BCO2

beta-carotene oxygenase 2

Basic information

Region (hg38): 11:112175509-112224699

Previous symbols: [ "BCDO2" ]

Links

ENSG00000197580 ∙ NCBI:83875 ∙ OMIM:611740 ∙ HGNC:18503 ∙ Uniprot:Q9BYV7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (25 variants)
• not provided (2 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			24	1		25
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in BCO2

This is a list of pathogenic ClinVar variants found in the BCO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-112175611-C-T		High density lipoprotein cholesterol level quantitative trait locus 6	Uncertain significance (Mar 23, 2024)
11-112175615-T-C		not specified	Uncertain significance (Feb 01, 2023)
11-112175648-C-T		not specified	Likely benign (Nov 10, 2022)
11-112175666-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-112179356-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-112179472-G-C		not specified	Uncertain significance (Dec 22, 2023)
11-112193478-A-G		not specified	Uncertain significance (Jun 01, 2023)
11-112193582-C-G		not specified	Uncertain significance (Apr 19, 2023)
11-112193598-A-G		not specified	Uncertain significance (Mar 07, 2023)
11-112193911-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-112194687-C-G		not specified	Uncertain significance (Apr 25, 2023)
11-112194731-A-C		not specified	Uncertain significance (Dec 14, 2022)
11-112194746-G-A		not specified	Uncertain significance (Sep 13, 2023)
11-112194751-A-C			Likely benign (Dec 01, 2022)
11-112199706-CTATAAGGT-C			Uncertain significance (Feb 08, 2023)
11-112199720-G-A		not specified	Uncertain significance (Dec 16, 2023)
11-112199792-C-G		not specified	Uncertain significance (Jan 31, 2023)
11-112200673-T-C		not specified	Uncertain significance (Nov 15, 2021)
11-112200690-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-112200718-G-A		not specified	Uncertain significance (Aug 16, 2022)
11-112200739-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-112202056-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-112202065-C-T		not specified	Uncertain significance (Jul 30, 2023)
11-112202149-C-G		not specified	Uncertain significance (Jul 19, 2023)
11-112213757-A-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

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: 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

• 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