SLCO2A1

Chr 3ADAR

solute carrier organic anion transporter family member 2A1

Also known as: MATR1, OATP2A1, PGT, PHOAD, PHOAR2, SLC21A2

NCBI Gene: 6578 ENSG00000174640 UniProt: Q92959 OMIM: 601460

This gene encodes a prostaglandin transporter that is a member of the 12-membrane-spanning superfamily of transporters. The encoded protein may be involved in mediating the uptake and clearance of prostaglandins in numerous tissues. [provided by RefSeq, Dec 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Hypertrophic osteoarthropathy, primary, autosomal dominantMIM #167100

PHOAR2-enteropathy syndromeMIM #614441

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Hypertrophic osteoarthropathy, primary, autosomal dominant; PHOAR2-enteropathy syndrome; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.05

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.05LOEUF

pLI 0.000

Z-score 1.32

OE 0.75 (0.54–1.05)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.52Z-score

OE missense 0.92 (0.84–1.01)

339 obs / 366.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.75 (0.54–1.05)

0≤0.351.4

Missense OE?0.92 (0.84–1.01)

0≤0.61.4

Synonymous OE?0.89

0≤1.21.6

LoF obs/exp: 24 / 32.1Missense obs/exp: 339 / 366.9Syn Z: 1.08

Background carrier burden — how many people carry a rare variant somewhere in SLCO2A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 62

799 rare PASS variants

Rare truncating (LoF)

1 in 2,000

112 rare PASS variants

Rare synonymous (reference)

1 in 97

334 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLCO2A1. 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 81	1 in 2,600
South Asian	~43k	1 in 52	1 in 1,800
Remaining (unassigned)	~30k	1 in 51	1 in 2,300
European (Finnish)	~27k	1 in 110	≈ 1 in 5,900
Admixed American	~22k	1 in 49	1 in 3,200
African / African American	~21k	1 in 65	1 in 610
East Asian	~20k	1 in 49	1 in 360
Ashkenazi Jewish	~13k	1 in 130	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 55	none seen

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): 13 of 14 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 14.? see exons ↓