GeneBe

CYP4F2

protein-coding

cytochrome P450 family 4 subfamily F member 2, the group of Cytochrome P450 family 4

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. The enzyme starts the process of inactivating and degrading leukotriene B4, a potent mediator of inflammation. This gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F11, is approximately 16 kb away. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001082.5

Inheritance

AD

ClinVar variants

U:73B:25

Top phenotype

Warfarin metabolism

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr19:15,878,023-15,898,077

External References & Databases

Ensembl (ENSG00000186115)NCBI Gene (8529)OMIM (604426)HGNC:2645GenCCUniProt (P78329)AlphaFoldClinVar (CYP4F2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~20.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Warfarin metabolismAD

Manifestation: General

Intervention: Pharmacogenomic

Rationale: Selection and dosing of medications (warfarin) may be affected by the presence of variants

Refs: 18250228; 19207028; 19300499; 22417713; 22534826; 22854539; 22855976Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CYP4F2 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 85
CYP4F2-related disorderTotal: 17
not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001082.5. 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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
3
clinvar
 20
missense
73
clinvar
3
clinvar
2
clinvar
 78
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total007320598
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001082.5RefSeqNP_001073.312MANE Select
ENST00000221700.11EnsemblENSP00000221700.312MANE Select
ENST00000011989.11EnsemblENSP00000011989.812Standard
ENST00000011989.12EnsemblENSP00000011989.812Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Arachidonic acid metabolism - Homo sapiens (human)
  • Etodolac Action Pathway
  • Ketoprofen Action Pathway
  • Ibuprofen Action Pathway
  • Rofecoxib Action Pathway

Biological Process

  • very long-chain fatty acid metabolic process
  • long-chain fatty acid metabolic process
  • renal water homeostasis
  • pressure natriuresis
  • icosanoid metabolic process

Molecular Function

  • monooxygenase activity
  • iron ion binding
  • protein binding
  • arachidonic acid epoxygenase activity
  • oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen

Cellular Component

  • cytoplasm
  • endoplasmic reticulum membrane
  • apical plasma membrane
  • organelle membrane
  • intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000221700
Coding exons
12
Length
20098
Individuals with no LoFs
125463
Homozygous LoFs
1
Heterozygous LoFs
283
Defined
125747
p
0.00113
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.3413473301.050.00002093414
Missense (PolyPhen)8486.5760.97024940
Synonymous-2.531661291.280.000007891016
Loss of Function0.07052525.40.9850.00000116279

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000860.00086rare
Latino/Admixed American0.00310.0031notable
Ashkenazi Jewish0.00180.0018notable
East Asian0.00220.0022notable
Finnish0.0000920.000092rare
European (Non-Finnish)0.000450.00043rare
South Asian0.000980.00098rare
Other0.00380.0038notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Omega-hydroxylase that oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids and xenobiotics. Plays a key role in vitamin K catabolism by mediating omega-hydroxylation of vitamin K1 (phylloquinone), and menaquinone-4 (MK-4), a form of vitamin K2. Hydroxylation of phylloquinone and MK-4 probably regulates blood coagulation (PubMed:19297519, PubMed:24138531). Also shows arachidonic acid omega-hydroxylase activity in kidney, by mediating conversion of arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE), possibly influencing blood pressure control (PubMed:10660572, PubMed:17341693, PubMed:18574070). Also acts as a leukotriene-B(4) omega-hydroxylase by mediating conversion of leukotriene-B(4) (LTB4) to its omega-hydroxylated metabolite 20-hydroxyleukotriene- B(4) (20-OH LTB4) (PubMed:8026587, PubMed:9799565). {ECO:0000269|PubMed:10660572, ECO:0000269|PubMed:17341693, ECO:0000269|PubMed:18574070, ECO:0000269|PubMed:19297519, ECO:0000269|PubMed:24138531, ECO:0000269|PubMed:8026587, ECO:0000269|PubMed:9799565}.;

Recessive Scores

pRec
0.213

Intolerance Scores

LoFtool
0.404
RVIS EVS
0.27
RVIS percentile EVS
70.73

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.929

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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