ABCB1

ATP binding cassette subfamily B member 1, the group of ATP binding cassette subfamily B|CD molecules

Basic information

Region (hg38): 7:87503016-87713323

Previous symbols: [ "PGY1", "MDR1", "CLCS" ]

Links

ENSG00000085563 ∙ NCBI:5243 ∙ OMIM:171050 ∙ HGNC:40 ∙ Uniprot:P08183 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the ABCB1 gene.

• Inborn genetic diseases (27 variants)
• not provided (25 variants)
• Tramadol response (8 variants)
• not specified (5 variants)
• Inflammatory bowel disease 13 (4 variants)
• Non-small cell lung carcinoma (1 variants)
• Neoplasm of ovary (1 variants)
• MDR1 POLYMORPHISM (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

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				10	4	14
missense			21		7	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			9	2	2	13
Total	0	0	30	12	13

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: gnomAD

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: dbNSFP

• 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