SLCO1B3

solute carrier organic anion transporter family member 1B3, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 12:20810701-20916911

Previous symbols: [ "SLC21A8" ]

Links

ENSG00000111700 ∙ NCBI:28234 ∙ OMIM:605495 ∙ HGNC:10961 ∙ Uniprot:Q9NPD5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Rotor syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperbilirubinemia, Rotor type, digenic	Digenic	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal	766621; 22232210
Inheritance involves SLCO1B1 and SLCO1B3

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLCO1B3 gene.

• Rotor syndrome (136 variants)
• not provided (60 variants)
• Inborn genetic diseases (22 variants)
• SLCO1B3-related condition (13 variants)
• not specified (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO1B3 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			6	5	6	17
missense			76	4	4	84
nonsense						0
start loss						0
frameshift	1		7			8
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1		1			2
splice region			6	3	2	11
non coding			22	2	45	69
Total	2	0	113	11	55

Highest pathogenic variant AF is 0.000131

Variants in SLCO1B3

This is a list of pathogenic ClinVar variants found in the SLCO1B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-20810704-G-A		Rotor syndrome	Benign (Jan 13, 2018)
12-20810779-G-C		Rotor syndrome	Uncertain significance (Jan 12, 2018)
12-20813517-T-G		Rotor syndrome	Benign (Jan 12, 2018)
12-20813557-A-T		Rotor syndrome	Uncertain significance (Jan 13, 2018)
12-20813559-G-C		Rotor syndrome	Uncertain significance (Mar 16, 2018)
12-20813573-GC-G		Rotor syndrome	Likely benign (Jun 14, 2016)
12-20813614-C-T		Rotor syndrome	Benign (Jan 13, 2018)
12-20815710-AATATTCACTTGGTATCTG-A		Rotor syndrome	Benign (Nov 30, 2023)
12-20815731-GTTTA-G		Rotor syndrome	Benign (Nov 30, 2023)
12-20815742-G-A		not specified	Uncertain significance (Apr 11, 2023)
12-20815749-A-G		Rotor syndrome	Likely benign (Sep 14, 2023)
12-20815764-A-C		Rotor syndrome	Uncertain significance (Jan 13, 2018)
12-20815805-C-T		Rotor syndrome	Uncertain significance (Mar 29, 2023)
12-20815807-C-T		Rotor syndrome	Benign/Likely benign (Jul 26, 2023)
12-20815821-A-C		Rotor syndrome	Uncertain significance (-)
12-20815894-C-T			Benign (Nov 12, 2018)
12-20815946-A-T			Benign (Nov 12, 2018)
12-20855040-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-20855042-C-T		Rotor syndrome	Uncertain significance (Apr 27, 2017)
12-20855051-C-G		Rotor syndrome • SLCO1B3-related disorder	Benign/Likely benign (Nov 03, 2023)
12-20855073-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-20855086-T-C		SLCO1B3-related disorder	Uncertain significance (Nov 21, 2022)
12-20855090-A-C		Rotor syndrome	Uncertain significance (Jan 13, 2018)
12-20855091-A-G		Rotor syndrome	Uncertain significance (Jan 12, 2018)
12-20855096-C-T		SLCO1B3-related disorder	Likely benign (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO1B3	protein_coding	protein_coding	ENST00000381545	14	279405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-24	0.0000949	124516	10	1211	125737	0.00487

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.16	412	351	1.17	0.0000164	4544
Missense in Polyphen		139	118.54	1.1726		1522
Synonymous	-0.606	132	123	1.07	0.00000618	1315
Loss of Function	-0.774	33	28.5	1.16	0.00000120	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00290	0.00288
Ashkenazi Jewish	0.00173	0.00169
East Asian	0.00109	0.00103
Finnish	0.0193	0.0191
European (Non-Finnish)	0.00566	0.00554
Middle Eastern	0.00109	0.00103
South Asian	0.00113	0.00105
Other	0.00776	0.00736

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the Na(+)-independent uptake of organic anions such as 17-beta-glucuronosyl estradiol, taurocholate, triiodothyronine (T3), leukotriene C4, dehydroepiandrosterone sulfate (DHEAS), methotrexate and sulfobromophthalein (BSP). Involved in the clearance of bile acids and organic anions from the liver. {ECO:0000269|PubMed:22232210}.
• Disease: DISEASE: Hyperbilirubinemia, Rotor type (HBLRR) [MIM:237450]: An autosomal recessive form of primary conjugated hyperbilirubinemia. Affected individuals develop mild jaundice not associated with hemolysis shortly after birth or in childhood. They have delayed plasma clearance of the unconjugated anionic dye bromsulphthalein and prominent urinary excretion of coproporphyrin I. Hepatic pigmentation is normal. {ECO:0000269|PubMed:22232210}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Methotrexate Pathway, Pharmacokinetics;Bile secretion - Homo sapiens (human);Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Rosuvastatin Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;Mycophenolic Acid Metabolism Pathway;Docetaxel Action Pathway;Paclitaxel Action Pathway;Metabolism of lipids;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Metabolism;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Metabolism of steroids;Bile acid biosynthesis;Porphyrin metabolism;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.793
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.74

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0808

Mouse Genome Informatics

• Gene name: Slco1b2
• Phenotype: liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: organic anion transport;bile acid and bile salt transport;sodium-independent organic anion transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane
• Molecular function: organic anion transmembrane transporter activity;bile acid transmembrane transporter activity;sodium-independent organic anion transmembrane transporter activity