CYP1B1
protein-codingcytochrome P450 family 1 subfamily B member 1, the group of Cytochrome P450 family 1
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. The enzyme encoded by this gene localizes to the endoplasmic reticulum and metabolizes procarcinogens such as polycyclic aromatic hydrocarbons and 17beta-estradiol. Mutations in this gene have been associated with primary congenital glaucoma; therefore it is thought that the enzyme also metabolizes a signaling molecule involved in eye development, possibly a steroid. [provided by RefSeq, Jul 2008]
- GLC3A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~42.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009277
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009277
Submitter: Laboratory for Molecular Medicine
This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.
Inheritance Pattern: AR
Disease ID:MONDO:0800472
Submitter: ClinGen
Pathogenic variants in the *CYP1B1* gene were first described as a cause of primary congenital glaucoma (PCG) by Stoilov et al. in 1997 (PMID: 9097971), through genetic linkage analysis and mutation screening. PCG pathogenicity in patients is associated with the presence of *CYP1B1* variants in the homozygous or compound heterozygous state. The clinical features of the disease include increased intraocular pressure, increased corneal diameter, enlarged globe, Haab striae (breaks in Descemet’s membrane), corneal edema, and optic nerve head cupping. Although most *CYP1B1* variants are associated with PCG, variants have been also described causing other disease phenotypes including aniridia (PMID:23767995; PMID:24001018), anterior segment dysgenesis 6 (ASGD6, OMIM #617315), Peter’s anomaly (PA, OMIM #617315), and primary open angle glaucoma with adult or juvenile onset (POAG, JOAG; OMIM# 231300; PMID: 24099281; PMID: 19643970). It is important to note, however, that the same variants can be associated with different disease phenotypes (PMID: 17914928), and that diverse disease phenotypes can occur among members of the same family (PMID: 26164761) or within the same individual (PMID: 20827438). Per criteria outlined by the ClinGen Lumping & Splitting Working Group, these findings as well as the similarities in inheritance pattern were found to point to a single disease spectrum rather than multiple distinct disease entities. For the purposes of this curation, this lumped disease entity has been referred to as CYP1B1-related glaucoma with or without anterior segment dysgenesis. More than 82 variants have been described in the literature (PMID: 17914928). Ten disease-causing variants were scored as part of this curation, which have been recurrently identified in multiple probands having different phenotypes (e.g. ASD6, PCG, PA, POAG) and have been shown *in vivo* to impair the proper functioning of the protein. Pathogenicity of the variants follows an autosomal recessive mode of inheritance in probands. The mechanism of pathogenicity includes missense, nonsense, and frameshift variants that disrupt or abolish protein function by reducing enzymatic activity (e.g p.Glu387Lys), decreasing protein stability (e.g. p.Pro437Leu), or triggering truncation of the protein product (e.g p.Ala179fs). The variants are observed at a low frequency that is consistent with the disease penetrance. Experimental evidence indicates that *CYP1B1* encodes a protein that is a member of the P450 family of enzymes which are involved in the metabolism of steroids, fatty acids, and retinoids. *CYP1B1* is highly expressed in the iris and ciliary body of the human eye. CYP1B1 is hypothesized to participate in the metabolism of a substrate that is important for the normal development and functioning of the anterior segment of the eye, which is further supported by evidence showing a higher expression of this gene in fetal than in adult eyes. Functional, functional alteration and animal models indicate that variants in *CYP1B1* interfere with the normal metabolism of other proteins known to be involved in pathogenesis (e.g. upregulation of MYOC, PMID: 23028769), result in disruption of microfibril fibers in the extracellular matrix in glaucoma patients compared to controls, or alter CYP1B1 expression in cultured cells resulting in lower protein activity and instability. Mice deficient in *Cyp1b1* expression show abnormalities during development of the ocular tissue (e.g. increased collagen loss resulting in severe atrophy of the trabecular meshwork in mice, PMID 24879660). In summary, *CYP1B1* is definitively associated with autosomal recessive CYP1B1-related glaucoma with or without anterior segment dysgenesis. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time without the emergence of contradictory evidence. This classification was approved by the ClinGen Glaucoma and Neuro-Ophthalmology Gene Curation Expert Panel on January 19th, 2023 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0009277
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0800472
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011414
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0020366
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: Ophthalmologic; Pharmacogenomic
Rationale: Early diagnosis and treatment with surgery (with the use of pre and postoperative agents to control intraocular pressure), or, if surgery is not effective, drainage implants or cyclodestruction, may be effective to decrease morbidity and mortality related to vision loss; Agents that may contribute to glaucoma, as well as alpha-2-agonists, should be avoided
Comments: Severe and difficult to treat glaucoma has been reported in many individuals with Peters anomaly; heterozygous variants may increase susceptibility to glaucoma; Digenic inheritance (with MYOC) has been reported; Variants may also act as disease modifiers (eg, related to Glaucoma, age of onset)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CYP1B1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000104.4. 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 | 2 | 203 | 3 | 209 | |
| missense | 17 | 36 | 143 | 14 | 1 | 211 |
| nonsense | 14 | 11 | 25 | |||
| start loss | 2 | 2 | 4 | |||
| frameshift | 19 | 22 | 2 | 43 | ||
| splice donor/acceptor (+/-2bp) | 2 | 2 | 1 | 5 | ||
| Total | 55 | 73 | 148 | 217 | 4 | 497 |
Highest pathogenic variant AF is 0.00040057572
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000095.2 | 2 | MANE Select | |
| Ensembl | ENSP00000478561.1 | 2 | MANE Select | |
| Ensembl | ENSP00000478839.2 | 2 | Standard | |
| Ensembl | ENSP00000478839.2 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Amodiaquine Pathway, Pharmacokinetics
- Tryptophan metabolism - Homo sapiens (human)
- Steroid hormone biosynthesis - Homo sapiens (human)
- Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human)
- Chemical carcinogenesis - Homo sapiens (human)
Biological Process
- angiogenesis
- trabecular meshwork development
- cellular aromatic compound metabolic process
- xenobiotic metabolic process
- nitric oxide biosynthetic process
Molecular Function
- monooxygenase activity
- iron ion binding
- oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
- oxygen binding
- heme binding
Cellular Component
- mitochondrion
- endoplasmic reticulum membrane
- organelle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000260630
- Coding exons
- 2
- Length
- 42929
- Individuals with no LoFs
- 125543
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 203
- Defined
- 125746
- p
- 0.000808
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.748 | 356 | 318 | 1.12 | 0.0000155 | 3494 |
| Missense (PolyPhen) | 139 | 133.73 | 1.0394 | 1509 | ||
| Synonymous | -1.92 | 171 | 142 | 1.21 | 0.00000711 | 1138 |
| Loss of Function | 1.10 | 9 | 13.4 | 0.674 | 7.10e-7 | 120 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.0011 | 0.0011 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.0012 | 0.0011 | notable |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, retinoid and xenobiotics. Preferentially oxidizes 17beta- estradiol to the carcinogenic 4-hydroxy derivative, and a variety of procarcinogenic compounds to their activated forms, including polycyclic aromatic hydrocarbons. Promotes angiogenesis by removing cellular oxygenation products, thereby decreasing oxidative stress, release of antiangiogenic factor THBS2, then allowing endothelial cells migration, cell adhesion and capillary morphogenesis. These changes are concommitant with the endothelial nitric oxide synthase activity and nitric oxide synthesis. Plays an important role in the regulation of perivascular cell proliferation, migration, and survival through modulation of the intracellular oxidative state and NF-kappa-B expression and/or activity, during angiogenesis. Contributes to oxidative homeostasis and ultrastructural organization and function of trabecular meshwork tissue through modulation of POSTN expression. {ECO:0000269|PubMed:10426814, ECO:0000269|PubMed:15258110, ECO:0000269|PubMed:22888116, ECO:0000269|PubMed:23821647}.;
- Disease
- DISEASE: Anterior segment dysgenesis 6 (ASGD6) [MIM:617315]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD6 patients predominantly manifest Peters anomaly. Peters anomaly consists of corneal leukoma, defects in the posterior structures of the cornea such as absence of the posterior corneal stroma and Descemet membrane, and a variable degree of iridocorneal and/or keratolenticular adhesions. Over 50% of patients develop glaucoma in childhood. {ECO:0000269|PubMed:11403040}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Glaucoma 3, primary congenital, A (GLC3A) [MIM:231300]: An autosomal recessive form of primary congenital glaucoma (PCG). PCG is characterized by marked increase of intraocular pressure at birth or early childhood, large ocular globes (buphthalmos) and corneal edema. It results from developmental defects of the trabecular meshwork and anterior chamber angle of the eye that prevent adequate drainage of aqueous humor. {ECO:0000269|PubMed:10227395, ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:11184479, ECO:0000269|PubMed:11527932, ECO:0000269|PubMed:11774072, ECO:0000269|PubMed:11980847, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:14640114, ECO:0000269|PubMed:15255109, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16490498, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:16735994, ECO:0000269|PubMed:16862072, ECO:0000269|PubMed:18470941, ECO:0000269|PubMed:9463332, ECO:0000269|PubMed:9497261}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry.; DISEASE: Glaucoma 1, open angle, A (GLC1A) [MIM:137750]: A form of primary open angle glaucoma (POAG). POAG is characterized by a specific pattern of optic nerve and visual field defects. The angle of the anterior chamber of the eye is open, and usually the intraocular pressure is increased. However, glaucoma can occur at any intraocular pressure. The disease is generally asymptomatic until the late stages, by which time significant and irreversible optic nerve damage has already taken place. {ECO:0000269|PubMed:11774072}. Note=The gene represented in this entry acts as a disease modifier. Digenic mutations in CYP1B1 and MYOC have been found in a family segregating both primary adult- onset and juvenile forms of open angle glaucoma (PubMed:11774072). All affected family members with mutations in both MYOC and CYP1B1 had juvenile glaucoma, whereas those with only the MYOC mutation had the adult-onset form (PubMed:11774072). {ECO:0000269|PubMed:11774072}.;
Recessive Scores
- pRec
- 0.620
Intolerance Scores
- LoFtool
- 0.351
- RVIS EVS
- 0.44
- RVIS percentile EVS
- 77.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.893
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |