SLCO2B1

Chr 11

solute carrier organic anion transporter family member 2B1

Also known as: OATP-B, OATP2B1, OATPB, SLC21A9

NCBI Gene: 11309 ENSG00000137491 UniProt: O94956 OMIM: 604988

This gene encodes an organic anion-transporting polypeptide that mediates sodium-independent transport of steroid sulfate conjugates, prostaglandins, and other organic anions across cell membranes in the placenta, liver, intestine, and blood-brain barrier. Mutations cause autosomal recessive primary hypertrophic osteoarthropathy, a connective tissue disorder characterized by digital clubbing, pachydermia (thickened skin), and periostosis (bone overgrowth). The gene shows low constraint against loss-of-function variants, consistent with the recessive inheritance pattern observed in disease.

OMIM ResearchSummary from RefSeq, UniProt

This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2010]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.67

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.67LOEUF

pLI 0.000

Z-score 3.04

OE 0.43 (0.28–0.67)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.95Z-score

OE missense 0.87 (0.80–0.95)

371 obs / 426.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.43 (0.28–0.67)

0≤0.351.4

Missense OE?0.87 (0.80–0.95)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 14 / 32.8Missense obs/exp: 371 / 426.0Syn Z: -0.04

Background carrier burden — how many people carry a rare variant somewhere in SLCO2B1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 51

896 rare PASS variants

Rare truncating (LoF)

1 in 1,900

94 rare PASS variants

Rare synonymous (reference)

1 in 110

409 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLCO2B1. 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 56	1 in 1,900
South Asian	~43k	1 in 54	1 in 2,000
Remaining (unassigned)	~30k	1 in 44	1 in 2,200
European (Finnish)	~27k	1 in 160	≈ 1 in 13,000
Admixed American	~22k	1 in 79	1 in 3,200
African / African American	~21k	1 in 64	1 in 620
East Asian	~20k	1 in 52	1 in 1,300
Ashkenazi Jewish	~13k	1 in 310	none seen
Middle Eastern	~2,884	1 in 64	≈ 1 in 2,900

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): All 14 coding exons well covered in gnomAD exomes and genomes.? see exons ↓