CYP4F11
protein-codingcytochrome P450 family 4 subfamily F member 11, the group of Cytochrome P450 family 4
Gene summary
This gene, CYP4F11, 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 gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F2, is approximately 16 kb away. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.5 kbGenCC 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 CYP4F11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021187.4. 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 | 1 | 1 | 2 | |||
| missense | 105 | 7 | 112 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 109 | 8 | 0 | 117 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_067010.3 | 12 | MANE Select | |
| Ensembl | ENSP00000384588.2 | 12 | MANE Select | |
| RefSeq | NP_001122404.1 | 12 | Standard | |
| Ensembl | ENSP00000248041.6 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Oxidation by Cytochrome P450
- Metapathway biotransformation Phase I and II
- Phase I - Functionalization of compounds
- Metabolism of lipids
- Synthesis of Leukotrienes (LT) and Eoxins (EX)
Biological Process
- fatty acid metabolic process
- inflammatory response
- blood coagulation
- menaquinone catabolic process
- phylloquinone catabolic process
Molecular Function
- monooxygenase activity
- fatty acid binding
- iron ion binding
- 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
- heme binding
Cellular Component
- endoplasmic reticulum membrane
- integral component of membrane
- organelle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000402119
- Coding exons
- 12
- Length
- 22501
- Individuals with no LoFs
- 125525
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 223
- Defined
- 125748
- p
- 0.000887
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.40 | 395 | 324 | 1.22 | 0.0000197 | 3442 |
| Missense (PolyPhen) | 104 | 86.563 | 1.2014 | 997 | ||
| Synonymous | -1.43 | 152 | 131 | 1.16 | 0.00000801 | 1016 |
| Loss of Function | -0.584 | 30 | 26.7 | 1.12 | 0.00000130 | 287 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0019 | 0.0019 | notable |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0.00060 | 0.00060 | rare |
| European (Non-Finnish) | 0.00065 | 0.00064 | rare |
| South Asian | 0.00065 | 0.00065 | rare |
| Other | 0.0033 | 0.0033 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Omega-hydroxylase that oxidizes a variety of structurally unrelated compounds, including 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:24138531). Catalyzes omega-hydroxylation of 3-hydroxy fatty acids, such as 3-hydroxypalmitate, 3-hydroxyoleate, 3- hydroxyarachidonate, and 3-hydroxystearate (PubMed:18065749, PubMed:19932081). Oxidizes drugs such as erythromycin, benzphetamine, ethylmorphine, chlorpromazine and imipramine (PubMed:15364545). {ECO:0000269|PubMed:15364545, ECO:0000269|PubMed:18065749, ECO:0000269|PubMed:19932081, ECO:0000269|PubMed:24138531}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.189
- RVIS EVS
- -0.64
- RVIS percentile EVS
- 16.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.152
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |