ABCB1
ATP binding cassette subfamily B member 1, the group of ATP binding cassette subfamily B|CD molecules
Basic information
Region (hg38): 7:87503017-87713323
Previous symbols: [ "PGY1", "MDR1", "CLCS" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Colchicine metabolism, association with | AD | Pharmacogenomic | Selection and dosing of medications (eg,colchicine) may be affected by the presence of variants | General | 7188928; 7129432; 17259950; 18973929; 21851199 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCB1 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 | 16 | 17 | ||||
| missense | 36 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 5 | 1 | 6 | |||
| non coding | 10 | 18 | ||||
| Total | 0 | 0 | 46 | 26 | 7 |
Variants in ABCB1
This is a list of pathogenic ClinVar variants found in the ABCB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-87503819-G-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503822-A-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503823-G-C | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503849-C-T | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503864-C-T | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503880-T-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503945-G-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503971-A-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87503976-A-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504020-G-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504050-T-C | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504054-T-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504057-T-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504059-TC-T | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504060-C-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504064-T-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504069-G-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504082-C-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504088-C-T | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504089-T-C | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504152-C-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504154-T-A | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504174-T-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504179-C-G | Tramadol response | drug response (Apr 28, 2018) | ||
| 7-87504180-T-G | Tramadol response | drug response (Apr 28, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ABCB1 | protein_coding | protein_coding | ENST00000265724 | 27 | 209437 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000126 | 1.00 | 125709 | 0 | 39 | 125748 | 0.000155 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.44 | 579 | 685 | 0.845 | 0.0000367 | 8394 |
| Missense in Polyphen | 149 | 222.02 | 0.6711 | 2586 | ||
| Synonymous | -0.185 | 245 | 241 | 1.02 | 0.0000125 | 2522 |
| Loss of Function | 4.98 | 21 | 64.0 | 0.328 | 0.00000365 | 772 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000420 | 0.000420 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.000176 | 0.000176 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells.;
- Disease
- DISEASE: Inflammatory bowel disease 13 (IBD13) [MIM:612244]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Citalopram Pathway, Pharmacokinetics;Methotrexate Pathway (Brain Cell), Pharmacokinetics;Methotrexate Pathway, Pharmacokinetics;Gastric cancer - Homo sapiens (human);Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Bile secretion - Homo sapiens (human);ABC transporters - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;MicroRNAs in cancer - Homo sapiens (human);Imatinib Pathway, Pharmacokinetics/Pharmacodynamics;Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Pravastatin Pathway, Pharmacokinetics;Warfarin Pathway, Pharmacokinetics;Codeine and Morphine Pathway, Pharmacokinetics;Vinka Alkaloid Pathway, Pharmacokinetics;Gefitinib Pathway, Pharmacokinetics;Proton Pump Inhibitor Pathway, Pharmacokinetics;Clopidogrel Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Erlotinib Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Mycophenolic acid Pathway, Pharmacokinetics;Tacrolimus/Cyclosporine Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Irinotecan Pathway, Pharmacodynamics;Statin Pathway, Pharmacodynamics;Doxorubicin Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Clopidogrel Metabolism Pathway;Clopidogrel Action Pathway;Irinotecan Action Pathway;Docetaxel Action Pathway;Paclitaxel Action Pathway;Vincristine Action Pathway;Vinblastine Action Pathway;Vinorelbine Action Pathway;Vindesine Action Pathway;Erlotinib Action Pathway;Venlafaxine Metabolism Pathway;Etoposide Action Pathway;Lamivudine Metabolism Pathway;Acetaminophen Metabolism Pathway;Irinotecan Metabolism Pathway;Etoposide Metabolism Pathway;Codeine and Morphine Metabolism;Drug Induction of Bile Acid Pathway;Allograft Rejection;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Imatinib and Chronic Myeloid Leukemia;LncRNA-mediated mechanisms of therapeutic resistance;Liver steatosis AOP;hypoxia and p53 in the cardiovascular system;multi-drug resistance factors;Abacavir transmembrane transport;Abacavir transport and metabolism;Metabolism;Transport of small molecules;ABC-family proteins mediated transport;HIF-1-alpha transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.680
Intolerance Scores
- loftool
- 0.0227
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 60.76
Haploinsufficiency Scores
- pHI
- 0.582
- hipred
- Y
- hipred_score
- 0.500
- ghis
- 0.387
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.519
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Abcb1a
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- abcb4
- Affected structure
- efflux transmembrane transporter activity
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;drug transmembrane transport;response to drug;xenobiotic transport;phospholipid translocation;regulation of response to osmotic stress;transmembrane transport;stem cell proliferation;ceramide translocation;positive regulation of anion channel activity;regulation of chloride transport
- Cellular component
- plasma membrane;cell surface;membrane;integral component of membrane;apical plasma membrane;extracellular exosome
- Molecular function
- transporter activity;protein binding;ATP binding;xenobiotic transmembrane transporting ATPase activity;ATPase activity, coupled to transmembrane movement of substances;phosphatidylcholine-translocating ATPase activity;phosphatidylethanolamine-translocating ATPase activity;ceramide-translocating ATPase activity