SLCO1B1
solute carrier organic anion transporter family member 1B1, the group of Solute carrier organic anion transporter family
Basic information
Region (hg38): 12:21131193-21239796
Previous symbols: [ "SLC21A6" ]
Links
Phenotypes
GenCC
Source:
- Rotor syndrome (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Statin-induced myopathy | AD | Pharmacogenomic | For Statin-induced myopathy, the presence of variants may indicate an increased risk of adverse events (eg, with statins), or may additionally be associated with indications for dosing/medication selection (eg, with rifampin) | Gastrointestinal | 766621; 18781850; 18823304; 18854776; 19238654; 18650507; 19901119; 21178985; 21142914; 19952871; 21243006; 21709081; 21386754; 22462750; 22232210; 22668755; 22749334; 22850760 |
| For Hyperbilirubinemia, Rotor type, digenic, inheritance involves SLCO1B1 and SLCO1B3 |
ClinVar
This is a list of variants' phenotypes submitted to
- Rotor syndrome (115 variants)
- not provided (46 variants)
- Inborn genetic diseases (16 variants)
- not specified (10 variants)
- Gilbert syndrome (2 variants)
- fluvastatin response - Toxicity (1 variants)
- rosuvastatin response - Metabolism/PK (1 variants)
- pitavastatin response - Metabolism/PK (1 variants)
- hmg coa reductase inhibitors response - Toxicity (1 variants)
- rosuvastatin response - Toxicity (1 variants)
- simvastatin response - Metabolism/PK (1 variants)
- simvastatin response - Toxicity (1 variants)
- lovastatin response - Toxicity (1 variants)
- pravastatin response - Toxicity (1 variants)
- Gestational diabetes mellitus uncontrolled (1 variants)
- lovastatin response - Metabolism/PK (1 variants)
- atorvastatin response - Toxicity (1 variants)
- simvastatin acid response - Metabolism/PK (1 variants)
- fluvastatin response - Metabolism/PK (1 variants)
- atorvastatin response - Metabolism/PK (1 variants)
- lovastatin acid response - Metabolism/PK (1 variants)
- Cardiovascular phenotype (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO1B1 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 | 17 | |||||
| missense | 58 | 69 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 12 | 36 | 56 | |||
| Total | 1 | 0 | 84 | 20 | 48 |
Highest pathogenic variant AF is 0.0000788
Variants in SLCO1B1
This is a list of pathogenic ClinVar variants found in the SLCO1B1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLCO1B1 | protein_coding | protein_coding | ENST00000256958 | 14 | 108045 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.11e-21 | 0.00114 | 124942 | 8 | 783 | 125733 | 0.00315 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.897 | 404 | 356 | 1.13 | 0.0000169 | 4482 |
| Missense in Polyphen | 141 | 124.16 | 1.1357 | 1516 | ||
| Synonymous | 0.319 | 119 | 124 | 0.963 | 0.00000586 | 1313 |
| Loss of Function | -0.0422 | 32 | 31.7 | 1.01 | 0.00000150 | 428 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0342 | 0.0339 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00514 | 0.00447 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000320 | 0.000317 |
| Middle Eastern | 0.00514 | 0.00447 |
| South Asian | 0.00265 | 0.00258 |
| Other | 0.00115 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates the Na(+)-independent uptake of organic anions such as pravastatin, taurocholate, methotrexate, dehydroepiandrosterone sulfate, 17-beta-glucuronosyl estradiol, estrone sulfate, prostaglandin E2, thromboxane B2, leukotriene C3, leukotriene E4, thyroxine and triiodothyronine. Involved in the clearance of bile acids and organic anions from the liver. {ECO:0000269|PubMed:10358072, ECO:0000269|PubMed:10601278, ECO:0000269|PubMed:12196548, ECO:0000269|PubMed:22232210}.;
- Pathway
- Methotrexate Pathway, Pharmacokinetics;Rosiglitazone Pharmacokinetic Pathway;Bile secretion - Homo sapiens (human);Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Rosuvastatin Pathway, Pharmacokinetics;Codeine and Morphine Pathway, Pharmacokinetics;Anti-diabetic Drug Repaglinide Pathway, Pharmacokinetics;Anti-diabetic Drug Nateglinide Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Rosiglitazone Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Irinotecan Action Pathway;Irinotecan Metabolism Pathway;Codeine and Morphine Metabolism;Drug Induction of Bile Acid Pathway;Irinotecan Pathway;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;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
- 0.198
Intolerance Scores
- loftool
- 0.994
- rvis_EVS
- 1.03
- rvis_percentile_EVS
- 91.07
Haploinsufficiency Scores
- pHI
- 0.0620
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0264
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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;thyroid hormone transport
- Cellular component
- plasma membrane;integral component of plasma membrane;membrane;basolateral plasma membrane
- Molecular function
- bile acid transmembrane transporter activity;sodium-independent organic anion transmembrane transporter activity;thyroid hormone transmembrane transporter activity