CYP20A1

Summary

CYP20A1 (cytochrome P450 family 20 subfamily A member 1, HGNC:20576) is a protein-coding gene on chromosome 2q33.2, encoding Cytochrome P450 20A1 (Q6UW02).

This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases that catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein lacks one amino acid of the conserved heme binding site. It also lacks the conserved I-helix motif AGX(D,E)T, suggesting that its substrate may carry its own oxygen.

Source: NCBI Gene 57404 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_177538

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20576
Approved symbol	CYP20A1
Name	cytochrome P450 family 20 subfamily A member 1
Location	2q33.2
Locus type	gene with protein product
Status	Approved
Aliases	CYP-M
Ensembl gene	ENSG00000119004
Ensembl biotype	protein_coding
Entrez	57404

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding, 3 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000356079, ENST00000428265, ENST00000429815, ENST00000431118, ENST00000443941, ENST00000449301, ENST00000461371, ENST00000463131, ENST00000489360, ENST00000875108, ENST00000875109, ENST00000956048

RefSeq mRNA: 13 — MANE Select: NM_177538 NM_001371695, NM_001371696, NM_001371697, NM_001371698, NM_001371699, NM_001371700, NM_001371701, NM_001371702, NM_001371703, NM_001371704, NM_001371705, NM_001371706, NM_177538

CCDS: CCDS2357, CCDS92931

Canonical transcript exons

ENST00000356079 — 13 exons

Exon	Start	End
ENSE00000803483	203246755	203246921
ENSE00001076405	203245846	203245895
ENSE00001554594	203296758	203306026
ENSE00001905806	203239018	203239134
ENSE00003493353	203280059	203280113
ENSE00003539280	203251967	203252109
ENSE00003573542	203296474	203296563
ENSE00003575020	203278573	203278688
ENSE00003661257	203266514	203266681
ENSE00003668160	203272670	203272748
ENSE00003671815	203292262	203292326
ENSE00003675193	203289765	203289876
ENSE00003785833	203285612	203285732

Expression profiles

Bgee: expression breadth ubiquitous, 225 present calls, max score 93.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.1715 / max 525.3354, expressed in 1816 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24746	9.5434	1799
24747	8.8754	1771
24748	0.7528	434

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	93.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.04	gold quality
adrenal tissue	UBERON:0018303	91.70	gold quality
colonic epithelium	UBERON:0000397	88.75	gold quality
monocyte	CL:0000576	85.80	gold quality
islet of Langerhans	UBERON:0000006	85.52	gold quality
mononuclear cell	CL:0000842	85.31	gold quality
leukocyte	CL:0000738	85.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.78	gold quality
tendon	UBERON:0000043	83.86	gold quality
body of pancreas	UBERON:0001150	83.17	gold quality
pancreas	UBERON:0001264	83.02	gold quality
adrenal gland	UBERON:0002369	82.82	gold quality
rectum	UBERON:0001052	82.74	gold quality
right adrenal gland cortex	UBERON:0035827	82.55	gold quality
right adrenal gland	UBERON:0001233	82.36	gold quality
left adrenal gland	UBERON:0001234	82.31	gold quality
left adrenal gland cortex	UBERON:0035825	81.95	gold quality
popliteal artery	UBERON:0002250	81.46	gold quality
tibial artery	UBERON:0007610	81.46	gold quality
gall bladder	UBERON:0002110	81.42	gold quality
adrenal cortex	UBERON:0001235	81.28	gold quality
stromal cell of endometrium	CL:0002255	81.06	gold quality
aorta	UBERON:0000947	80.87	gold quality
left coronary artery	UBERON:0001626	80.82	gold quality
right testis	UBERON:0004534	80.80	gold quality
sural nerve	UBERON:0015488	80.62	gold quality
thoracic aorta	UBERON:0001515	80.26	gold quality
ascending aorta	UBERON:0001496	80.20	gold quality
left ovary	UBERON:0002119	80.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.83

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TCF3

Literature-anchored findings (GeneRIF, showing 2)

• Multiple Alu Exonization in 3’UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge. (PMID:33434274)
• The association study between CYP20A1, CYP4F2, CYP2D6 gene polymorphisms and coronary heart disease risk in the Han population in southern China. (PMID:34302632)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cyp20a1	ENSDARG00000006040
mus_musculus	Cyp20a1	ENSMUSG00000049439
rattus_norvegicus	Cyp20a1	ENSRNOG00000017631

Protein

Protein identifiers

Cytochrome P450 20A1 — Q6UW02 (reviewed: Q6UW02)

All UniProt accessions (5): Q6UW02, C9J8K7, E9PHG5, F2Z3K6, F8WBE2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the cytochrome P450 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UW02-1	1	yes
Q6UW02-2	2

RefSeq proteins (13): NP_001358624, NP_001358625, NP_001358626, NP_001358627, NP_001358628, NP_001358629, NP_001358630, NP_001358631, NP_001358632, NP_001358633, NP_001358634, NP_001358635, NP_803882* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001128	Cyt_P450	Family
IPR002401	Cyt_P450_E_grp-I	Family
IPR036396	Cyt_P450_sf	Homologous_superfamily
IPR052666	CYP450_20A1-like	Family

Pfam: PF00067

UniProt features (9 total): sequence conflict 3, sequence variant 2, chain 1, transmembrane region 1, binding site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UW02-F1	89.00	0.64

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): 409 (axial binding residue)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, CUI_TCF21_TARGETS_2_DN, GOMF_TETRAPYRROLE_BINDING, GOMF_IRON_ION_BINDING, GOMF_MONOOXYGENASE_ACTIVITY, CCACACA_MIR147, KASLER_HDAC7_TARGETS_1_UP, PTEN_DN.V2_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_UP, GSE14415_INDUCED_TREG_VS_FAILED_INDUCED_TREG_UP, GSE14415_ACT_VS_CTRL_NATURAL_TREG_UP, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_DN, GSE13547_2H_VS_12_H_ANTI_IGM_STIM_BCELL_DN

GO Biological Process (0):

GO Molecular Function (7): monooxygenase activity (GO:0004497), iron ion binding (GO:0005506), oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705), heme binding (GO:0020037), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), metal ion binding (GO:0046872)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
oxidoreductase activity	2
transition metal ion binding	1
tetrapyrrole binding	1
binding	1
catalytic activity	1
cation binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1512 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CYP20A1	ICA1L	Q8NDH6	544
CYP20A1	GK5	Q6ZS86	542
CYP20A1	CYP39A1	Q9NYL5	532
CYP20A1	C17orf75	Q9HAS0	521
CYP20A1	DCAF10	Q5QP82	514
CYP20A1	ZNF429	Q86V71	497
CYP20A1	CYP7A1	P22680	490
CYP20A1	ZNF850	A8MQ14	461
CYP20A1	PPIH	O43447	453
CYP20A1	ZNF714	Q96N38	449
CYP20A1	CYB5D2	Q8WUJ1	444
CYP20A1	CIAO1	O76071	443
CYP20A1	CACNG8	Q8WXS5	438
CYP20A1	FKBP14	Q9NWM8	437
CYP20A1	HSD3B7	Q9H2F3	437

IntAct

18 interactions, top by confidence:

A	B	Type	Score
VSIG1	TTI1	psi-mi:“MI:0914”(association)	0.640
CYP20A1	PIEZO1	psi-mi:“MI:0915”(physical association)	0.590
BTNL3	FAM171A2	psi-mi:“MI:0914”(association)	0.530
VSIG1	TNPO2	psi-mi:“MI:0914”(association)	0.530
Rrbp1	PIPSL	psi-mi:“MI:0914”(association)	0.350
COPE	ESYT2	psi-mi:“MI:0914”(association)	0.350
TMED10	PGRMC1	psi-mi:“MI:0914”(association)	0.350
SLC11A2	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC16A6	RER1	psi-mi:“MI:0914”(association)	0.350
SLC17A3	ADCY3	psi-mi:“MI:0914”(association)	0.350
SLC44A1	UPK3BL1	psi-mi:“MI:0914”(association)	0.350
SLC7A8	SPTLC1	psi-mi:“MI:0914”(association)	0.350
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (31): CYP20A1 (Synthetic Growth Defect), CYP20A1 (Affinity Capture-MS), PIEZO1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-RNA), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), PIEZO1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS), CYP20A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1V6PBE7, A0A5B8ND22, A0A9Y1LLN2, A8WGA0, E1BHJ4, F1RE08, G3V7X8, I1GQE7, M1W080, O02766, O23051, O46491, O75881, O88962, O93323, P0DOX0, P0DXH8, P18125, P22680, P46634, P48416, P51542, P79739, Q07973, Q08D50, Q09128, Q09660, Q4G0S4, Q50EK5, Q5E980, Q60991, Q62969, Q63688, Q64441, Q64505, Q6EIG3, Q6JD68, Q6P7D4, Q6UW02, Q7YRB2

Diamond homologs: A0A159AKG3, A0A1Z3GBS4, A0A218NGS0, A8NCK6, B5UAQ8, C8VJR0, E9Q5K4, F1B282, H2DH19, H2DH24, H2KYS3, O04773, O18809, O18963, O18993, O46515, O65012, O70537, O77809, O77810, P04800, P05181, P05182, P05183, P0DO35, P0DO40, P0DO41, P0DO42, P11509, P20853, P24454, P24462, P24470, P33266, P37123, P51538, P79102, Q05555, Q05556, Q16696

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2159 predictions. Top by Δscore:

Variant	Effect	Δscore
2:203245844:A:G	acceptor_gain	1.0000
2:203245891:GAAAA:G	donor_gain	1.0000
2:203245894:AA:A	donor_gain	1.0000
2:203245896:G:GG	donor_gain	1.0000
2:203246922:G:GG	donor_gain	1.0000
2:203251965:A:AG	acceptor_gain	1.0000
2:203251965:AGC:A	acceptor_gain	1.0000
2:203251966:G:GA	acceptor_gain	1.0000
2:203251966:GC:G	acceptor_gain	1.0000
2:203251966:GCG:G	acceptor_gain	1.0000
2:203252107:AAGG:A	donor_loss	1.0000
2:203252108:AGG:A	donor_loss	1.0000
2:203252110:G:C	donor_loss	1.0000
2:203252111:T:A	donor_loss	1.0000
2:203266512:A:AG	acceptor_gain	1.0000
2:203266513:G:GC	acceptor_gain	1.0000
2:203266513:GC:G	acceptor_gain	1.0000
2:203266513:GCT:G	acceptor_gain	1.0000
2:203266513:GCTT:G	acceptor_gain	1.0000
2:203266513:GCTTT:G	acceptor_gain	1.0000
2:203266649:G:GT	donor_gain	1.0000
2:203266677:GCACA:G	donor_gain	1.0000
2:203266678:CACA:C	donor_gain	1.0000
2:203266679:ACA:A	donor_gain	1.0000
2:203266679:ACAGT:A	donor_loss	1.0000
2:203266680:CA:C	donor_gain	1.0000
2:203266681:AGT:A	donor_loss	1.0000
2:203266682:G:GG	donor_gain	1.0000
2:203266682:GTAA:G	donor_loss	1.0000
2:203266683:T:A	donor_loss	1.0000

AlphaMissense

3040 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:203246870:A:C	S80R	0.998
2:203246872:T:A	S80R	0.998
2:203246872:T:G	S80R	0.998
2:203239085:C:A	A8D	0.989
2:203246868:T:A	V79D	0.989
2:203266538:T:A	W153R	0.989
2:203266538:T:C	W153R	0.989
2:203246760:G:A	G43D	0.988
2:203246764:T:A	N44K	0.988
2:203246764:T:G	N44K	0.988
2:203289797:G:C	R335P	0.988
2:203296475:T:C	F384L	0.983
2:203296477:T:A	F384L	0.983
2:203296477:T:G	F384L	0.983
2:203246760:G:T	G43V	0.981
2:203246805:T:C	L58P	0.979
2:203292269:T:A	V364D	0.976
2:203246801:T:C	F57L	0.968
2:203246803:C:A	F57L	0.968
2:203246803:C:G	F57L	0.968
2:203246843:T:C	F71L	0.967
2:203246845:C:A	F71L	0.967
2:203246845:C:G	F71L	0.967
2:203289788:A:T	E332V	0.967
2:203246759:G:C	G43R	0.965
2:203239115:C:A	A18D	0.964
2:203296490:T:C	F389L	0.962
2:203296492:T:A	F389L	0.962
2:203296492:T:G	F389L	0.962
2:203296532:T:C	F403L	0.959

dbSNP variants (sampled 300 via entrez): RS1000065184 (2:203297639 C>A,G,T), RS1000080031 (2:203274172 A>C), RS1000088013 (2:203281945 T>A), RS1000101987 (2:203261973 C>A,G), RS1000352902 (2:203268987 C>T), RS1000376085 (2:203286184 G>A), RS1000378391 (2:203293428 G>A,T), RS1000399951 (2:203286221 C>T), RS1000447371 (2:203293336 C>T), RS1000493735 (2:203252884 C>T), RS1000499607 (2:203292898 G>A), RS1000597383 (2:203297804 C>A), RS1000608156 (2:203255605 C>G,T), RS1000663071 (2:203239278 G>A,C,T), RS1000684495 (2:203280303 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST000839_5	Height	2.000000e-06
GCST007094_143	Diastolic blood pressure	7.000000e-06
GCST007096_201	Pulse pressure	3.000000e-09
GCST007097_26	Pulse pressure	8.000000e-06
GCST008876_22	Non-lobar intracerebral hemorrhage (MTAG)	1.000000e-06
GCST010101_5	White matter hyperintensities	4.000000e-13
GCST010102_1	White matter integrity (fractional anisotropy)	7.000000e-08
GCST010698_18	Subcortical volume (min-P)	1.000000e-08
GCST010699_69	Brain morphology (min-P)	9.000000e-20
GCST010700_6	Cortical thickness (MOSTest)	2.000000e-14
GCST010701_36	Cortical surface area (MOSTest)	2.000000e-24
GCST010702_146	Subcortical volume (MOSTest)	2.000000e-13
GCST010703_42	Brain morphology (MOSTest)	1.000000e-08
GCST010726_18	Periventricular white matter hyperintensities	7.000000e-08
GCST90000025_865	Appendicular lean mass	7.000000e-15
GCST90011900_136	Serum alkaline phosphatase levels	5.000000e-24
GCST90013406_59	Liver enzyme levels (alkaline phosphatase)	7.000000e-30

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0010178	non-lobar intracerebral hemorrhage
EFO:0005665	white matter hyperintensity measurement
EFO:0004641	white matter integrity
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0004980	appendicular lean mass
EFO:0004533	alkaline phosphatase measurement

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 — CYP11, CYP17, CYP19, CYP20 and CYP21 families

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	3
Valproic Acid	affects expression, decreases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
bisphenol A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression	1
perfluorooctane sulfonic acid	increases expression	1
fipronil	affects cotreatment, decreases expression	1
2-palmitoylglycerol	increases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Cisplatin	affects expression	1
DEET	affects cotreatment, decreases expression	1
Diethylstilbestrol	decreases expression	1
Endosulfan	increases expression	1
Gallic Acid	decreases expression	1
Manganese	increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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