GeneBe

SLCO1B3

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

Basic information

Region (hg38): 12:20810702-20916911

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hyperbilirubinemia, Rotor type, digenicDigenicGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingGastrointestinal766621; 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 (112 variants)
  • SLCO1B3-related_disorder (74 variants)
  • not_specified (72 variants)
  • not_provided (22 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. These statistics are base on transcript: NM_000019844.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
30
clinvar
1
clinvar
 36
missense
132
clinvar
16
clinvar
 148
nonsense
0
start loss
0
frameshift
1
clinvar
5
clinvar
 6
splice donor/acceptor (+/-2bp)
2
clinvar
3
clinvar
 5
Total 3 3 142 46 1

Highest pathogenic variant AF is 0.00010369863

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLCO1B3protein_codingprotein_codingENST00000381545 14279405
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.32e-240.00009491245161012111257370.00487
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.164123511.170.00001644544
Missense in Polyphen139118.541.17261522
Synonymous-0.6061321231.070.000006181315
Loss of Function-0.7743328.51.160.00000120422

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002900.00288
Ashkenazi Jewish0.001730.00169
East Asian0.001090.00103
Finnish0.01930.0191
European (Non-Finnish)0.005660.00554
Middle Eastern0.001090.00103
South Asian0.001130.00105
Other0.007760.00736

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
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
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