BCO2

Chr 11

beta-carotene oxygenase 2

Also known as: B-DIOX-II, BCDO2

NCBI Gene: 83875 ENSG00000197580 UniProt: Q9BYV7 OMIM: 611740

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.28

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.28LOEUF

pLI 0.000

Z-score 0.35

OE 0.93 (0.69–1.28)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.41Z-score

OE missense 0.94 (0.85–1.03)

295 obs / 315.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.93 (0.69–1.28)

0≤0.351.4

Missense OE?0.94 (0.85–1.03)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 28 / 30.1Missense obs/exp: 295 / 315.5Syn Z: 0.59

Background carrier burden — how many people carry a rare variant somewhere in BCO2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 65

720 rare PASS variants

Rare truncating (LoF)

1 in 530

138 rare PASS variants

Rare synonymous (reference)

1 in 160

227 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for BCO2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 130	1 in 950
South Asian	~43k	1 in 60	1 in 540
Remaining (unassigned)	~30k	1 in 61	1 in 260
European (Finnish)	~27k	1 in 230	1 in 3,800
Admixed American	~22k	1 in 55	1 in 290
African / African American	~21k	1 in 68	1 in 350
East Asian	~20k	1 in 61	1 in 480
Ashkenazi Jewish	~13k	1 in 220	≈ 1 in 4,400
Middle Eastern	~2,884	1 in 69	1 in 290

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 10 of 12 coding exons well covered in gnomAD exomes; exons 4, 5 marginal. Genomes: 11 of 12 (exon 9 below).? see exons ↓