CYP3A7

cytochrome P450 family 3 subfamily A member 7, the group of Cytochrome P450 family 3

Basic information

Region (hg38): 7:99705035-99735196

Links

ENSG00000160870 ∙ NCBI:1551 ∙ OMIM:605340 ∙ HGNC:2640 ∙ Uniprot:P24462 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP3A7 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP3A7 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			19	3	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	4	1

Variants in CYP3A7

This is a list of pathogenic ClinVar variants found in the CYP3A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99705580-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-99707864-G-T		not specified	Uncertain significance (Dec 03, 2021)
7-99707900-A-G		not specified	Uncertain significance (Oct 20, 2023)
7-99707903-C-A		not specified	Uncertain significance (Feb 03, 2022)
7-99707915-C-T		not specified	Uncertain significance (Dec 15, 2022)
7-99707950-G-C		not specified	Uncertain significance (Apr 07, 2022)
7-99709134-C-T		not specified	Uncertain significance (May 31, 2023)
7-99709175-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-99709214-C-T		not specified	Uncertain significance (Jan 31, 2023)
7-99709231-A-T		not specified	Likely benign (Oct 18, 2021)
7-99710814-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-99710827-T-C		not specified	Uncertain significance (Mar 23, 2023)
7-99710889-A-C		not specified	Uncertain significance (Apr 25, 2022)
7-99713475-G-A		not specified	Uncertain significance (Nov 13, 2023)
7-99713477-G-T		not specified	Uncertain significance (Jan 31, 2022)
7-99714574-C-T		not specified	Uncertain significance (Nov 01, 2022)
7-99714599-A-T		not specified	Uncertain significance (Sep 29, 2023)
7-99714617-T-C		not specified	Uncertain significance (Aug 02, 2021)
7-99714656-G-A		not specified	Likely benign (Dec 13, 2022)
7-99715770-C-T		not specified	Uncertain significance (Jan 05, 2022)
7-99715775-G-T		not specified	Uncertain significance (Jan 23, 2024)
7-99715821-A-G		not specified	Uncertain significance (Aug 02, 2021)
7-99715853-C-T		not specified	Likely benign (Oct 14, 2021)
7-99717214-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-99717532-G-A			Likely benign (Aug 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP3A7	protein_coding	protein_coding	ENST00000336374	13	30160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.12e-14	0.0580	125667	0	71	125738	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.268	279	267	1.05	0.0000139	3307
Missense in Polyphen		67	77.492	0.86461		1062
Synonymous	-0.391	97	92.2	1.05	0.00000471	959
Loss of Function	0.525	22	24.8	0.886	0.00000125	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000478	0.000478
Ashkenazi Jewish	0.00	0.00
East Asian	0.00180	0.00180
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00180	0.00180
South Asian	0.000425	0.000425
Other	0.00	0.00

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: Retinol metabolism - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Carbamazepine Pathway, Pharmacokinetics;Phenytoin Pathway, Pharmacokinetics;Citalopram Action Pathway;Methadone Metabolism Pathway;Citalopram Metabolism Pathway;Methadone Action Pathway;Carbamazepine Metabolism Pathway;Levomethadyl Acetate Metabolism Pathway;Vitamin A Deficiency;Retinol Metabolism;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;Oxidation by Cytochrome P450;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;Vitamin A (retinol) metabolism;Xenobiotics metabolism;Tryptophan degradation;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.202

Intolerance Scores

• loftool: 0.906
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp3a13
• Phenotype: homeostasis/metabolism 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); normal phenotype

Gene ontology

• Biological process: lipid hydroxylation;xenobiotic metabolic process;steroid metabolic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;organelle membrane
• Molecular function: monooxygenase activity;iron ion binding;steroid hydroxylase activity;oxygen binding;heme binding;aromatase activity;estrogen 16-alpha-hydroxylase activity