SLCO4A1

protein-coding

solute carrier organic anion transporter family member 4A1, the group of Solute carrier organic anion transporter family

Gene summary

Enables prostaglandin transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Located in cell junction. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SLC21A12

MANE transcript

NM_016354.4

Inheritance

—

ClinVar variants

U:115B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr20:62,642,503-62,685,785

External References & Databases

Ensembl (ENSG00000101187)

Transcript & Mutation Effects

hg38 • Region Span ~43.3 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 SLCO4A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 129

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016354.4. 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	3 clinvar		4
missense			111 clinvar	16 clinvar		127
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	115	19	0	134

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016354.4	RefSeq	NP_057438.3	11	MANE Select
ENST00000217159.6	Ensembl	ENSP00000217159.1	11	MANE Select
ENST00000370507.5	Ensembl	ENSP00000359538.1	11	Standard
ENST00000370507.6	Ensembl	ENSP00000359538.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tyrosine metabolism
Androgen and estrogen biosynthesis and metabolism
Transport of vitamins, nucleosides, and related molecules
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

sodium-independent organic anion transport
transmembrane transport
thyroid hormone transport

Molecular Function

sodium-independent organic anion transmembrane transporter activity
thyroid hormone 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: ENST00000217159
Coding exons: 11
Length: 43341
Individuals with no LoFs: 125563
Homozygous LoFs: 0
Heterozygous LoFs: 182
Defined: 125745
p: 0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.430	437	463	0.944	0.0000305	4594
Missense (PolyPhen)		147	166.33	0.8838		1724
Synonymous	-1.09	244	223	1.09	0.0000174	1527
Loss of Function	1.56	20	29.1	0.688	0.00000152	297

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00056	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0.0016	0.0015	notable
European (Non-Finnish)	0.00094	0.00090	rare
South Asian	0.00043	0.00042	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the Na(+)-independent transport of organic anions such as the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and of estrone-3-sulfate and taurocholate.;

Recessive Scores

pRec: 0.143

Intolerance Scores

LoFtool: 0.726
RVIS EVS: -1.32
RVIS percentile EVS: 4.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.199

Gene Damage Prediction

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