CYP3A5
Basic information
Region (hg38): 7:99648194-99679996
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
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
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 | 3 | |||||
missense | 19 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 7 | |||||
Total | 0 | 0 | 20 | 14 | 2 |
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) | ||
7-99664087-G-T | not specified | Uncertain significance (Dec 04, 2024) | ||
7-99665175-G-T | not specified | Uncertain significance (Oct 09, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
- Phenotype
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