BCO2

beta-carotene oxygenase 2

Basic information

Region (hg38): 11:112175510-112224699

Previous symbols: [ "BCDO2" ]

Links

ENSG00000197580NCBI:83875OMIM:611740HGNC:18503Uniprot:Q9BYV7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCO2 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
58
clinvar
5
clinvar
63
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 60 7 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BCO2protein_codingprotein_codingENST00000357685 1249233
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.78e-180.010012541203361257480.00134
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4102953150.9350.00001613813
Missense in Polyphen113121.950.92661602
Synonymous0.5931021100.9280.000005231099
Loss of Function0.3482830.10.9310.00000163339

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01160.0117
Ashkenazi Jewish0.002280.00228
East Asian0.001470.00147
Finnish0.00004620.0000462
European (Non-Finnish)0.0004670.000457
Middle Eastern0.001470.00147
South Asian0.0006540.000653
Other0.0009770.000978

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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