SLCO3A1

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

Basic information

Region (hg38): 15:91853707-92172435

Previous symbols: [ "SLC21A11" ]

Links

ENSG00000176463 ∙ NCBI:28232 ∙ OMIM:612435 ∙ HGNC:10952 ∙ Uniprot:Q9UIG8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLCO3A1 gene.

• Inborn genetic diseases (15 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO3A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	15	2	1

Variants in SLCO3A1

This is a list of pathogenic ClinVar variants found in the SLCO3A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-91916276-C-T		not specified	Uncertain significance (Jul 13, 2022)
15-91916284-G-T		not specified	Uncertain significance (Aug 16, 2022)
15-91916299-C-A		not specified	Uncertain significance (Mar 23, 2022)
15-91916330-C-T		not specified	Uncertain significance (Dec 16, 2022)
15-92061300-T-C		Vascular endothelial growth factor (VEGF) inhibitor response	association (-)
15-92104376-G-C		not specified	Uncertain significance (Oct 12, 2022)
15-92104419-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-92104496-C-A		not specified	Uncertain significance (Dec 14, 2023)
15-92120510-C-T		not specified	Uncertain significance (Dec 09, 2023)
15-92126108-C-T		not specified	Uncertain significance (Dec 22, 2023)
15-92126247-C-A		not specified	Uncertain significance (Jan 16, 2024)
15-92128357-A-G			Likely benign (Mar 01, 2023)
15-92128463-G-C		not specified	Uncertain significance (Dec 15, 2023)
15-92128494-TGGGATGGGGCAG-T			Benign (Jan 30, 2018)
15-92146991-C-T		not specified	Uncertain significance (Jul 12, 2023)
15-92147025-G-C		not specified	Uncertain significance (Oct 12, 2021)
15-92147035-G-A		not specified	Uncertain significance (Jan 24, 2024)
15-92147149-A-G			Likely benign (Mar 01, 2023)
15-92150944-A-G			Benign (Apr 10, 2018)
15-92150982-T-G		not specified	Uncertain significance (Nov 29, 2023)
15-92162768-C-T		not specified	Uncertain significance (Jan 26, 2023)
15-92162833-C-A		not specified	Uncertain significance (Aug 17, 2022)
15-92162834-A-G		not specified	Uncertain significance (Aug 17, 2022)
15-92162863-G-A		not specified	Uncertain significance (Jan 29, 2024)
15-92162897-C-T		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO3A1	protein_coding	protein_coding	ENST00000318445	10	318741

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.390	0.610	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	277	447	0.619	0.0000285	4579
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000562	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000369	0.0000352
Middle Eastern	0.0000562	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.132
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.78

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.673
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco3a1

Gene ontology

• Biological process: prostaglandin transport;sodium-independent organic anion transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: sodium-independent organic anion transmembrane transporter activity