SLCO3A1

Chr 15

solute carrier organic anion transporter family member 3A1

Also known as: OATP-D, OATP-RP3, OATP3A1, OATPD, OATPRP3, SLC21A11

NCBI Gene: 28232ENSG00000176463UniProt: Q9UIG8

Enables organic anion transmembrane transporter activity and prostaglandin transmembrane transporter activity. Involved in positive regulation of MAPK cascade; positive regulation of canonical NF-kappaB signal transduction; and prostaglandin transport. Located in basal plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

116
ClinVar variants
41
Pathogenic / LP
0.39
pLI score
0
Active trials
Clinical Summary— SLCO3A1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.22) despite low pLI — interpret in context.
📋
ClinVar Variants
41 Pathogenic / Likely Pathogenic· 68 VUS of 116 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.44LOEUF
pLI 0.390
Z-score 3.72
OE 0.22 (0.12–0.44)
Moderately constrained

More LoF-intolerant than ~75% of genes

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.
2.86Z-score
OE missense 0.62 (0.56–0.68)
277 obs / 447.3 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

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.0.22 (0.12–0.44)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.62 (0.56–0.68)
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.1.10
0≤1.21.6
LoF obs/exp: 6 / 26.8Missense obs/exp: 277 / 447.3Syn Z: -1.12

ClinVar Variant Classifications

116 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic37
Likely Pathogenic4
VUS68
Likely Benign4
Benign3
37
Pathogenic
4
Likely Pathogenic
68
VUS
4
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
37
0
37
Likely Pathogenic
0
0
4
0
4
VUS
0
65
3
0
68
Likely Benign
0
2
1
1
4
Benign
0
0
3
0
3
Total067481116

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

View in ClinVar →

Protein Context — Lollipop Plot

SLCO3A1 · 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
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
SLCO3A1, A novel crohn's disease-associated gene, regulates nf-κB activity and associates with intestinal perforation.
Wei SC et al.·PLoS One
2014
Genetic Variants Associated with Suspected Neonatal Hypoxic Ischaemic Encephalopathy: A Study in a South African Context.
Foden CJ et al.·Int J Mol Sci
2025
A Genome-Wide Association Study of Nausea Incidence in Varenicline-Treated Cigarette Smokers.
Chenoweth MJ et al.·Nicotine Tob Res
2021
Genome-wide association study of antisocial personality disorder diagnostic criteria provides evidence for shared risk factors across disorders.
Li W et al.·Psychiatr Genet
2023
CircRNA expression profiling and bioinformatics analysis indicate the potential biological role and clinical significance of circRNA in influenza A virus-induced lung injury.
Wang J et al.·J Biosci
2021
Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia.
Volpi S et al.·Mol Psychiatry
2009Clinical trial
ABCB1 and ABCC1 variants associated with virological failure of first-line protease inhibitors antiretroviral regimens in Northeast Brazil patients.
Coelho AV et al.·J Clin Pharmacol
2013Cohort
Weight loss after gastric bypass is associated with a variant at 15q26.1.
Hatoum IJ et al.·Am J Hum Genet
2013
Identification of circRNA-lncRNA-miRNA-mRNA competitive endogenous RNA networks as prognostic bio-markers in head and neck squamous cell carcinoma.
Ge Y et al.·Technol Health Care
2023
Epigenome-wide analysis reveals functional modulators of drug sensitivity and post-treatment survival in chronic lymphocytic leukaemia.
Barrow TM et al.·Br J Cancer
2021Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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