CYP26C1

gene
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Summary

CYP26C1 (cytochrome P450 family 26 subfamily C member 1, HGNC:20577) is a protein-coding gene on chromosome 10q23.33, encoding Cytochrome P450 26C1 (Q6V0L0). A cytochrome P450 monooxygenase involved in the metabolism of retinoates (RAs), the active metabolites of vitamin A, and critical signaling molecules in animals.

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. This enzyme is involved in the catabolism of all-trans- and 9-cis-retinoic acid, and thus contributes to the regulation of retinoic acid levels in cells and tissues. This gene is adjacent to a related gene on chromosome 10q23.33.

Source: NCBI Gene 340665 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): focal facial dermal dysplasia type IV (Strong, GenCC)
  • GWAS associations: 7
  • Clinical variants (ClinVar): 122 total — 1 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 19
  • MANE Select transcript: NM_183374

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20577
Approved symbolCYP26C1
Namecytochrome P450 family 26 subfamily C member 1
Location10q23.33
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000187553
Ensembl biotypeprotein_coding
OMIM608428
Entrez340665

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000624358, ENST00000651965

RefSeq mRNA: 1 — MANE Select: NM_183374 NM_183374

CCDS: CCDS7425

Canonical transcript exons

ENST00000651965 — 6 exons

ExonStartEnd
ENSE000010923309306201093062234
ENSE000013275799306272093062995
ENSE000013766089306438193064536
ENSE000018035389306595693066285
ENSE000038436679306832093069540
ENSE000038446789306079893061467

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 54.83.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0737 / max 13.2966, expressed in 34 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1062680.073734

Top tissues by expression

113 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099154.83silver quality
colonic epitheliumUBERON:000039748.90gold quality
prefrontal cortexUBERON:000045145.02silver quality
olfactory segment of nasal mucosaUBERON:000538642.64silver quality
bone marrow cellCL:000209242.12gold quality
placentaUBERON:000198742.02silver quality
frontal cortexUBERON:000187040.14silver quality
cortical plateUBERON:000534339.96gold quality
gall bladderUBERON:000211038.94gold quality
superior frontal gyrusUBERON:000266138.78gold quality
stromal cell of endometriumCL:000225538.75gold quality
spleenUBERON:000210638.60silver quality
cerebral cortexUBERON:000095637.68silver quality
skeletal muscle tissueUBERON:000113437.55gold quality
bloodUBERON:000017837.22gold quality
duodenumUBERON:000211437.20silver quality
myometriumUBERON:000129636.72silver quality
ventricular zoneUBERON:000305336.48gold quality
muscle tissueUBERON:000238536.42gold quality
right coronary arteryUBERON:000162536.04gold quality
sural nerveUBERON:001548835.97gold quality
substantia nigraUBERON:000203835.73gold quality
C1 segment of cervical spinal cordUBERON:000646935.57silver quality
ganglionic eminenceUBERON:000402335.49gold quality
hindlimb stylopod muscleUBERON:000425235.39gold quality
lymph nodeUBERON:000002935.10gold quality
bone marrowUBERON:000237134.79gold quality
Ammon’s hornUBERON:000195434.64silver quality
endometriumUBERON:000129534.08gold quality
granulocyteCL:000009434.03gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.97

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 9)

  • may play a specific role in catabolizing both all-trans and 9-cis isomers of retinoic acid. (PMID:14532297)
  • CYP26A1 and CYP26C1 play a pivotal role in the pathogenesis of nonsyndromic bilateral and unilateral optic nerve aplasia. (PMID:21850183)
  • Focal facial dermal dysplasia, type IV results from the loss of function mutations in CYP26C1. (PMID:23161670)
  • Elevated expression of CYP26C1 in primary breast carcinomas (PMID:26009309)
  • Together, these findings describe CYP26C1 as the first genetic modifier for SHOX deficiency. (PMID:27861128)
  • findings suggest that CYP26C1 is a 4-oxo-atRA hydroxylase and may be important in regulating the concentrations of this active retinoid in human tissues (PMID:29476041)
  • CYP26C1 missense variants and one splicing variant were identified in six independent individuals with idiopathic short stature. (PMID:29706635)
  • This review highlights the current knowledge of structure-function of CYP26 enzymes and focuses on their role in human retinoid metabolism in different tissues. (PMID:31419517)
  • Association of CYP26C1 Promoter Hypomethylation with Small Vessel Occlusion in Korean Subjects. (PMID:34681016)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocyp26c1ENSDARG00000056029
mus_musculusCyp26c1ENSMUSG00000062432
rattus_norvegicusCyp26c1ENSRNOG00000030698

Paralogs (2): CYP26B1 (ENSG00000003137), CYP26A1 (ENSG00000095596)

Protein

Protein identifiers

Cytochrome P450 26C1Q6V0L0 (reviewed: Q6V0L0)

All UniProt accessions (2): A0A096LNL5, Q6V0L0

UniProt curated annotations — full annotation on UniProt →

Function. A cytochrome P450 monooxygenase involved in the metabolism of retinoates (RAs), the active metabolites of vitamin A, and critical signaling molecules in animals. RAs exist as at least four different isomers: all-trans-RA (atRA), 9-cis-RA, 13-cis-RA, and 9,13-dicis-RA, where atRA is considered to be the biologically active isomer, although 9-cis-RA and 13-cis-RA also have activity. Catalyzes the oxidation of atRA primarily at C-4. Oxidation of atRA limits its biological activity and initiates a degradative process leading to its eventual elimination, thereby contributes to the regulation of atRA homeostasis and signaling. Able to metabolize other RAs such as 9-cis with high efficiency. Can oxidize all-trans-13,14-dihydroretinoate (DRA) to metabolites which could include all-trans-4-oxo-DRA, all-trans-4-hydroxy-DRA, all-trans-5,8-epoxy-DRA, and all-trans-18-hydroxy-DRA. Shares sequence similarity with other CYP26 family members, but has higher affinity to 9-cis-RA and is much less sensitive to the inhibitory effects of ketoconazole. In cooperation with Cyp26a1, contributes to the CNS patterning and the development of regions of higher visual acuity.

Subcellular location. Membrane.

Tissue specificity. Detected in most tissues at very low level.

Disease relevance. Focal facial dermal dysplasia 4 (FFDD4) [MIM:614974] A form of focal facial dermal dysplasia, a group of developmental defects characterized by bitemporal or preauricular skin lesions resembling aplasia cutis congenita. Skin defects occur at the sites of facial fusion during embryogenesis, with temporal lesions situated at the junction between the frontonasal and maxillary facial prominences, and preauricular lesions at the meeting point of the maxillary and mandibular prominences. The ectodermal lesions show consistent histologic abnormalities: atrophy and flattening of the epidermis, replacement of the dermis by loose connective tissue, reduced levels of fragmented elastic tissue and absence of the subcutaneous tissues and adnexal structures. FFDD4 is characterized by isolated, preauricular skin lesions. The disease is caused by variants affecting the gene represented in this entry.

Induction. By retinoic acid.

Similarity. Belongs to the cytochrome P450 family.

RefSeq proteins (1): NP_899230* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001128Cyt_P450Family
IPR002403Cyt_P450_E_grp-IVFamily
IPR017972Cyt_P450_CSConserved_site
IPR036396Cyt_P450_sfHomologous_superfamily

Pfam: PF00067

Catalyzed reactions (Rhea), 7 shown:

  • an organic molecule + reduced [NADPH–hemoprotein reductase] + O2 = an alcohol + oxidized [NADPH–hemoprotein reductase] + H2O + H(+) (RHEA:17149)
  • all-trans-retinoate + reduced [NADPH–hemoprotein reductase] + O2 = all-trans-4-hydroxyretinoate + oxidized [NADPH–hemoprotein reductase] + H2O + H(+) (RHEA:51984)
  • 9-cis-retinoate + reduced [NADPH–hemoprotein reductase] + O2 = 9-cis-4-hydroxyretinoate + oxidized [NADPH–hemoprotein reductase] + H2O + H(+) (RHEA:75847)
  • all-trans-4-hydroxyretinoate + reduced [NADPH–hemoprotein reductase] + O2 = all-trans-4-oxoretinoate + oxidized [NADPH–hemoprotein reductase] + 2 H2O + H(+) (RHEA:75851)
  • 9-cis-4-hydroxyretinoate + reduced [NADPH–hemoprotein reductase] + O2 = 9-cis-4-oxoretinoate + oxidized [NADPH–hemoprotein reductase] + 2 H2O + H(+) (RHEA:75855)
  • all-trans-4-hydroxy-13,14-dihydroretinoate + reduced [NADPH–hemoprotein reductase] + O2 = all-trans-4-oxo-13,14-dihydroretinoate + oxidized [NADPH–hemoprotein reductase] + 2 H2O + H(+) (RHEA:75859)
  • all-trans-13,14-dihydroretinoate + reduced [NADPH–hemoprotein reductase] + O2 = all-trans-4-hydroxy-13,14-dihydroretinoate + oxidized [NADPH–hemoprotein reductase] + H2O + H(+) (RHEA:75863)

UniProt features (5 total): chain 1, transmembrane region 1, binding site 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6V0L0-F189.340.77

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 459 (axial binding residue)

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-211916Vitamins
R-HSA-5365859RA biosynthesis pathway
R-HSA-5579004Defective CYP26C1 causes FFDD4

MSigDB gene sets: 126 (showing top): REACTOME_BIOLOGICAL_OXIDATIONS, BENPORATH_ES_WITH_H3K27ME3, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_REGULATION_OF_RETINOIC_ACID_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_HORMONE_LEVELS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_HORMONE_MEDIATED_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_RETINOIC_ACID_RECEPTOR_SIGNALING_PATHWAY, GOBP_MESENCHYMAL_CELL_DIFFERENTIATION, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, GOBP_RETINOIC_ACID_METABOLIC_PROCESS, GOBP_RESPONSE_TO_HORMONE

GO Biological Process (8): vitamin metabolic process (GO:0006766), central nervous system development (GO:0007417), anterior/posterior pattern specification (GO:0009952), neural crest cell development (GO:0014032), retinoic acid catabolic process (GO:0034653), organelle fusion (GO:0048284), negative regulation of retinoic acid receptor signaling pathway (GO:0048387), lipid metabolic process (GO:0006629)

GO Molecular Function (9): retinoic acid binding (GO:0001972), monooxygenase activity (GO:0004497), iron ion binding (GO:0005506), retinoic acid 4-hydroxylase activity (GO:0008401), 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 (GO:0016712), heme binding (GO:0020037), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705), metal ion binding (GO:0046872)

GO Cellular Component (2): endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Cytochrome P450 - arranged by substrate type1
Signaling by Retinoic Acid1
Metabolic disorders of biological oxidation enzymes1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
oxidoreductase activity2
monooxygenase activity2
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen2
small molecule metabolic process1
nervous system development1
system development1
regionalization1
neural crest cell differentiation1
stem cell development1
diterpenoid catabolic process1
fat-soluble vitamin catabolic process1
retinoic acid metabolic process1
monocarboxylic acid catabolic process1
organelle organization1
retinoic acid receptor signaling pathway1
regulation of retinoic acid receptor signaling pathway1
negative regulation of intracellular signal transduction1
primary metabolic process1
retinoid binding1
monocarboxylic acid binding1
transition metal ion binding1
tetrapyrrole binding1
catalytic activity1
cation binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

1196 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYP26C1ALDH1A2O94788825
CYP26C1STRA8Q7Z7C7823
CYP26C1CRABP2P29373722
CYP26C1CRABP1P29762701
CYP26C1ALDH1A3P47895640
CYP26C1RDH10Q8IZV5637
CYP26C1RBP2P50120634
CYP26C1RARS1P54136608
CYP26C1RARBP10826531
CYP26C1RARGP13631519
CYP26C1HOXB1P14653501
CYP26C1STRA6Q9BX79500
CYP26C1LRRC30A6NM36497
CYP26C1SDR9C7Q8NEX9495
CYP26C1ALDH1A1P00352490

IntAct

3 interactions, top by confidence:

ABTypeScore
Mpsi-mi:“MI:0914”(association)0.350
GPC3PXDNLpsi-mi:“MI:0914”(association)0.350

BioGRID (1): CYP26C1 (Protein-peptide)

ESM2 similar proteins: B2RXA7, E1BHJ4, F1RE08, G3V7X8, I1GQE7, O02766, O15528, O35084, O35132, O43174, O55127, O88962, O93323, P00191, P03940, P08686, P0DOX0, P12394, P15540, P30437, P51871, P70085, P98187, Q07973, Q08D50, Q09128, Q16678, Q2LA59, Q2LA60, Q2LCM1, Q3MID2, Q4G0S4, Q5VRM7, Q60991, Q64429, Q64441, Q64562, Q64678, Q6EIG3, Q6V0L0

Diamond homologs: A0A087X1C5, A0A098CZ12, A0A0B5KYT4, A0A179HLW2, A0A1B4XBH1, A0A1L7VEQ8, A0A1L9URA0, A0A1U8QFC3, A0A1W5T1Y6, A0A2L0P0J8, A0A2Z5D854, A0A2Z6FZ19, A0A343URW7, A0A384JQH2, A0A3Q9FEJ4, A0A3Q9R4N5, A0A411KZZ4, A0A481WNM6, A0A517FNC7, A7VMU4, A8CDR5, B2RXA7, B3FWR7, B4FVP3, C9K202, F4JW83, G1XU01, G3JUI6, G3XSI3, K0E684, M2V0Z8, O18992, O22307, O23066, O46658, O55071, P04167, P05185, P10635, P11715

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

122 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic3
Uncertain significance91
Likely benign15
Benign5

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
2081971NM_183374.3(CYP26C1):c.457_481del (p.Ala153fs)Pathogenic
3065284NM_183374.3(CYP26C1):c.1191+1G>ALikely pathogenic
4685469NM_183374.3(CYP26C1):c.1238_1260del (p.Asp413fs)Likely pathogenic
4845661NM_183374.3(CYP26C1):c.1056C>A (p.Cys352Ter)Likely pathogenic

SpliceAI

749 predictions. Top by Δscore:

VariantEffectΔscore
10:93064532:TGAAG:Tdonor_loss1.0000
10:93064537:G:Adonor_loss1.0000
10:93066283:GAC:Gdonor_gain1.0000
10:93066286:G:GGdonor_gain1.0000
10:93061466:AG:Adonor_loss0.9900
10:93061467:GGTGA:Gdonor_loss0.9900
10:93061469:T:Adonor_loss0.9900
10:93062008:AG:Aacceptor_gain0.9900
10:93062009:GG:Gacceptor_gain0.9900
10:93062231:CAAG:Cdonor_loss0.9900
10:93062232:AAGG:Adonor_loss0.9900
10:93062233:AGG:Adonor_loss0.9900
10:93062236:T:Adonor_loss0.9900
10:93062992:CAAGG:Cdonor_loss0.9900
10:93062993:AAGGT:Adonor_loss0.9900
10:93062994:AGGTA:Adonor_loss0.9900
10:93062996:GTAC:Gdonor_loss0.9900
10:93062997:T:Gdonor_loss0.9900
10:93064371:T:Aacceptor_gain0.9900
10:93064376:A:AGacceptor_gain0.9900
10:93064376:ATCAG:Aacceptor_gain0.9900
10:93064377:T:Gacceptor_gain0.9900
10:93065955:GGA:Gacceptor_gain0.9900
10:93066282:CGAC:Cdonor_gain0.9900
10:93066283:GACG:Gdonor_gain0.9900
10:93066284:AC:Adonor_gain0.9900
10:93066284:ACGT:Adonor_loss0.9900
10:93066285:CGTA:Cdonor_loss0.9900
10:93066286:GTA:Gdonor_loss0.9900
10:93066287:TAAG:Tdonor_loss0.9900

AlphaMissense

3314 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:93068482:T:CF452L0.998
10:93068484:C:AF452L0.998
10:93068484:C:GF452L0.998
10:93062019:T:CF72L0.997
10:93062021:C:AF72L0.997
10:93062021:C:GF72L0.997
10:93062055:T:CF84L0.997
10:93062057:C:AF84L0.997
10:93062057:C:GF84L0.997
10:93066257:G:CR388P0.997
10:93066256:C:AR388S0.996
10:93068356:A:CS410R0.996
10:93068358:C:AS410R0.996
10:93068358:C:GS410R0.996
10:93066001:A:CS303R0.995
10:93066003:T:AS303R0.995
10:93066003:T:GS303R0.995
10:93068482:T:AF452I0.994
10:93062089:G:CR95P0.992
10:93066007:A:CS305R0.992
10:93066009:C:AS305R0.992
10:93066009:C:GS305R0.992
10:93066217:G:AE375K0.992
10:93066218:A:TE375V0.992
10:93066226:C:AR378S0.992
10:93068341:T:AW405R0.992
10:93068341:T:CW405R0.992
10:93068572:T:AW482R0.992
10:93068572:T:CW482R0.992
10:93062020:T:CF72S0.991

dbSNP variants (sampled 300 via entrez): RS1000279251 (10:93059535 G>A), RS1000323921 (10:93065038 T>C), RS1000435806 (10:93065352 A>G), RS1000488109 (10:93065139 C>A), RS1000661834 (10:93063788 G>T), RS1000820102 (10:93066454 GCTGA>G), RS1000956189 (10:93060501 G>T), RS1001292721 (10:93069401 A>G), RS1001830774 (10:93065732 TC>T), RS1001946936 (10:93066050 T>C), RS1002140565 (10:93059421 G>A), RS1002451601 (10:93063887 T>C), RS1002454116 (10:93063356 T>C), RS1002718943 (10:93060859 C>G), RS1002775906 (10:93069388 A>G)

Disease associations

OMIM: gene MIM:608428 | disease phenotypes: MIM:614974

GenCC curated gene-disease

DiseaseClassificationInheritance
focal facial dermal dysplasia type IVStrongAutosomal recessive

Mondo (1): focal facial dermal dysplasia type IV (MONDO:0013997)

Orphanet (3): Microphthalmia-anophthalmia-coloboma (Orphanet:98555), Focal facial dermal dysplasia (Orphanet:398166), Focal facial dermal dysplasia type IV (Orphanet:398189)

HPO phenotypes

19 total (19 of 19 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000175Cleft palate
HP:0000204Cleft upper lip
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000331Short chin
HP:0001028Hemangioma
HP:0001269Hemiparesis
HP:0002170Intracranial hemorrhage
HP:0003764Nevus
HP:0004426Abnormal cheek morphology
HP:0007359Focal-onset seizure
HP:0008066Abnormal blistering of the skin
HP:0011124Abnormal epidermal morphology
HP:0011336Bitemporal forceps marks
HP:0025167Fragmented elastic fibers in the dermis
HP:0100494Abnormal mast cell morphology
HP:0100699Scarring
HP:3000019Abnormal buccal mucosa morphology

GWAS associations

7 associations (top):

StudyTraitp-value
GCST005407_1Glaucoma (primary open-angle)2.000000e-06
GCST006003_19Triglyceride levels4.000000e-16
GCST007876_115Estimated glomerular filtration rate1.000000e-09
GCST010002_297Refractive error3.000000e-23
GCST010241_431Apolipoprotein A1 levels6.000000e-12
GCST010796_3318Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08
GCST011345_14Triglyceride levels5.000000e-18

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0004327electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — CYP24, CYP26 and CYP27 families

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Alitretinoinaffects binding, decreases reaction, increases metabolic processing, increases expression2
Tretinoinaffects binding, decreases reaction, increases metabolic processing, increases expression2
aristolochic acid Idecreases expression1
bisphenol Aincreases methylation1
potassium perchloratedecreases expression1
aflatoxin B2decreases methylation1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Biological Factorsdecreases expression1
Ketoconazoledecreases reaction, increases metabolic processing1
Leadaffects expression1
Ozoneaffects expression, increases abundance1
Aflatoxin B1increases methylation1
Asbestos, Serpentinedecreases methylation1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.