CYP2A7

protein-coding

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

Gene summary

This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum; its substrate has not yet been determined. This gene, which produces two transcript variants, is part of a large cluster of cytochrome P450 genes from the CYP2A, CYP2B and CYP2F subfamilies on chromosome 19q. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000764.3

Inheritance

—

ClinVar variants

U:112B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr19:40,875,439-40,882,752

External References & Databases

Ensembl (ENSG00000198077)

Transcript & Mutation Effects

hg38 • Region Span ~7.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CYP2A7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 115

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000764.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			110 clinvar	10 clinvar	2 clinvar	122
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	112	10	4	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000764.3	RefSeq	NP_000755.2	9	MANE Select
ENST00000301146.9	Ensembl	ENSP00000301146.4	9	MANE Select
NM_030589.3	RefSeq	NP_085079.2	8	Standard
ENST00000291764.3	Ensembl	ENSP00000291764.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin A Deficiency
Retinol Metabolism
Oxidation by Cytochrome P450
Metapathway biotransformation Phase I and II
Phase I - Functionalization of compounds

Biological Process

organic acid metabolic process
xenobiotic metabolic process
coumarin metabolic process
epoxygenase P450 pathway
exogenous drug catabolic process

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

Cellular Component

cytoplasm
endoplasmic reticulum membrane
organelle membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301146
Coding exons: 9
Length: 7314
Individuals with no LoFs: 125570
Homozygous LoFs: 2
Heterozygous LoFs: 176
Defined: 125748
p: 0.000708

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.70	381	298	1.28	0.0000171	3238
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0020	0.0019	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00039	0.00037	rare
South Asian	0.0016	0.0016	notable
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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.;

Intolerance Scores

LoFtool: 0.959
RVIS EVS: 3.43
RVIS percentile EVS: 99.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.989

Gene Damage Prediction

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