CYP4F2

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

Basic information

Region (hg38): 19:15878022-15898077

Links

ENSG00000186115 ∙ NCBI:8529 ∙ OMIM:604426 ∙ HGNC:2645 ∙ Uniprot:P78329 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Warfarin metabolism	AD	Pharmacogenomic	Selection and dosing of medications (warfarin) may be affected by the presence of variants	General	18250228; 19207028; 19300499; 22417713; 22534826; 22854539; 22855976

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP4F2 gene.

• Inborn genetic diseases (20 variants)
• not provided (8 variants)
• warfarin response - Dosage (1 variants)
• acenocoumarol response - Dosage (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4F2 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	2	3
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	20	2	4

Variants in CYP4F2

This is a list of pathogenic ClinVar variants found in the CYP4F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15878763-T-C		CYP4F2-related disorder	Likely benign (Feb 04, 2021)
19-15878779-G-T		CYP4F2-related disorder	Likely benign (May 05, 2023)
19-15878791-G-T		CYP4F2-related disorder	Likely benign (Mar 18, 2020)
19-15878832-T-C		not specified	Uncertain significance (Apr 06, 2022)
19-15878848-T-C		not specified	Uncertain significance (Feb 13, 2024)
19-15878864-G-A		CYP4F2-related disorder	Likely benign (Sep 13, 2021)
19-15878865-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-15878891-G-A		CYP4F2-related disorder	Likely benign (Dec 18, 2020)
19-15878898-T-G		not specified	Uncertain significance (Dec 19, 2022)
19-15878920-T-C		CYP4F2-related disorder	Likely benign (Oct 17, 2019)
19-15878940-G-C		CYP4F2-related disorder	Benign (Jul 12, 2019)
19-15879401-C-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
19-15879621-C-T		warfarin response - Dosage • acenocoumarol response - Dosage • CYP4F2-related disorder	drug response (Mar 24, 2021)
19-15879668-C-A			Uncertain significance (Jan 01, 2019)
19-15879771-G-A		CYP4F2-related disorder	Likely benign (Jul 12, 2019)
19-15879888-C-T			Benign (Jan 25, 2018)
19-15879897-C-A		not specified	Uncertain significance (Dec 22, 2023)
19-15885914-C-T		CYP4F2-related disorder	Benign (Jul 12, 2019)
19-15885946-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-15885947-G-A		CYP4F2-related disorder	Likely benign (Aug 13, 2019)
19-15885985-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-15886010-G-A		CYP4F2-related disorder	Benign (Oct 18, 2019)
19-15886018-G-C			Benign (Jul 16, 2018)
19-15886024-A-G		not specified	Uncertain significance (Nov 08, 2022)
19-15886041-G-A		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4F2	protein_coding	protein_coding	ENST00000221700	12	20098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.58e-17	0.00819	125463	1	283	125747	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.341	347	330	1.05	0.0000209	3414
Missense in Polyphen		84	86.576	0.97024		940
Synonymous	-2.53	166	129	1.28	0.00000789	1016
Loss of Function	0.0705	25	25.4	0.985	0.00000116	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00397	0.00396
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.00223	0.00223
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000448	0.000431
Middle Eastern	0.00223	0.00223
South Asian	0.000980	0.000980
Other	0.00375	0.00375

dbNSFP

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}.
• Pathway: Arachidonic acid metabolism - Homo sapiens (human);Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Prostaglandin Leukotriene metabolism;Synthesis of Leukotrienes (LT) and Eoxins (EX);Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE);Arachidonic acid metabolism;Fatty acids;Eicosanoids;Miscellaneous substrates;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;α-tocopherol degradation;Fatty acid metabolism;Putative anti-Inflammatory metabolites formation from EPA;Vitamin E metabolism;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.73

Haploinsufficiency Scores

• pHI: 0.0961
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp4f18
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: very long-chain fatty acid metabolic process;long-chain fatty acid metabolic process;renal water homeostasis;pressure natriuresis;icosanoid metabolic process;leukotriene metabolic process;blood coagulation;regulation of blood pressure;drug metabolic process;arachidonic acid metabolic process;epoxygenase P450 pathway;negative regulation of icosanoid secretion;positive regulation of icosanoid secretion;leukotriene B4 catabolic process;vitamin E metabolic process;menaquinone catabolic process;phylloquinone catabolic process;vitamin K catabolic process;sodium ion homeostasis;oxidation-reduction process;omega-hydroxylase P450 pathway
• Cellular component: cytoplasm;endoplasmic reticulum membrane;apical plasma membrane;organelle membrane;intracellular membrane-bounded organelle
• 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;alkane 1-monooxygenase activity;heme binding;leukotriene-B4 20-monooxygenase activity;arachidonic acid omega-hydroxylase activity;alpha-tocopherol omega-hydroxylase activity;tocotrienol omega-hydroxylase activity;20-hydroxy-leukotriene B4 omega oxidase activity;20-aldehyde-leukotriene B4 20-monooxygenase activity