BCO2
Basic information
Region (hg38): 11:112175510-112224699
Previous symbols: [ "BCDO2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (3 variants)
- HIGH_DENSITY_LIPOPROTEIN_CHOLESTEROL_LEVEL_QUANTITATIVE_TRAIT_LOCUS_6 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCO2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031938.7. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 58 | 63 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 60 | 7 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BCO2 | protein_coding | protein_coding | ENST00000357685 | 12 | 49233 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.78e-18 | 0.0100 | 125412 | 0 | 336 | 125748 | 0.00134 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.410 | 295 | 315 | 0.935 | 0.0000161 | 3813 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0116 | 0.0117 |
Ashkenazi Jewish | 0.00228 | 0.00228 |
East Asian | 0.00147 | 0.00147 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000467 | 0.000457 |
Middle Eastern | 0.00147 | 0.00147 |
South Asian | 0.000654 | 0.000653 |
Other | 0.000977 | 0.000978 |
dbNSFP
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}.;
- Pathway
- Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- rvis_EVS
- 1.69
- rvis_percentile_EVS
- 96.41
Haploinsufficiency Scores
- pHI
- 0.0499
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.411
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.330
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bco2
- Phenotype
- immune system phenotype; liver/biliary system phenotype; reproductive system phenotype; hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- retinoid metabolic process;carotenoid metabolic process;carotene metabolic process;carotene catabolic process;xanthophyll metabolic process;retinoic acid metabolic process;retinal metabolic process;regulation of mitochondrial membrane potential;oxidation-reduction process;regulation of reactive oxygen species metabolic process
- Cellular component
- mitochondrion;mitochondrial matrix
- 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;beta,beta-carotene-9',10'-cleaving oxygenase activity