CYP4F3

cytochrome P450 family 4 subfamily F member 3, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 19:15640896-15662825

Previous symbols: [ "LTB4H" ]

Links

ENSG00000186529 ∙ NCBI:4051 ∙ OMIM:601270 ∙ HGNC:2646 ∙ Uniprot:Q08477 ∙ 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 CYP4F3 gene.

• Inborn genetic diseases (22 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4F3 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	1	3
missense			24	3	2	29
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	24	5	4

Variants in CYP4F3

This is a list of pathogenic ClinVar variants found in the CYP4F3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15641438-C-T		not specified	Uncertain significance (Dec 15, 2022)
19-15641555-G-A			Likely benign (Jun 01, 2018)
19-15641555-G-T			Uncertain significance (May 01, 2021)
19-15641570-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-15641579-C-G		not specified	Uncertain significance (Feb 07, 2023)
19-15641603-A-T		not specified	Uncertain significance (Jan 26, 2022)
19-15643959-A-T		not specified	Uncertain significance (Oct 05, 2023)
19-15644007-G-A		not specified	Uncertain significance (Mar 28, 2023)
19-15644024-A-C		not specified	Likely benign (Oct 13, 2023)
19-15644024-A-T		not specified	Uncertain significance (Mar 13, 2023)
19-15645768-C-T			Uncertain significance (May 01, 2021)
19-15647199-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-15647253-A-C		not specified	Uncertain significance (Mar 29, 2023)
19-15647318-C-A			Likely benign (Jun 20, 2018)
19-15649205-A-G			Benign (Jul 21, 2018)
19-15649952-T-G		not specified	Uncertain significance (Aug 08, 2022)
19-15650005-A-G		not specified	Uncertain significance (Mar 04, 2024)
19-15650060-C-A		not specified	Uncertain significance (May 08, 2023)
19-15650073-G-A			Benign/Likely benign (Feb 01, 2023)
19-15650077-T-C			Likely benign (Jul 31, 2018)
19-15650085-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-15650088-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-15650089-G-A			Uncertain significance (-)
19-15650137-C-A		not specified	Uncertain significance (Jan 30, 2024)
19-15650164-A-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4F3	protein_coding	protein_coding	ENST00000221307	12	21929

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-16	0.0105	125414	0	334	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.896	371	326	1.14	0.0000205	3415
Missense in Polyphen		97	82.279	1.1789		954
Synonymous	0.0598	129	130	0.993	0.00000788	1026
Loss of Function	0.0793	24	24.4	0.983	0.00000104	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00503	0.00498
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000218	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000917	0.000897
Middle Eastern	0.000218	0.000217
South Asian	0.00164	0.00163
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform CYP4F3A: Catalyzes the omega-hydroxylation of leukotriene-B(4), a potent chemoattractant for polymorphonuclear leukocytes, it has low activity for arachidonic acid. {ECO:0000269|PubMed:11461919, ECO:0000269|PubMed:8486631}.
• 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);Arachidonic acid metabolism;Fatty acids;Eicosanoids;Miscellaneous substrates;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;Putative anti-Inflammatory metabolites formation from EPA;Vitamin E metabolism;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.328
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.69

Haploinsufficiency Scores

• pHI: 0.439
• hipred: N
• hipred_score: 0.131
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp4f13

Gene ontology

• Biological process: icosanoid metabolic process;leukotriene metabolic process;leukotriene B4 catabolic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane
• Molecular function: monooxygenase activity;iron ion binding;heme binding;leukotriene-B4 20-monooxygenase activity;20-hydroxy-leukotriene B4 omega oxidase activity;20-aldehyde-leukotriene B4 20-monooxygenase activity