BCO2
protein-codingbeta-carotene oxygenase 2
Gene summary
This gene encodes an enzyme which oxidizes carotenoids such as beta-carotene during the biosynthesis of vitamin A. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
- BCDO2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.2 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 BCO2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031938.7. 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 | ||||
| missense | 73 | 7 | 80 | |||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 77 | 9 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_114144.5 | 12 | MANE Select | |
| Ensembl | ENSP00000350314.5 | 12 | MANE Select | |
| RefSeq | NP_001032367.3 | 11 | Standard | |
| RefSeq | NP_001243326.2 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin A and Carotenoid Metabolism
- Signaling by GPCR
- Signal Transduction
- Metabolism of fat-soluble vitamins
- Metabolism
Biological Process
- retinoid metabolic process
- carotenoid metabolic process
- carotene metabolic process
- carotene catabolic process
- xanthophyll metabolic process
Molecular Function
- beta-carotene 15,15'-monooxygenase activity
- retinal isomerase activity
- carotenoid dioxygenase activity
- oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
- metal ion binding
Cellular Component
- mitochondrion
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000357685
- Coding exons
- 12
- Length
- 49233
- Individuals with no LoFs
- 125412
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 336
- Defined
- 125748
- p
- 0.00134
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.410 | 295 | 315 | 0.935 | 0.0000161 | 3813 |
| Missense (PolyPhen) | 113 | 121.95 | 0.9266 | 1602 | ||
| Synonymous | 0.593 | 102 | 110 | 0.928 | 0.00000523 | 1099 |
| Loss of Function | 0.348 | 28 | 30.1 | 0.931 | 0.00000163 | 339 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.011 | 0.011 | notable |
| Latino/Admixed American | 0.0010 | 0.0010 | notable |
| Ashkenazi Jewish | 0.0023 | 0.0023 | notable |
| East Asian | 0.0015 | 0.0015 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00047 | 0.00046 | rare |
| South Asian | 0.00065 | 0.00065 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Asymmetrically cleaves beta-carotene at the 9',10' double bond resulting in the formation of beta-apo-10'-carotenal and beta-ionone. Besides beta-carotene, lycopene is also oxidatively cleaved. The apocarotenals formed by this enzyme may be the precursors for the biosynthesis of retinoic acid or exert unknown physiological effects. {ECO:0000269|PubMed:21106934}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- RVIS EVS
- 1.69
- RVIS percentile EVS
- 96.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.330
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |