CYP2B6

cytochrome P450 family 2 subfamily B member 6, the group of Cytochrome P450 family 2

Basic information

Region (hg38): 19:40991281-41018398

Previous symbols: [ "CYP2B" ]

Links

ENSG00000197408 ∙ NCBI:1555 ∙ OMIM:123930 ∙ HGNC:2615 ∙ Uniprot:P20813 ∙ 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
Efavirenz, poor metabolism of	AD	Pharmacogenomic	It has been suggested that CYP2B6 genotype should be considered in efavirenz treatment	General	15622315; 20639527; 20860463; 23080225; 23152403

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP2B6 gene.

• Inborn genetic diseases (23 variants)
• not provided (3 variants)
• not specified (2 variants)
• Efavirenz response (2 variants)
• nevirapine response - Toxicity (1 variants)
• efavirenz response - Toxicity (1 variants)
• efavirenz response - Metabolism/PK (1 variants)
• nevirapine response - Metabolism/PK (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP2B6 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				1		1
missense			23	2	1	26
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	3

Variants in CYP2B6

This is a list of pathogenic ClinVar variants found in the CYP2B6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40991351-T-C		CYP2B6-related disorder	Likely benign (Jun 28, 2019)
19-40991359-C-A		CYP2B6-related disorder	Likely benign (Nov 25, 2019)
19-40991367-A-T		CYP2B6-related disorder	Likely benign (May 09, 2019)
19-40991387-G-GGC		not specified	Benign (Jan 02, 2020)
19-40991389-CCG-C		not specified	Benign (Jan 02, 2020)
19-40991435-C-G		not specified	Uncertain significance (Aug 17, 2022)
19-41004015-T-A		Efavirenz response	drug response (Oct 11, 2012)
19-41004031-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-41004122-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-41004133-G-T		not specified	Uncertain significance (Aug 10, 2023)
19-41004142-G-C		not specified	Uncertain significance (Sep 13, 2023)
19-41004158-G-T		Efavirenz response	drug response (May 15, 2015)
19-41004161-A-G		not specified	Uncertain significance (Mar 20, 2023)
19-41004303-T-C		Efavirenz response	drug response (May 15, 2015)
19-41004377-A-G		CYP2B6-related disorder	Likely benign (Feb 15, 2022)
19-41004381-G-A			Likely benign (Jan 01, 2023)
19-41004407-G-A		not specified	Uncertain significance (Jan 07, 2022)
19-41004423-T-C		not specified	Uncertain significance (Mar 11, 2024)
19-41004434-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-41004445-G-T		not specified	Uncertain significance (Nov 09, 2021)
19-41006910-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-41006936-G-T		Efavirenz response • efavirenz response - Metabolism/PK • efavirenz response - Toxicity • nevirapine response - Metabolism/PK • CYP2B6-related disorder	drug response (Mar 24, 2021)
19-41006943-A-G		not specified	Uncertain significance (Aug 01, 2023)
19-41006968-T-G		Efavirenz response	drug response (May 15, 2015)
19-41007013-T-C		Efavirenz response	drug response (Jan 01, 2006)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP2B6	protein_coding	protein_coding	ENST00000324071	9	27100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-10	0.232	125354	5	389	125748	0.00157

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.976	332	286	1.16	0.0000177	3221
Missense in Polyphen		100	93.172	1.0733		1180
Synonymous	-1.50	131	111	1.18	0.00000679	984
Loss of Function	0.737	17	20.6	0.825	0.00000135	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0254	0.0142
Ashkenazi Jewish	0.00576	0.00577
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000512	0.000466
Middle Eastern	0.000272	0.000272
South Asian	0.000555	0.000523
Other	0.00228	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase. {ECO:0000269|PubMed:11695850, ECO:0000269|PubMed:20061448, ECO:0000269|PubMed:21875942, ECO:0000269|PubMed:22909231}.
• Pathway: Artemisinin and Derivatives Pathway, Pharmacokinetics;Retinol metabolism - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Carbamazepine Pathway, Pharmacokinetics;Phenytoin Pathway, Pharmacokinetics;Tamoxifen Pathway, Pharmacokinetics;Clopidogrel Pathway, Pharmacokinetics;Tramadol Pharmacokinetics;Nevirapine Pathway, Pharmacokinetics;Sorafenib Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Nicotine Pathway, Pharmacokinetics;Cyclophosphamide Pathway, Pharmacokinetics;Ifosfamide Pathway, Pharmacokinetics;Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Clopidogrel Metabolism Pathway;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Methadone Metabolism Pathway;Nicotine Metabolism Pathway;Clopidogrel Action Pathway;Nicotine Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Tamoxifen Action Pathway;Methadone Action Pathway;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Tramadol Metabolism Pathway;Valproic Acid Metabolism Pathway;Carbamazepine Metabolism Pathway;Cyclophosphamide Action Pathway;Ifosfamide Action Pathway;Sorafenib Metabolism Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Vitamin A Deficiency;Nevirapine Metabolism Pathway;Tamoxifen Metabolism Pathway;Cyclophosphamide Metabolism Pathway;Ifosfamide Metabolism Pathway;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Retinol Metabolism;Piroxicam Action Pathway;Nicotine Metabolism;Liver X Receptor Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Valproic acid pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Liver steatosis AOP;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;bupropion degradation;Xenobiotics;Tyrosine metabolism;Fatty acids;Androgen and estrogen biosynthesis and metabolism;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;Tryptophan degradation;CYP2E1 reactions;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.888
• rvis_EVS: 2.36
• rvis_percentile_EVS: 98.44

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.203

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.303

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cyp2b10

Gene ontology

• Biological process: organic acid metabolic process;xenobiotic metabolic process;steroid metabolic process;drug metabolic process;epoxygenase P450 pathway;cellular ketone metabolic process;exogenous drug catabolic process;oxidation-reduction process
• Cellular component: cytoplasm;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: monooxygenase activity;iron ion binding;arachidonic acid epoxygenase activity;steroid hydroxylase activity;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;heme binding