ACOX3
protein-codingacyl-CoA oxidase 3, pristanoyl
Gene summary
Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~74.4 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 ACOX3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003501.3. 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 | 2 | 9 | 2 | 13 | ||
| missense | 151 | 11 | 3 | 165 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 155 | 20 | 5 | 180 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003492.2 | 17 | MANE Select | |
| Ensembl | ENSP00000348775.4 | 17 | MANE Select | |
| RefSeq | NP_001095137.1 | 15 | Standard | |
| RefSeq | NP_001362712.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Biosynthesis of unsaturated fatty acids - Homo sapiens (human)
- Fatty acid degradation - Homo sapiens (human)
- cAMP signaling pathway - Homo sapiens (human)
- alpha-Linolenic acid metabolism - Homo sapiens (human)
Biological Process
- protein targeting to peroxisome
- fatty acid beta-oxidation using acyl-CoA oxidase
- lipid homeostasis
Molecular Function
- acyl-CoA oxidase activity
- signaling receptor binding
- fatty acid binding
- pristanoyl-CoA oxidase activity
- flavin adenine dinucleotide binding
Cellular Component
- peroxisome
- peroxisomal matrix
- cytosol
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356406
- Coding exons
- 17
- Length
- 74442
- Individuals with no LoFs
- 125484
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 263
- Defined
- 125748
- p
- 0.00105
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.445 | 469 | 443 | 1.06 | 0.0000289 | 4483 |
| Missense (PolyPhen) | 133 | 125.42 | 1.0604 | 1275 | ||
| Synonymous | -0.941 | 205 | 189 | 1.09 | 0.0000135 | 1433 |
| Loss of Function | 1.25 | 28 | 36.1 | 0.775 | 0.00000186 | 410 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.00046 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0091 | 0.0076 | notable |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.00061 | 0.00060 | rare |
| South Asian | 0.00034 | 0.00033 | rare |
| Other | 0.00093 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Oxidizes the CoA-esters of 2-methyl-branched fatty acids. {ECO:0000250, ECO:0000269|PubMed:9271077}.;
Recessive Scores
- pRec
- 0.634
Intolerance Scores
- LoFtool
- 0.188
- RVIS EVS
- -0.79
- RVIS percentile EVS
- 12.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.828
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |