CYP3A5

cytochrome P450 family 3 subfamily A member 5, the group of Cytochrome P450 family 3

Basic information

Region (hg38): 7:99648193-99679998

Links

ENSG00000106258 ∙ NCBI:1577 ∙ OMIM:605325 ∙ HGNC:2638 ∙ Uniprot:P20815 ∙ 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
Drug metabolism, CYP3A5-related	AD	Pharmacogenomic	Selection and dosing of many medications may be affected by the presence of variants	General	11740341; 15284534; 12065767; 20212519; 21412232; 22015057; 22210422; 22304537; 22407409; 22706623; 22875663; 23033116

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP3A5 gene.

• Inborn genetic diseases (16 variants)
• not provided (5 variants)
• Essential hypertension (1 variants)
• CYP3A5-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP3A5 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			14	3		17
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1		1	2
Total	0	0	15	5	1

Variants in CYP3A5

This is a list of pathogenic ClinVar variants found in the CYP3A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99648381-G-A		not specified	Uncertain significance (Nov 13, 2023)
7-99648403-A-G			Benign (Jul 31, 2018)
7-99650089-G-T		not specified	Uncertain significance (Aug 30, 2022)
7-99650155-A-G		not specified	Uncertain significance (Oct 14, 2023)
7-99652563-G-A		not specified	Uncertain significance (Dec 11, 2023)
7-99652600-G-A			Likely benign (Jun 23, 2018)
7-99652615-T-G		CYP3A5-related disorder	Likely benign (Sep 17, 2019)
7-99652632-A-G		not specified	Uncertain significance (Apr 07, 2023)
7-99652641-G-A		Essential hypertension	not provided (-)
7-99652664-A-G		not specified	Uncertain significance (Sep 27, 2021)
7-99652766-T-C		not specified	Uncertain significance (Oct 02, 2023)
7-99652770-T-TA		CYP3A5-related disorder	Likely benign (Jul 21, 2021)
7-99652775-G-T		not specified	Uncertain significance (Feb 16, 2023)
7-99660519-C-A		not specified	Uncertain significance (Jun 29, 2023)
7-99660599-G-T		not specified	Uncertain significance (Sep 20, 2022)
7-99660630-A-C		not specified	Uncertain significance (Feb 27, 2023)
7-99663009-C-T		CYP3A5-related disorder	Likely benign (Mar 25, 2022)
7-99663987-C-T		not specified	Uncertain significance (Jun 18, 2021)
7-99664001-T-A		not specified	Likely benign (Mar 02, 2023)
7-99664072-CTG-C		CYP3A5-related disorder	Likely benign (Jan 24, 2020)
7-99665212-C-T		CYP3A5-related disorder	Likely benign (Jul 21, 2021)
7-99665261-T-C		not specified	Uncertain significance (Aug 16, 2022)
7-99666617-G-A		not specified	Uncertain significance (Jul 07, 2022)
7-99666668-A-G		not specified	Uncertain significance (Nov 07, 2022)
7-99667025-A-G		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP3A5	protein_coding	protein_coding	ENST00000222982	13	31805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.29e-17	0.00734	122011	93	3644	125748	0.0150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	216	270	0.800	0.0000136	3285
Missense in Polyphen		55	69.339	0.7932		912
Synonymous	0.629	92	100	0.920	0.00000524	965
Loss of Function	0.0330	25	25.2	0.993	0.00000121	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.113	0.113
Ashkenazi Jewish	0.00745	0.00747
East Asian	0.00789	0.00791
Finnish	0.00393	0.00393
European (Non-Finnish)	0.0109	0.0109
Middle Eastern	0.00789	0.00791
South Asian	0.00679	0.00669
Other	0.0111	0.0108

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.
• Pathway: Artemisinin and Derivatives Pathway, Pharmacokinetics;Benzodiazepine Pathway, Pharmacokinetics;Retinol metabolism - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Carbamazepine Pathway, Pharmacokinetics;Imatinib Pathway, Pharmacokinetics/Pharmacodynamics;Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Phenytoin Pathway, Pharmacokinetics;Tamoxifen Pathway, Pharmacokinetics;Vinka Alkaloid Pathway, Pharmacokinetics;Gefitinib Pathway, Pharmacokinetics;Clopidogrel Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Erlotinib Pathway, Pharmacokinetics;Fluoxetine Pathway, Pharmacokinetics;Nevirapine Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Tacrolimus/Cyclosporine Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Cyclophosphamide Pathway, Pharmacokinetics;Ifosfamide Pathway, Pharmacokinetics;Artemether Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Fluoxetine Action Pathway;Clopidogrel Metabolism Pathway;Clopidogrel Action Pathway;Irinotecan Action Pathway;Tamoxifen Action Pathway;Carbamazepine Metabolism Pathway;Etoposide Action Pathway;Teniposide Action Pathway;Ifosfamide Action Pathway;Vitamin A Deficiency;Fluoxetine Metabolism Pathway;Nevirapine Metabolism Pathway;Teniposide Metabolism Pathway;Irinotecan Metabolism Pathway;Etoposide Metabolism Pathway;Tamoxifen Metabolism Pathway;Ifosfamide Metabolism Pathway;Retinol Metabolism;Irinotecan Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;Oxidation by Cytochrome P450;Tamoxifen metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Xenobiotics;Tyrosine metabolism;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;Aflatoxin activation and detoxification;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.909
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.0379
• hipred: N
• hipred_score: 0.112
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.330

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp3a44

Gene ontology

• Biological process: lipid hydroxylation;xenobiotic metabolic process;steroid metabolic process;alkaloid catabolic process;drug catabolic process;oxidative demethylation
• Cellular component: endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: monooxygenase activity;iron ion binding;oxidoreductase activity;oxygen binding;heme binding;aromatase activity;estrogen 16-alpha-hydroxylase activity