partially stable and may have a regulatory/inhibitory function. Most patient-derived COQ6 mutations retain residual enzymatic activity (hypomorphic alleles), and mutant COQ6 proteins allow assembly of the CoQ biosynthetic complex. Vanillic acid and 3,4-dihydroxybenzoic acid restore respiratory growth of yeast expressing mutant human COQ6.","method":"Yeast complementation assay with human COQ6 isoforms and patient mutations, bypass rescue with hydroxylated precursor analogs, protein stability assessment","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic functional characterization of multiple isoforms and patient alleles with complementation and rescue assays, multiple orthogonal readouts","pmids":["24140869"],"is_preprint":false},{"year":2015,"finding":"Coq6, in addition to C5-hydroxylation, catalyzes the C4-deamination reaction when para-aminobenzoic acid (pABA) is used as the CoQ precursor; this reaction requires molecular oxygen. Specific mutations in Coq6 can selectively abrogate C4-deamination while preserving C5-hydroxylation activity. Deletion of Coq9 impairs Coq6-mediated C4-deamination, indicating Coq9 impacts Coq6 function.","method":"18O2 isotope labeling experiments, site-directed mutagenesis of Coq6, yeast genetic analysis (Δcoq9), functional growth assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — isotope labeling establishing reaction mechanism, mutagenesis dissecting dual catalytic activities, genetic epistasis with COQ9","pmids":["26260787"],"is_preprint":false},{"year":2016,"finding":"Coq6 is a flavoprotein using FAD as a cofactor. Homology modeling and molecular dynamics simulations identified a putative substrate access channel for the bulky hydrophobic substrate 3-hexaprenyl-4-hydroxyphenol. Computational mutations G248R and L382E at the channel entrance partially block substrate access; the G248R-L382E double mutant completely blocks access. In vivo assays confirmed these mutations decrease or abolish enzymatic activity, consistent with the structural model.","method":"Biochemical FAD cofactor characterization, homology modeling, molecular dynamics simulation, substrate docking, in vivo functional assay of computationally predicted mutations","journal":"PLoS computational biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — FAD binding confirmed biochemically, mutagenesis validated computationally predicted channel in vivo, but structural model is homology-based not experimental","pmids":["26808124"],"is_preprint":false},{"year":2019,"finding":"CRISPR/Cas9-generated human cells lacking functional COQ6 cannot synthesize CoQ and display severe ATP deficiency and increased ROS production. These cells accumulate 3-decaprenyl-1,4-benzoquinone, indicating that in mammals the decarboxylation and C1-hydroxylation reactions occur before or independently of the C5-hydroxylation catalyzed by COQ6. Vanillic acid treatment recovers CoQ biosynthesis, ATP production, and normalizes ROS. COQ6 isoform c does not encode an active enzyme.","method":"CRISPR/Cas9 knockout in human cell line, CoQ biosynthesis measurement, ATP quantification, ROS measurement, metabolite accumulation analysis, isoform complementation assay, vanillic acid rescue","journal":"Oxidative medicine and cellular longevity","confidence":"High","confidence_rationale":"Tier 2 / Strong — human cell knockout with multiple orthogonal metabolic readouts (CoQ, ATP, ROS, metabolite intermediates) establishing reaction order in mammalian cells","pmids":["31379988"],"is_preprint":false},{"year":2019,"finding":"Podocyte-specific knockout of Coq6 in mice causes FSGS and massive proteinuria (>46-fold increase in albuminuria). COQ6 knockdown in human podocytes impairs podocyte migration rate. Treatment with 2,4-dihydroxybenzoic acid (a CoQ precursor analog) prevents renal dysfunction and reverses the migration defect in both mice and cells.","method":"Conditional knockout mouse (podocyte-specific Coq6 KO), albuminuria measurement, siRNA knockdown in human podocyte cell line, podocyte migration assay, pharmacological rescue with 2,4-diHB","journal":"Journal of the American Society of Nephrology : JASN","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional KO with quantitative disease readout plus in vitro mechanistic assay and pharmacological rescue, multiple orthogonal methods","pmids":["30737270"],"is_preprint":false},{"year":2017,"finding":"In yeast, Coq7 modulates CoQ6 levels through a phosphorylation cycle regulated by the mitochondrial phosphatase Ptc7; dephosphorylation of Coq7 Ser/Thr residues by Ptc7 increases CoQ6 biosynthesis levels. A constitutively active (permanently dephosphorylated) Coq7 mutant causes 2.5-fold elevated CoQ6 levels but decreases mitochondrial respiratory chain activity and increases endogenous ROS, shortening chronological lifespan. Loss of Ptc7 reduces CoQ6 biosynthesis rate and also shortens chronological lifespan.","method":"Yeast site-directed mutagenesis (Ser/Thr to Ala in Coq7), CoQ6 level quantification, respiratory chain activity assay, ROS measurement, chronological lifespan assay, PTC7 deletion and overexpression","journal":"Microbial cell (Graz, Austria)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic manipulation of upstream regulator with direct measurement of CoQ6 levels and mitochondrial function, single lab study","pmids":["28357388"],"is_preprint":false}],"current_model":"COQ6 encodes a mitochondrial FAD-dependent flavoprotein monooxygenase that catalyzes two distinct reactions in the coenzyme Q (CoQ/ubiquinone) biosynthesis pathway: C5-hydroxylation of the benzene ring precursor and, when para-aminobenzoic acid is used as precursor, C4-deamination; it localizes to the matrix side of the inner mitochondrial membrane, receives electrons from the ferredoxin/ferredoxin reductase pair (Yah1/Arh1 in yeast), and is regulated post-translationally through the Coq7 phosphorylation cycle; loss of COQ6 in human cells abolishes CoQ synthesis, causing ATP deficiency and ROS overproduction, while bypass with hydroxylated precursor analogs (vanillic acid, 2,4-dihydroxybenzoic acid) can restore CoQ biosynthesis and rescue cellular and organismal phenotypes."},"narrative":{"mechanistic_narrative":"COQ6 encodes a mitochondrial FAD-dependent flavoprotein monooxygenase that performs ring-modification steps in coenzyme Q (ubiquinone) biosynthesis, and its loss abolishes CoQ synthesis with downstream bioenergetic failure [PMID:12721307, PMID:21944752, PMID:31379988]. The protein is imported into mitochondria in a membrane-potential-dependent manner and acts as a peripheral membrane protein on the matrix side of the inner mitochondrial membrane, where coq6 loss causes accumulation of the early intermediate 3-hexaprenyl-4-hydroxybenzoic acid [PMID:12721307]. Its principal catalytic role is the C5-hydroxylation of the CoQ benzene-ring precursor, receiving electrons in vivo from the ferredoxin/ferredoxin reductase pair Yah1/Arh1, and it additionally catalyzes an oxygen-dependent C4-deamination when para-aminobenzoic acid serves as precursor — two activities separable by point mutations and modulated by Coq9 [PMID:21944752, PMID:26260787]. Substrate handling depends on a hydrophobic access channel for the bulky prenylated substrate, and enzymatic function requires the FAD cofactor [PMID:26808124]. In human cells, COQ6 knockout abolishes CoQ, producing ATP deficiency and ROS overproduction with accumulation of 3-decaprenyl-1,4-benzoquinone, indicating that decarboxylation and C1-hydroxylation precede the COQ6-catalyzed C5-hydroxylation in mammals [PMID:31379988]. Loss-of-function COQ6 mutations cause a CoQ-deficiency disease presenting as steroid-resistant nephrotic syndrome/FSGS with sensorineural deafness, with COQ6 acting in podocytes and inner-ear stria vascularis; podocyte-specific deletion in mice produces FSGS and massive proteinuria [PMID:21540551, PMID:30737270]. Across yeast, cultured human cells, and mouse models, hydroxylated precursor analogs (vanillic acid, 3,4-dihydroxybenzoic acid, 2,4-dihydroxybenzoic acid) bypass COQ6 deficiency and restore CoQ biosynthesis, respiration, and organ function [PMID:21944752, PMID:24140869, PMID:31379988, PMID:30737270].","teleology":[{"year":2003,"claim":"Established that COQ6 is a flavin-dependent monooxygenase required for CoQ biosynthesis and pinned its position downstream of the 3-hexaprenyl-4-hydroxybenzoic acid intermediate, defining where in the pathway it acts.","evidence":"Functional complementation cloning, mitochondrial import and submitochondrial fractionation, and metabolite accumulation analysis in yeast","pmids":["12721307"],"confidence":"High","gaps":["Did not assign the specific chemical reaction catalyzed","Electron donors not identified"]},{"year":2011,"claim":"Resolved COQ6's specific reaction as the C5-hydroxylation step and identified its in vivo electron donors, also showing that hydroxylated precursor analogs bypass the deficiency.","evidence":"Yeast genetic complementation, metabolic labeling, bypass assays with substrate analogs, and electron-donor mutant analysis","pmids":["21944752"],"confidence":"High","gaps":["Direct in vitro reconstitution of the hydroxylase reaction not reported","Did not address additional catalytic activities"]},{"year":2011,"claim":"Connected human COQ6 loss-of-function to disease by showing patient mutations fail to complement yeast and cause podocyte/zebrafish apoptosis rescuable by CoQ10, establishing a CoQ-deficiency nephropathy with cochlear involvement.","evidence":"Yeast complementation of patient alleles, siRNA and zebrafish morpholino knockdown, tissue immunolocalization, and CoQ10 rescue","pmids":["21540551"],"confidence":"High","gaps":["Reported Golgi/cell-process localization in podocytes alongside mitochondrial role not mechanistically reconciled","Genotype-phenotype correlation across alleles incomplete"]},{"year":2013,"claim":"Characterized human COQ6 isoforms and patient alleles, showing most disease mutations are hypomorphic and that an FAD-domain-truncated isoform is inactive, clarifying residual-activity biology and rescue potential.","evidence":"Yeast complementation with human isoforms and patient mutations, protein stability assessment, and analog bypass rescue","pmids":["24140869"],"confidence":"High","gaps":["Proposed regulatory/inhibitory role of inactive isoform b not directly demonstrated","Endogenous human isoform abundances not quantified"]},{"year":2015,"claim":"Demonstrated a second catalytic activity—oxygen-dependent C4-deamination on the pABA-derived precursor—separable from C5-hydroxylation by mutation and influenced by Coq9, expanding COQ6 to a bifunctional enzyme.","evidence":"18O2 isotope labeling, site-directed mutagenesis dissecting the two activities, and Δcoq9 genetic epistasis in yeast","pmids":["26260787"],"confidence":"High","gaps":["Molecular basis of Coq9 influence on COQ6 not defined","Relevance of C4-deamination in mammals using pABA not established"]},{"year":2016,"claim":"Provided a structural rationale for substrate handling by modeling a hydrophobic access channel and validating channel-blocking mutations in vivo, linking enzyme architecture to function.","evidence":"Biochemical FAD cofactor characterization, homology modeling, molecular dynamics with substrate docking, and in vivo assays of predicted mutations","pmids":["26808124"],"confidence":"Medium","gaps":["No experimental structure; model is homology-based","Channel and catalytic mechanism not confirmed by crystallography or cryo-EM"]},{"year":2017,"claim":"Identified post-translational regulation of CoQ output via a Coq7 phosphorylation cycle controlled by the phosphatase Ptc7, linking COQ6/CoQ levels to mitochondrial function and lifespan.","evidence":"Yeast Ser/Thr mutagenesis of Coq7, CoQ6 quantification, respiratory and ROS assays, and PTC7 deletion/overexpression","pmids":["28357388"],"confidence":"Medium","gaps":["Regulation acts on Coq7 rather than direct COQ6 modification","Single-lab yeast study; mammalian conservation untested"]},{"year":2019,"claim":"Defined the mammalian reaction order and bioenergetic consequences of COQ6 loss using human knockouts, showing intermediate accumulation, ATP deficiency, ROS rise, and analog rescue.","evidence":"CRISPR/Cas9 knockout in human cells with CoQ, ATP, ROS, and metabolite measurements plus vanillic acid rescue","pmids":["31379988"],"confidence":"High","gaps":["Enzymes for the upstream decarboxylation/C1-hydroxylation not assigned here","In vitro enzymatic kinetics not measured"]},{"year":2019,"claim":"Established organ-level causality and a non-canonical podocyte phenotype by showing podocyte-specific Coq6 deletion causes FSGS/proteinuria and a migration defect, both rescued by 2,4-dihydroxybenzoic acid.","evidence":"Podocyte-specific conditional knockout mice with albuminuria readout, human podocyte knockdown migration assay, and 2,4-diHB pharmacological rescue","pmids":["30737270"],"confidence":"High","gaps":["Mechanism linking CoQ deficiency to impaired podocyte migration not resolved","Hearing phenotype not addressed in this model"]},{"year":null,"claim":"How COQ6's two catalytic activities and its substrate channel are coordinated within the CoQ biosynthetic complex, and the molecular basis of Coq9-dependent regulation, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No experimental atomic structure of COQ6","Direct enzymatic reconstitution and kinetics absent","Mechanism of Coq9 modulation undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[0,1,4,6]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1,6]}],"complexes":["CoQ biosynthetic complex"],"partners":["COQ9","COQ7","YAH1","ARH1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2Z9","full_name":"Ubiquinone biosynthesis monooxygenase COQ6, mitochondrial","aliases":["2-methoxy-6-polyprenolphenol 4-hydroxylase","Coenzyme Q10 monooxygenase 6"],"length_aa":468,"mass_kda":50.9,"function":"FAD-dependent monooxygenase required for two non-consecutive steps during ubiquinone biosynthesis (PubMed:26260787, PubMed:38425362). Required for the C5-ring hydroxylation during ubiquinone biosynthesis by catalyzing the hydroxylation of 4-hydroxy-3-(all-trans-decaprenyl)benzoic acid to 3,4-dihydroxy-5-(all-trans-decaprenyl)benzoic acid (PubMed:26260787, PubMed:38425362). Also acts downstream of COQ4, for the C1-hydroxylation during ubiquinone biosynthesis by catalyzing the hydroxylation of 2-methoxy-6-(all-trans-decaprenyl)phenol to 2-methoxy-6-(all-trans-decaprenyl)benzene-1,4-diol (PubMed:38425362). The electrons required for the hydroxylation reaction are funneled indirectly to COQ6 from NADPH via a ferredoxin/ferredoxin reductase system composed of FDX2 and FDXR (PubMed:26260787, PubMed:38425362)","subcellular_location":"Mitochondrion inner membrane; Golgi apparatus; Cell projection","url":"https://www.uniprot.org/uniprotkb/Q9Y2Z9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/COQ6","classification":"Not Classified","n_dependent_lines":44,"n_total_lines":1208,"dependency_fraction":0.03642384105960265},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/COQ6","total_profiled":1310},"omim":[{"mim_id":"615567","title":"COENZYME Q8B; COQ8B","url":"https://www.omim.org/entry/615567"},{"mim_id":"614650","title":"COENZYME Q10 DEFICIENCY, PRIMARY, 6; COQ10D6","url":"https://www.omim.org/entry/614650"},{"mim_id":"614647","title":"COENZYME Q6, MONOOXYGENASE; COQ6","url":"https://www.omim.org/entry/614647"},{"mim_id":"607426","title":"COENZYME Q10 DEFICIENCY, PRIMARY, 1; COQ10D1","url":"https://www.omim.org/entry/607426"},{"mim_id":"162091","title":"SCHWANNOMATOSIS 1; SWN1","url":"https://www.omim.org/entry/162091"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/COQ6"},"hgnc":{"alias_symbol":["CGI-10"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2Z9","domains":[{"cath_id":"3.50.50.60","chopping":"35-468","consensus_level":"medium","plddt":87.581,"start":35,"end":468}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2Z9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2Z9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2Z9-F1-predicted_aligned_error_v6.png","plddt_mean":83.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=COQ6","jax_strain_url":"https://www.jax.org/strain/search?query=COQ6"},"sequence":{"accession":"Q9Y2Z9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2Z9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2Z9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2Z9"}},"corpus_meta":[{"pmid":"21540551","id":"PMC_21540551","title":"COQ6 mutations in human patients produce nephrotic syndrome with sensorineural deafness.","date":"2011","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/21540551","citation_count":299,"is_preprint":false},{"pmid":"21944752","id":"PMC_21944752","title":"Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency.","date":"2011","source":"Chemistry & biology","url":"https://pubmed.ncbi.nlm.nih.gov/21944752","citation_count":97,"is_preprint":false},{"pmid":"24140869","id":"PMC_24140869","title":"Effect of vanillic acid on COQ6 mutants identified in patients with coenzyme Q10 deficiency.","date":"2013","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/24140869","citation_count":69,"is_preprint":false},{"pmid":"12721307","id":"PMC_12721307","title":"The Saccharomyces cerevisiae COQ6 gene encodes a mitochondrial flavin-dependent monooxygenase required for coenzyme Q biosynthesis.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12721307","citation_count":62,"is_preprint":false},{"pmid":"30737270","id":"PMC_30737270","title":"Treatment with 2,4-Dihydroxybenzoic Acid Prevents FSGS Progression and Renal Fibrosis in Podocyte-Specific Coq6 Knockout Mice.","date":"2019","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/30737270","citation_count":45,"is_preprint":false},{"pmid":"31379988","id":"PMC_31379988","title":"Vanillic Acid Restores Coenzyme Q Biosynthesis and ATP Production in Human Cells Lacking COQ6.","date":"2019","source":"Oxidative medicine and cellular longevity","url":"https://pubmed.ncbi.nlm.nih.gov/31379988","citation_count":44,"is_preprint":false},{"pmid":"28117207","id":"PMC_28117207","title":"COQ6 Mutations in Children With Steroid-Resistant Focal Segmental Glomerulosclerosis and Sensorineural Hearing Loss.","date":"2017","source":"American journal of kidney diseases : the official journal of the National Kidney Foundation","url":"https://pubmed.ncbi.nlm.nih.gov/28117207","citation_count":40,"is_preprint":false},{"pmid":"26260787","id":"PMC_26260787","title":"Coq6 is responsible for the C4-deamination reaction in coenzyme Q biosynthesis in Saccharomyces cerevisiae.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26260787","citation_count":39,"is_preprint":false},{"pmid":"24763291","id":"PMC_24763291","title":"A germline missense mutation in COQ6 is associated with susceptibility to familial schwannomatosis.","date":"2014","source":"Genetics in medicine : official journal of the American College of Medical Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24763291","citation_count":20,"is_preprint":false},{"pmid":"30232548","id":"PMC_30232548","title":"CoQ10-related sustained remission of proteinuria in a child with COQ6 glomerulopathy-a case report.","date":"2018","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/30232548","citation_count":19,"is_preprint":false},{"pmid":"28357388","id":"PMC_28357388","title":"Balanced CoQ6 biosynthesis is required for lifespan and mitophagy in yeast.","date":"2017","source":"Microbial cell (Graz, Austria)","url":"https://pubmed.ncbi.nlm.nih.gov/28357388","citation_count":16,"is_preprint":false},{"pmid":"32685349","id":"PMC_32685349","title":"COQ6 mutation in patients with nephrotic syndrome, sensorineural deafness, and optic atrophy.","date":"2020","source":"JIMD reports","url":"https://pubmed.ncbi.nlm.nih.gov/32685349","citation_count":15,"is_preprint":false},{"pmid":"28173653","id":"PMC_28173653","title":"[Coenzyme Q(10) treatment for one child with COQ6 gene mutation induced nephrotic syndrome and literature review].","date":"2017","source":"Zhonghua er ke za zhi = Chinese journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/28173653","citation_count":12,"is_preprint":false},{"pmid":"30584653","id":"PMC_30584653","title":"Pair analysis and custom array CGH can detect a small copy number variation in COQ6 gene.","date":"2018","source":"Clinical and experimental nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/30584653","citation_count":12,"is_preprint":false},{"pmid":"35111204","id":"PMC_35111204","title":"A Family Segregating Lethal Primary Coenzyme Q10 Deficiency Due to Two Novel COQ6 Variants.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35111204","citation_count":10,"is_preprint":false},{"pmid":"26808124","id":"PMC_26808124","title":"Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6.","date":"2016","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/26808124","citation_count":10,"is_preprint":false},{"pmid":"21944743","id":"PMC_21944743","title":"Coq6 hydroxylase: unmasked and bypassed.","date":"2011","source":"Chemistry & biology","url":"https://pubmed.ncbi.nlm.nih.gov/21944743","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10189,"output_tokens":2807,"usd":0.036336,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10236,"output_tokens":3411,"usd":0.068227,"stage2_stop_reason":"end_turn"},"total_usd":0.104563,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"COQ6 encodes a flavin-dependent monooxygenase that localizes to mitochondria; the Coq6 polypeptide is imported into mitochondria in a membrane potential-dependent manner and functions as a peripheral membrane protein on the matrix side of the inner mitochondrial membrane. coq6 mutants accumulate the Q biosynthetic intermediate 3-hexaprenyl-4-hydroxybenzoic acid, establishing COQ6 as required for a step after that intermediate in the CoQ biosynthesis pathway.\",\n      \"method\": \"Functional complementation cloning, mitochondrial import assay, submitochondrial fractionation, metabolic intermediate accumulation analysis in yeast\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (complementation, fractionation, import assay, metabolite profiling) in a single focused study establishing subcellular localization and pathway position\",\n      \"pmids\": [\"12721307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Coq6 is required exclusively for the C5-hydroxylation reaction in CoQ biosynthesis. The ferredoxin Yah1 and ferredoxin reductase Arh1 serve as the in vivo electron donors for Coq6. Hydroxylated analogs of 4-hydroxybenzoic acid (vanillic acid or 3,4-dihydroxybenzoic acid) can bypass Coq6 deficiency and restore Q biosynthesis and respiration in coq6 yeast mutants.\",\n      \"method\": \"Yeast genetic complementation, metabolic labeling, bypass assay with substrate analogs, in vivo functional assay with electron donor mutants\",\n      \"journal\": \"Chemistry & biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — biochemical reaction assignment with genetic epistasis through electron donor mutants and bypass rescue, replicated across multiple experimental approaches\",\n      \"pmids\": [\"21944752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"COQ6 is a monooxygenase responsible for the C5-hydroxylation step of CoQ biosynthesis; human COQ6 mutations fail to complement coq6-deficient yeast, demonstrating loss of function. In podocytes, COQ6 localizes to cell processes and the Golgi apparatus; in the inner ear it localizes to stria vascularis cells. Knockdown of Coq6 in podocyte cell lines and zebrafish causes apoptosis partially reversed by CoQ10 treatment.\",\n      \"method\": \"Yeast complementation assay, siRNA knockdown in podocyte cell lines, zebrafish morpholino knockdown, immunolocalization in rat tissue, CoQ10 rescue experiment\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (yeast complementation, cell line KD, zebrafish KD, tissue localization, pharmacological rescue) across vertebrate models\",\n      \"pmids\": [\"21540551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Human COQ6 isoform a can partially complement coq6-deficient yeast, while isoform b (lacking part of the FAD-binding domain) is enzymatically inactive but partially stable and may have a regulatory/inhibitory function. Most patient-derived COQ6 mutations retain residual enzymatic activity (hypomorphic alleles), and mutant COQ6 proteins allow assembly of the CoQ biosynthetic complex. Vanillic acid and 3,4-dihydroxybenzoic acid restore respiratory growth of yeast expressing mutant human COQ6.\",\n      \"method\": \"Yeast complementation assay with human COQ6 isoforms and patient mutations, bypass rescue with hydroxylated precursor analogs, protein stability assessment\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic functional characterization of multiple isoforms and patient alleles with complementation and rescue assays, multiple orthogonal readouts\",\n      \"pmids\": [\"24140869\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Coq6, in addition to C5-hydroxylation, catalyzes the C4-deamination reaction when para-aminobenzoic acid (pABA) is used as the CoQ precursor; this reaction requires molecular oxygen. Specific mutations in Coq6 can selectively abrogate C4-deamination while preserving C5-hydroxylation activity. Deletion of Coq9 impairs Coq6-mediated C4-deamination, indicating Coq9 impacts Coq6 function.\",\n      \"method\": \"18O2 isotope labeling experiments, site-directed mutagenesis of Coq6, yeast genetic analysis (Δcoq9), functional growth assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — isotope labeling establishing reaction mechanism, mutagenesis dissecting dual catalytic activities, genetic epistasis with COQ9\",\n      \"pmids\": [\"26260787\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Coq6 is a flavoprotein using FAD as a cofactor. Homology modeling and molecular dynamics simulations identified a putative substrate access channel for the bulky hydrophobic substrate 3-hexaprenyl-4-hydroxyphenol. Computational mutations G248R and L382E at the channel entrance partially block substrate access; the G248R-L382E double mutant completely blocks access. In vivo assays confirmed these mutations decrease or abolish enzymatic activity, consistent with the structural model.\",\n      \"method\": \"Biochemical FAD cofactor characterization, homology modeling, molecular dynamics simulation, substrate docking, in vivo functional assay of computationally predicted mutations\",\n      \"journal\": \"PLoS computational biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — FAD binding confirmed biochemically, mutagenesis validated computationally predicted channel in vivo, but structural model is homology-based not experimental\",\n      \"pmids\": [\"26808124\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CRISPR/Cas9-generated human cells lacking functional COQ6 cannot synthesize CoQ and display severe ATP deficiency and increased ROS production. These cells accumulate 3-decaprenyl-1,4-benzoquinone, indicating that in mammals the decarboxylation and C1-hydroxylation reactions occur before or independently of the C5-hydroxylation catalyzed by COQ6. Vanillic acid treatment recovers CoQ biosynthesis, ATP production, and normalizes ROS. COQ6 isoform c does not encode an active enzyme.\",\n      \"method\": \"CRISPR/Cas9 knockout in human cell line, CoQ biosynthesis measurement, ATP quantification, ROS measurement, metabolite accumulation analysis, isoform complementation assay, vanillic acid rescue\",\n      \"journal\": \"Oxidative medicine and cellular longevity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — human cell knockout with multiple orthogonal metabolic readouts (CoQ, ATP, ROS, metabolite intermediates) establishing reaction order in mammalian cells\",\n      \"pmids\": [\"31379988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Podocyte-specific knockout of Coq6 in mice causes FSGS and massive proteinuria (>46-fold increase in albuminuria). COQ6 knockdown in human podocytes impairs podocyte migration rate. Treatment with 2,4-dihydroxybenzoic acid (a CoQ precursor analog) prevents renal dysfunction and reverses the migration defect in both mice and cells.\",\n      \"method\": \"Conditional knockout mouse (podocyte-specific Coq6 KO), albuminuria measurement, siRNA knockdown in human podocyte cell line, podocyte migration assay, pharmacological rescue with 2,4-diHB\",\n      \"journal\": \"Journal of the American Society of Nephrology : JASN\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional KO with quantitative disease readout plus in vitro mechanistic assay and pharmacological rescue, multiple orthogonal methods\",\n      \"pmids\": [\"30737270\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In yeast, Coq7 modulates CoQ6 levels through a phosphorylation cycle regulated by the mitochondrial phosphatase Ptc7; dephosphorylation of Coq7 Ser/Thr residues by Ptc7 increases CoQ6 biosynthesis levels. A constitutively active (permanently dephosphorylated) Coq7 mutant causes 2.5-fold elevated CoQ6 levels but decreases mitochondrial respiratory chain activity and increases endogenous ROS, shortening chronological lifespan. Loss of Ptc7 reduces CoQ6 biosynthesis rate and also shortens chronological lifespan.\",\n      \"method\": \"Yeast site-directed mutagenesis (Ser/Thr to Ala in Coq7), CoQ6 level quantification, respiratory chain activity assay, ROS measurement, chronological lifespan assay, PTC7 deletion and overexpression\",\n      \"journal\": \"Microbial cell (Graz, Austria)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic manipulation of upstream regulator with direct measurement of CoQ6 levels and mitochondrial function, single lab study\",\n      \"pmids\": [\"28357388\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"COQ6 encodes a mitochondrial FAD-dependent flavoprotein monooxygenase that catalyzes two distinct reactions in the coenzyme Q (CoQ/ubiquinone) biosynthesis pathway: C5-hydroxylation of the benzene ring precursor and, when para-aminobenzoic acid is used as precursor, C4-deamination; it localizes to the matrix side of the inner mitochondrial membrane, receives electrons from the ferredoxin/ferredoxin reductase pair (Yah1/Arh1 in yeast), and is regulated post-translationally through the Coq7 phosphorylation cycle; loss of COQ6 in human cells abolishes CoQ synthesis, causing ATP deficiency and ROS overproduction, while bypass with hydroxylated precursor analogs (vanillic acid, 2,4-dihydroxybenzoic acid) can restore CoQ biosynthesis and rescue cellular and organismal phenotypes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COQ6 encodes a mitochondrial FAD-dependent flavoprotein monooxygenase that performs ring-modification steps in coenzyme Q (ubiquinone) biosynthesis, and its loss abolishes CoQ synthesis with downstream bioenergetic failure [#0, #1, #6]. The protein is imported into mitochondria in a membrane-potential-dependent manner and acts as a peripheral membrane protein on the matrix side of the inner mitochondrial membrane, where coq6 loss causes accumulation of the early intermediate 3-hexaprenyl-4-hydroxybenzoic acid [#0]. Its principal catalytic role is the C5-hydroxylation of the CoQ benzene-ring precursor, receiving electrons in vivo from the ferredoxin/ferredoxin reductase pair Yah1/Arh1, and it additionally catalyzes an oxygen-dependent C4-deamination when para-aminobenzoic acid serves as precursor — two activities separable by point mutations and modulated by Coq9 [#1, #4]. Substrate handling depends on a hydrophobic access channel for the bulky prenylated substrate, and enzymatic function requires the FAD cofactor [#5]. In human cells, COQ6 knockout abolishes CoQ, producing ATP deficiency and ROS overproduction with accumulation of 3-decaprenyl-1,4-benzoquinone, indicating that decarboxylation and C1-hydroxylation precede the COQ6-catalyzed C5-hydroxylation in mammals [#6]. Loss-of-function COQ6 mutations cause a CoQ-deficiency disease presenting as steroid-resistant nephrotic syndrome/FSGS with sensorineural deafness, with COQ6 acting in podocytes and inner-ear stria vascularis; podocyte-specific deletion in mice produces FSGS and massive proteinuria [#2, #7]. Across yeast, cultured human cells, and mouse models, hydroxylated precursor analogs (vanillic acid, 3,4-dihydroxybenzoic acid, 2,4-dihydroxybenzoic acid) bypass COQ6 deficiency and restore CoQ biosynthesis, respiration, and organ function [#1, #3, #6, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that COQ6 is a flavin-dependent monooxygenase required for CoQ biosynthesis and pinned its position downstream of the 3-hexaprenyl-4-hydroxybenzoic acid intermediate, defining where in the pathway it acts.\",\n      \"evidence\": \"Functional complementation cloning, mitochondrial import and submitochondrial fractionation, and metabolite accumulation analysis in yeast\",\n      \"pmids\": [\"12721307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not assign the specific chemical reaction catalyzed\", \"Electron donors not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved COQ6's specific reaction as the C5-hydroxylation step and identified its in vivo electron donors, also showing that hydroxylated precursor analogs bypass the deficiency.\",\n      \"evidence\": \"Yeast genetic complementation, metabolic labeling, bypass assays with substrate analogs, and electron-donor mutant analysis\",\n      \"pmids\": [\"21944752\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct in vitro reconstitution of the hydroxylase reaction not reported\", \"Did not address additional catalytic activities\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connected human COQ6 loss-of-function to disease by showing patient mutations fail to complement yeast and cause podocyte/zebrafish apoptosis rescuable by CoQ10, establishing a CoQ-deficiency nephropathy with cochlear involvement.\",\n      \"evidence\": \"Yeast complementation of patient alleles, siRNA and zebrafish morpholino knockdown, tissue immunolocalization, and CoQ10 rescue\",\n      \"pmids\": [\"21540551\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reported Golgi/cell-process localization in podocytes alongside mitochondrial role not mechanistically reconciled\", \"Genotype-phenotype correlation across alleles incomplete\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Characterized human COQ6 isoforms and patient alleles, showing most disease mutations are hypomorphic and that an FAD-domain-truncated isoform is inactive, clarifying residual-activity biology and rescue potential.\",\n      \"evidence\": \"Yeast complementation with human isoforms and patient mutations, protein stability assessment, and analog bypass rescue\",\n      \"pmids\": [\"24140869\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Proposed regulatory/inhibitory role of inactive isoform b not directly demonstrated\", \"Endogenous human isoform abundances not quantified\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated a second catalytic activity—oxygen-dependent C4-deamination on the pABA-derived precursor—separable from C5-hydroxylation by mutation and influenced by Coq9, expanding COQ6 to a bifunctional enzyme.\",\n      \"evidence\": \"18O2 isotope labeling, site-directed mutagenesis dissecting the two activities, and Δcoq9 genetic epistasis in yeast\",\n      \"pmids\": [\"26260787\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of Coq9 influence on COQ6 not defined\", \"Relevance of C4-deamination in mammals using pABA not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Provided a structural rationale for substrate handling by modeling a hydrophobic access channel and validating channel-blocking mutations in vivo, linking enzyme architecture to function.\",\n      \"evidence\": \"Biochemical FAD cofactor characterization, homology modeling, molecular dynamics with substrate docking, and in vivo assays of predicted mutations\",\n      \"pmids\": [\"26808124\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No experimental structure; model is homology-based\", \"Channel and catalytic mechanism not confirmed by crystallography or cryo-EM\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identified post-translational regulation of CoQ output via a Coq7 phosphorylation cycle controlled by the phosphatase Ptc7, linking COQ6/CoQ levels to mitochondrial function and lifespan.\",\n      \"evidence\": \"Yeast Ser/Thr mutagenesis of Coq7, CoQ6 quantification, respiratory and ROS assays, and PTC7 deletion/overexpression\",\n      \"pmids\": [\"28357388\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Regulation acts on Coq7 rather than direct COQ6 modification\", \"Single-lab yeast study; mammalian conservation untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the mammalian reaction order and bioenergetic consequences of COQ6 loss using human knockouts, showing intermediate accumulation, ATP deficiency, ROS rise, and analog rescue.\",\n      \"evidence\": \"CRISPR/Cas9 knockout in human cells with CoQ, ATP, ROS, and metabolite measurements plus vanillic acid rescue\",\n      \"pmids\": [\"31379988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Enzymes for the upstream decarboxylation/C1-hydroxylation not assigned here\", \"In vitro enzymatic kinetics not measured\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established organ-level causality and a non-canonical podocyte phenotype by showing podocyte-specific Coq6 deletion causes FSGS/proteinuria and a migration defect, both rescued by 2,4-dihydroxybenzoic acid.\",\n      \"evidence\": \"Podocyte-specific conditional knockout mice with albuminuria readout, human podocyte knockdown migration assay, and 2,4-diHB pharmacological rescue\",\n      \"pmids\": [\"30737270\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking CoQ deficiency to impaired podocyte migration not resolved\", \"Hearing phenotype not addressed in this model\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COQ6's two catalytic activities and its substrate channel are coordinated within the CoQ biosynthetic complex, and the molecular basis of Coq9-dependent regulation, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No experimental atomic structure of COQ6\", \"Direct enzymatic reconstitution and kinetics absent\", \"Mechanism of Coq9 modulation undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [0, 1, 4, 6]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1, 6]}\n    ],\n    \"complexes\": [\"CoQ biosynthetic complex\"],\n    \"partners\": [\"COQ9\", \"COQ7\", \"YAH1\", \"ARH1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}