CYP20A1

protein-coding

cytochrome P450 family 20 subfamily A member 1, the group of Cytochrome P450 family 20

Gene summary

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. [provided by RefSeq, Jul 2008]

MANE transcript

NM_177538.3

Inheritance

—

ClinVar variants

U:56B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr2:203,238,977-203,306,026

External References & Databases

Ensembl (ENSG00000119004)

Transcript & Mutation Effects

hg38 • Region Span ~67.0 kb

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GenCC 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 CYP20A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_177538.3. 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						0
missense			53 clinvar	2 clinvar	2 clinvar	57
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	56	2	2	60

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_177538.3	RefSeq	NP_803882.1	13	MANE Select
ENST00000356079.9	Ensembl	ENSP00000348380.4	13	MANE Select
NM_001371695.1	RefSeq	NP_001358624.1	13	Standard
NM_001371696.1	RefSeq	NP_001358625.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
cyp20a1	Danio rerio	Structure: whole organism Quality: increased behavioural activity abnormal

Gene / Model

Organism

Observed Phenotype

cyp20a1

Danio rerio

Structure: whole organism

Quality: increased behavioural activity

abnormal

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

oxidation-reduction process

Molecular Function

monooxygenase activity
iron ion binding
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
heme binding

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356079
Coding exons: 13
Length: 59347
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 100
Defined: 125747
p: 0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.375	215	231	0.931	0.0000109	3011
Missense (PolyPhen)		47	55.416	0.84813		715
Synonymous	0.230	79	81.6	0.968	0.00000379	860
Loss of Function	0.103	25	25.6	0.978	0.00000132	319

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00051	0.00043	rare
Latino/Admixed American	0.00025	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00044	0.00042	rare
South Asian	0.00085	0.00082	rare
Other	0.00055	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.205

Intolerance Scores

LoFtool: 0.865
RVIS EVS: 0.26
RVIS percentile EVS: 70.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0473

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High