CYP2A7

cytochrome P450 family 2 subfamily A member 7, the group of Cytochrome P450 family 2

Basic information

Region (hg38): 19:40875439-40882752

Links

ENSG00000198077 ∙ NCBI:1549 ∙ OMIM:608054 ∙ HGNC:2611 ∙ Uniprot:P20853 ∙ 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 CYP2A7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP2A7 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					2	2
missense			67	4	6	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	4	8

Variants in CYP2A7

This is a list of pathogenic ClinVar variants found in the CYP2A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40875698-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-40875706-A-C		not specified	Uncertain significance (Jan 23, 2024)
19-40875707-A-G		not specified	Uncertain significance (Jan 10, 2022)
19-40875712-A-C		not specified	Uncertain significance (Nov 21, 2023)
19-40875713-T-C		not specified	Uncertain significance (Jan 19, 2022)
19-40875742-A-C			Benign (Dec 31, 2019)
19-40875758-A-G		not specified	Uncertain significance (Aug 22, 2022)
19-40875762-G-C		not specified	Uncertain significance (Jan 30, 2025)
19-40875812-C-T			Likely benign (Dec 01, 2022)
19-40875848-G-T		not specified	Uncertain significance (Oct 09, 2024)
19-40875857-C-T		not specified	Uncertain significance (Jan 18, 2023)
19-40875858-G-C		not specified	Uncertain significance (Jul 14, 2024)
19-40875866-T-A			Benign (Dec 31, 2019)
19-40876559-T-C		not specified	Uncertain significance (Aug 20, 2024)
19-40876573-G-C		not specified	Likely benign (Jun 18, 2021)
19-40876578-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-40876638-C-T			Likely benign (Jul 01, 2023)
19-40876639-G-A			Benign (Aug 22, 2018)
19-40877194-G-A		not specified	Uncertain significance (Apr 08, 2024)
19-40877236-C-T			Benign (Jun 15, 2018)
19-40877255-T-A		not specified	Uncertain significance (Apr 24, 2024)
19-40877266-A-G		not specified	Uncertain significance (Nov 15, 2023)
19-40877280-G-T		not specified	Uncertain significance (Apr 04, 2024)
19-40877311-G-C		not specified	Uncertain significance (Dec 09, 2024)
19-40877323-A-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP2A7	protein_coding	protein_coding	ENST00000301146	9	7314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.78e-15	0.00596	125570	2	176	125748	0.000708

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.70	381	298	1.28	0.0000171	3238
Missense in Polyphen		125	106.81	1.1703		1173
Synonymous	-2.43	153	119	1.28	0.00000724	929
Loss of Function	-0.414	21	19.1	1.10	9.34e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00264	0.00264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000392	0.000369
Middle Eastern	0.000326	0.000326
South Asian	0.00161	0.00160
Other	0.000489	0.000489

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: Vitamin A Deficiency;Retinol Metabolism;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;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: 0.959
• rvis_EVS: 3.43
• rvis_percentile_EVS: 99.46

Haploinsufficiency Scores

• pHI: 0.0572
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp2a5
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: organic acid metabolic process;xenobiotic metabolic process;coumarin metabolic process;epoxygenase P450 pathway;exogenous drug catabolic process;oxidation-reduction process
• Cellular component: cytoplasm;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: 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;oxygen binding;heme binding;aromatase activity