CYP2F1

protein-coding

cytochrome P450 family 2 subfamily F member 1, 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 and is known to dehydrogenate 3-methylindole, an endogenous toxin derived from the fermentation of tryptophan, as well as xenobiotic substrates such as naphthalene and ethoxycoumarin. This gene 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]

Previous symbols:

CYP2F

MANE transcript

NM_000774.5

Inheritance

—

ClinVar variants

U:91B:8

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr19:41,114,432-41,128,381

External References & Databases

Ensembl (ENSG00000197446)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 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 CYP2F1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000774.5. 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	1 clinvar	1 clinvar	4
missense			88 clinvar	3 clinvar	3 clinvar	94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	91	4	4	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000774.5	RefSeq	NP_000765.2	9	MANE Select
ENST00000331105.7	Ensembl	ENSP00000333534.2	9	MANE Select
ENST00000439903.2	Ensembl	ENSP00000443424.1	3	Standard
ENST00000532164.2	Ensembl	ENSP00000471416.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human)
Oxidation by Cytochrome P450
Tryptophan metabolism
Metapathway biotransformation Phase I and II
Phase I - Functionalization of compounds

Biological Process

organic acid metabolic process
xenobiotic metabolic process
response to toxic substance
naphthalene metabolic process
trichloroethylene metabolic process

Molecular Function

monooxygenase activity
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

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: ENST00000331105
Coding exons: 9
Length: 13935
Individuals with no LoFs: 79498
Homozygous LoFs: 6001
Heterozygous LoFs: 40249
Defined: 125748
p: 0.205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00200	311	311	1.00	0.0000196	3188
Missense (PolyPhen)		95	100.87	0.94178		1029
Synonymous	0.785	124	136	0.914	0.00000893	1006
Loss of Function	0.771	15	18.6	0.807	9.39e-7	207

Population LoF Frequency

Population	CAF	p-value	Status
African	0.40	0.40	notable
Latino/Admixed American	0.14	0.14	notable
Ashkenazi Jewish	0.17	0.16	notable
East Asian	0.25	0.25	notable
Finnish	0.24	0.24	notable
European (Non-Finnish)	0.19	0.19	notable
South Asian	0.23	0.23	notable
Other	0.19	0.19	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the metabolism of various pneumotoxicants including naphthalene. Is able to dealkylate ethoxycoumarin, propoxycoumarin, and pentoxyresorufin but possesses no activity toward ethoxyresorufin and only trace dearylation activity toward benzyloxyresorufin. Bioactivates 3- methylindole (3MI) by dehydrogenation to the putative electrophile 3-methylene-indolenine. {ECO:0000269|PubMed:1974816}.;

Intolerance Scores

LoFtool: 0.824
RVIS EVS: 1
RVIS percentile EVS: 90.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.317

Gene Damage Prediction

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