BCO1

Chr 16AD

beta-carotene oxygenase 1

Also known as: BCDO, BCDO1, BCMO, BCMO1, BCO

NCBI Gene: 53630ENSG00000135697UniProt: Q9HAY6

Vitamin A metabolism is important for vital processes such as vision, embryonic development, cell differentiation, and membrane and skin protection. The protein encoded by this gene is a key enzyme in beta-carotene metabolism to vitamin A. It catalyzes the oxidative cleavage of beta,beta-carotene into two retinal molecules. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

?Hypercarotenemia and vitamin A deficiency, autosomal dominantMIM #115300
AD
219
ClinVar variants
40
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— BCO1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
40 Pathogenic / Likely Pathogenic· 129 VUS of 219 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.18LOEUF
pLI 0.000
Z-score 0.87
OE 0.81 (0.57–1.18)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.90Z-score
OE missense 1.15 (1.05–1.25)
346 obs / 302.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.81 (0.57–1.18)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.15 (1.05–1.25)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.21
0≤1.21.6
LoF obs/exp: 20 / 24.6Missense obs/exp: 346 / 302.1Syn Z: -1.88

ClinVar Variant Classifications

219 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35
Likely Pathogenic5
VUS129
Likely Benign15
Benign34
Conflicting1
35
Pathogenic
5
Likely Pathogenic
129
VUS
15
Likely Benign
34
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
35
0
35
Likely Pathogenic
0
0
5
0
5
VUS
0
100
29
0
129
Likely Benign
0
7
3
5
15
Benign
0
4
27
3
34
Conflicting
—1
Total0111998219

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BCO1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

?Hypercarotenemia and vitamin A deficiency, autosomal dominant

MIM #115300

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Association of MARC1, ADCY5, and BCO1 Variants with the Lipid Profile, Suggests an Additive Effect for Hypertriglyceridemia in Mexican Adult Men.
Rivera-Paredez B et al.·Int J Mol Sci
2022
Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients.
Tang J et al.·Genes (Basel)
2022Review
β-Carotene Oxygenase 1 Activity Modulates Circulating Cholesterol Concentrations in Mice and Humans.
Amengual J et al.·J Nutr
2020
Single Nucleotide Polymorphisms in β-Carotene Oxygenase 1 are Associated with Plasma Lycopene Responses to a Tomato-Soy Juice Intervention in Men with Prostate Cancer.
Moran NE et al.·J Nutr
2019
Common variant rs6564851 near the beta-carotene oxygenase 1 gene is associated with plasma triglycerides levels in middle-aged Mexican men adults.
León-Reyes G et al.·Nutr Res
2022
Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.
Qian M et al.·Appl Environ Microbiol
2025
RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout.
Ahmed RO et al.·BMC Genomics
2023Functional
Unveiling BCO2 function in macular pigment metabolism: Mitochondrial processing and expression in the primate retina.
Shen C et al.·Biochim Biophys Acta Mol Cell Biol Lipids
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Single-cell transcriptomics reveals the regulation of bco1 and bco2 genes in the carotenoid metabolism of koi carp.
Luo M et al.·Int J Biol Macromol
2025
Genetic variants in the PKD1L2/BCO1 region are associated with β-carotene, lutein, and zeaxanthin: A genome-wide association study of plasma carotenoids.
Jamnik J et al.·Nutr Res
2024
LncRNA (BCO1-AS) regulate inflammatory responses in bacterial infection through caspase-1 in turbot (Scophthalmus maximus).
Wang B et al.·Int J Biol Macromol
2024
β-Cryptoxanthin Attenuates Cigarette-Smoke-Induced Lung Lesions in the Absence of Carotenoid Cleavage Enzymes (BCO1/BCO2) in Mice.
Chiaverelli RA et al.·Molecules
2023🔓 Open Access
The BCO2 Genotype and the Expression of BCO1, BCO2, LRAT, and TTPA Genes in the Adipose Tissue and Brain of Rabbits Fed a Diet with Marigold Flower Extract.
Strychalski J et al.·Int J Mol Sci
2023🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools