CYP4F12

cytochrome P450 family 4 subfamily F member 12, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 19:15673018-15697174

Links

ENSG00000186204 ∙ NCBI:66002 ∙ OMIM:611485 ∙ HGNC:18857 ∙ Uniprot:Q9HCS2 ∙ 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 CYP4F12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4F12 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		1
missense			45	4		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	5	0

Variants in CYP4F12

This is a list of pathogenic ClinVar variants found in the CYP4F12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15673696-A-C		not specified	Uncertain significance (Feb 23, 2023)
19-15678315-T-C		not specified	Likely benign (Nov 08, 2022)
19-15678354-T-C		not specified	Likely benign (Nov 08, 2022)
19-15678385-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-15680277-G-A		not specified	Uncertain significance (Jan 20, 2025)
19-15680281-C-A		not specified	Uncertain significance (Nov 13, 2024)
19-15680430-C-T		not specified	Uncertain significance (May 24, 2023)
19-15680434-A-G		not specified	Uncertain significance (Aug 08, 2022)
19-15680445-C-G		not specified	Uncertain significance (Aug 08, 2022)
19-15680481-T-A		not specified	Uncertain significance (Jul 27, 2024)
19-15680503-G-A		not specified	Uncertain significance (Jul 17, 2024)
19-15682453-T-G		not specified	Uncertain significance (Sep 08, 2024)
19-15682465-A-G		not specified	Uncertain significance (Nov 10, 2024)
19-15682501-A-C		not specified	Uncertain significance (May 31, 2023)
19-15682504-G-T		not specified	Uncertain significance (May 17, 2023)
19-15683497-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-15683553-C-A		not specified	Uncertain significance (Oct 07, 2024)
19-15683567-A-C		not specified	Uncertain significance (Feb 23, 2025)
19-15683571-C-G		not specified	Uncertain significance (Jun 29, 2023)
19-15683590-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-15683606-G-A		not specified	Likely benign (Nov 30, 2022)
19-15683659-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-15683678-T-C		not specified	Uncertain significance (Feb 05, 2024)
19-15683741-T-C		not specified	Uncertain significance (Aug 20, 2024)
19-15683753-T-C		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4F12	protein_coding	protein_coding	ENST00000550308	12	24418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-17	0.00602	125270	0	478	125748	0.00190

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.762	365	326	1.12	0.0000199	3422
Missense in Polyphen		104	94.748	1.0976		1050
Synonymous	-0.449	136	130	1.05	0.00000790	1010
Loss of Function	0.0432	26	26.2	0.991	0.00000138	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0186	0.0172
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000614	0.000607
Middle Eastern	0.000382	0.000381
South Asian	0.00184	0.00170
Other	0.00119	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes leukotriene B4 omega-hydroxylation and arachidonic acid omega-hydroxylation but with an activity much lower than that of CYP4F2. Catalyzes the hydroxylation of the antihistamine ebastine.
• Pathway: Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;Oxidation by Cytochrome P450;Tryptophan metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Tyrosine metabolism;Fatty acids;Eicosanoids;Androgen and estrogen biosynthesis and metabolism;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;Tryptophan degradation;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.442
• rvis_EVS: 3.74
• rvis_percentile_EVS: 99.59

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.112
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0495

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp4f14
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; digestive/alimentary phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: very long-chain fatty acid metabolic process;long-chain fatty acid metabolic process;renal water homeostasis;pressure natriuresis;drug metabolic process;arachidonic acid metabolic process;epoxygenase P450 pathway;leukotriene B4 catabolic process;vitamin E metabolic process;sodium ion homeostasis;oxidation-reduction process
• Cellular component: cytoplasm;endoplasmic reticulum membrane;integral component of membrane;apical plasma membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: monooxygenase activity;iron ion binding;arachidonic acid epoxygenase activity;alkane 1-monooxygenase activity;heme binding;leukotriene-B4 20-monooxygenase activity;aromatase activity