CYP27C1
protein-codingcytochrome P450 family 27 subfamily C member 1, the group of Cytochrome P450 family 27
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. [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 ~36.5 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 CYP27C1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001367502.1. 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 | ||||
| missense | 59 | 2 | 1 | 62 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 59 | 3 | 1 | 63 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001354431.1 | 9 | MANE Select | |
| Ensembl | ENSP00000499243.1 | 9 | MANE Select | |
| RefSeq | NP_001001665.3 | 7 | Standard | |
| RefSeq | NP_001354430.1 | 7 | 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
Biological Process
- retinol metabolic process
- retinoic acid metabolic process
- retinal metabolic process
- oxidation-reduction process
Molecular Function
- retinoic acid binding
- monooxygenase activity
- 11-cis retinal binding
- all-trans retinal binding
- iron ion binding
Cellular Component
- cellular_component
- membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335247
- Coding exons
- 7
- Length
- 35959
- Individuals with no LoFs
- 125707
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 41
- Defined
- 125748
- p
- 0.000163
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.685 | 198 | 227 | 0.872 | 0.0000139 | 2417 |
| Missense (PolyPhen) | 82 | 101.59 | 0.80717 | 1099 | ||
| Synonymous | 0.427 | 87 | 92.2 | 0.943 | 0.00000571 | 754 |
| Loss of Function | 1.31 | 12 | 18.0 | 0.667 | 9.49e-7 | 198 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the conversion of all-trans retinol (also called vitamin A1, the precursor of 11-cis retinal) to 3,4- didehydroretinol (also called vitamin A2, the precursor of 11-cis 3,4-didehydroretinal). Also acts on all-trans retinal and all- trans retinoic acid. {ECO:0000269|PubMed:27059013}.;
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- LoFtool
- 0.607
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 50.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.300
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |