COQ3
protein-codingcoenzyme Q3, methyltransferase, the group of 7BS small molecule methyltransferases
Gene summary
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.[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COQ3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017421.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 51 | 3 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 54 | 4 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_059117.3 | 7 | MANE Select | |
| Ensembl | ENSP00000254759.3 | 7 | MANE Select | |
| Ensembl | ENSP00000358243.1 | 3 | Standard | |
| Ensembl | ENSP00000358243.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human)
- Ubiquinone Biosynthesis
- Metabolism
- Ubiquinol biosynthesis
- Metabolism of cofactors
Biological Process
- glycerol metabolic process
- ubiquinone biosynthetic process
- regulation of ubiquinone biosynthetic process
- methylation
Molecular Function
- hexaprenyldihydroxybenzoate methyltransferase activity
- protein binding
- O-methyltransferase activity
- 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity
- 3-demethylubiquinone-9 3-O-methyltransferase activity
Cellular Component
- mitochondrion
- mitochondrial matrix
- extrinsic component of mitochondrial inner membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254759
- Coding exons
- 7
- Length
- 24805
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125747
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0749 | 192 | 189 | 1.02 | 0.00000876 | 2373 |
| Missense (PolyPhen) | 49 | 44.046 | 1.1125 | 545 | ||
| Synonymous | -1.01 | 83 | 72.1 | 1.15 | 0.00000356 | 725 |
| Loss of Function | 0.561 | 13 | 15.4 | 0.846 | 6.48e-7 | 201 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. {ECO:0000255|HAMAP- Rule:MF_03190}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.864
- RVIS EVS
- 0.62
- RVIS percentile EVS
- 83.25
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.735
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |