SLCO3A1

protein-coding

solute carrier organic anion transporter family member 3A1, the group of Solute carrier organic anion transporter family

Gene summary

Enables prostaglandin transmembrane transporter activity. Involved in carboxylic acid transport and positive regulation of intracellular signal transduction. Located in apical plasma membrane and basolateral plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SLC21A11

MANE transcript

NM_013272.4

Inheritance

—

ClinVar variants

U:74B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr15:91,853,708-92,172,435

External References & Databases

Ensembl (ENSG00000176463)

Transcript & Mutation Effects

hg38 • Region Span ~318.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLCO3A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013272.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			68 clinvar	2 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	74	3	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013272.4	RefSeq	NP_037404.2	10	MANE Select
ENST00000318445.11	Ensembl	ENSP00000320634.6	10	MANE Select
NM_001145044.1	RefSeq	NP_001138516.1	11	Standard
ENST00000424469.2	Ensembl	ENSP00000387846.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Androgen and estrogen biosynthesis and metabolism
Transport of vitamins, nucleosides, and related molecules
SLC-mediated transmembrane transport
Transport of small molecules
Prostaglandin formation from arachidonate

Biological Process

prostaglandin transport
sodium-independent organic anion transport
transmembrane transport

Molecular Function

sodium-independent organic anion transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318445
Coding exons: 10
Length: 318741
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.86	277	447	0.619	0.0000285	4579
Missense (PolyPhen)		76	213.2	0.35647		2224
Synonymous	-1.12	224	204	1.10	0.0000152	1467
Loss of Function	3.72	6	26.8	0.224	0.00000123	303

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000056	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the Na(+)-independent transport of organic anions such as estrone-3-sulfate (PubMed:10873595). Mediates transport of prostaglandins (PG) E1 and E2, thyroxine (T4), deltorphin II, BQ-123 and vasopressin, but not DPDPE (a derivative of enkephalin lacking an N-terminal tyrosine residue), estrone-3- sulfate, taurocholate, digoxin nor DHEAS (PubMed:16971491). {ECO:0000269|PubMed:10873595, ECO:0000269|PubMed:16971491}.;

Recessive Scores

pRec: 0.146

Intolerance Scores

LoFtool: 0.132
RVIS EVS: -0.58
RVIS percentile EVS: 18.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.273

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium