CYP1A1

cytochrome P450 family 1 subfamily A member 1, the group of Cytochrome P450 family 1

Basic information

Region (hg38): 15:74719541-74725536

Previous symbols: [ "CYP1" ]

Links

ENSG00000140465 ∙ NCBI:1543 ∙ OMIM:108330 ∙ HGNC:2595 ∙ Uniprot:P04798 ∙ 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 CYP1A1 gene.

• Inborn genetic diseases (15 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP1A1 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	2
missense			15	1	5	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	6

Variants in CYP1A1

This is a list of pathogenic ClinVar variants found in the CYP1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74720496-C-A			Benign (Jun 13, 2018)
15-74720555-G-A		CYP1A1-related disorder	Benign (Jan 24, 2020)
15-74720572-C-T		not specified	Uncertain significance (Mar 07, 2024)
15-74720584-C-T		CYP1A1-related disorder	Benign (Jun 11, 2019)
15-74720586-C-G		not specified	Uncertain significance (Jun 06, 2023)
15-74720590-A-G		not specified	Uncertain significance (Apr 12, 2023)
15-74720599-G-A		CYP1A1-related disorder	Likely benign (Mar 23, 2023)
15-74720638-G-T		CYP1A1-related disorder	Benign (Sep 10, 2019)
15-74720644-T-C		CYP1A1-related disorder	Benign (Oct 18, 2019)
15-74720646-G-T		CYP1A1-related disorder	Benign (Oct 28, 2019)
15-74720654-G-A		CYP1A1-related disorder	Likely benign (Oct 28, 2019)
15-74720656-TA-T		CYP1A1-related disorder	Likely benign (Jul 14, 2022)
15-74720671-C-G		not specified	Uncertain significance (Aug 12, 2021)
15-74720710-C-T		CYP1A1-related disorder	Likely benign (Jun 30, 2019)
15-74720737-G-A		not specified	Uncertain significance (Apr 12, 2022)
15-74720972-A-T		not specified	Uncertain significance (Oct 25, 2022)
15-74721003-C-T		not specified	Uncertain significance (Jun 07, 2023)
15-74721022-A-G		not specified	Uncertain significance (Apr 25, 2023)
15-74721026-G-C		CYP1A1-related disorder	Likely benign (May 30, 2019)
15-74721053-G-C		not specified	Uncertain significance (Dec 26, 2023)
15-74721203-G-A		not specified	Uncertain significance (Apr 28, 2023)
15-74721217-G-T		not specified	Uncertain significance (Jan 22, 2024)
15-74721301-C-T		not specified	Uncertain significance (Feb 10, 2023)
15-74721446-G-T		not specified	Uncertain significance (Dec 28, 2022)
15-74721686-A-G			Benign/Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP1A1	protein_coding	protein_coding	ENST00000379727	6	6069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-17	0.000695	125219	2	527	125748	0.00211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.357	322	304	1.06	0.0000179	3359
Missense in Polyphen		129	110.18	1.1708		1262
Synonymous	-0.0685	123	122	1.01	0.00000667	1044
Loss of Function	-1.11	23	17.9	1.28	9.33e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00321	0.00321
Ashkenazi Jewish	0.000795	0.000794
East Asian	0.00125	0.00120
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00244	0.00244
Middle Eastern	0.00125	0.00120
South Asian	0.00337	0.00334
Other	0.00473	0.00408

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: Amodiaquine Pathway, Pharmacokinetics;Tryptophan metabolism - Homo sapiens (human);Retinol metabolism - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Warfarin Pathway, Pharmacokinetics;Estrogen Metabolism Pathway;Gefitinib Pathway, Pharmacokinetics;Erlotinib Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Tryptophan Metabolism;Fatty Acid Omega Oxidation;Aryl Hydrocarbon Receptor;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Aryl Hydrocarbon Receptor Pathway;Vitamin D Receptor Pathway;Estrogen Receptor Pathway;Nuclear Receptors Meta-Pathway;Melatonin metabolism and effects;Cannabinoid receptor signaling;Liver steatosis AOP;Oxidative Stress;Oxidation by Cytochrome P450;Tryptophan metabolism;Tamoxifen metabolism;Benzo(a)pyrene metabolism;Estrogen metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE);Arachidonic acid metabolism;Xenobiotics;Tyrosine metabolism;Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET);Androgen and estrogen biosynthesis and metabolism;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Biosynthesis of protectins;Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Vitamin A (retinol) metabolism;Xenobiotics metabolism;Tryptophan degradation;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.835

Intolerance Scores

• loftool: 0.627
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

• pHI: 0.0886
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.671

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp1a1
• 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; hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to hypoxia;lipid hydroxylation;porphyrin-containing compound metabolic process;aging;steroid metabolic process;cell population proliferation;amine metabolic process;response to wounding;response to virus;response to nematode;response to herbicide;ethylene metabolic process;coumarin metabolic process;flavonoid metabolic process;response to iron(III) ion;insecticide metabolic process;drug metabolic process;regulation of lipid metabolic process;dibenzo-p-dioxin catabolic process;epoxygenase P450 pathway;response to food;response to lipopolysaccharide;response to vitamin A;response to immobilization stress;vitamin D metabolic process;response to drug;long-chain fatty acid biosynthetic process;9-cis-retinoic acid biosynthetic process;camera-type eye development;response to antibiotic;response to arsenic-containing substance;digestive tract development;hydrogen peroxide biosynthetic process;response to hyperoxia;oxidation-reduction process;maternal process involved in parturition;hepatocyte differentiation;demethylation;cellular response to copper ion;cellular response to organic cyclic compound;omega-hydroxylase P450 pathway;positive regulation of G1/S transition of mitotic cell cycle
• Cellular component: mitochondrion;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: monooxygenase activity;iron ion binding;protein binding;oxidoreductase activity;oxidoreductase activity, acting on diphenols and related substances as donors;flavonoid 3'-monooxygenase activity;oxygen binding;enzyme binding;heme binding;demethylase activity;aromatase activity;vitamin D 24-hydroxylase activity;estrogen 16-alpha-hydroxylase activity