CYP20A1

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

Basic information

Region (hg38): 2:203238977-203306026

Links

ENSG00000119004 ∙ NCBI:57404 ∙ ∙ HGNC:20576 ∙ Uniprot:Q6UW02 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYP20A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP20A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24		2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	2

Variants in CYP20A1

This is a list of pathogenic ClinVar variants found in the CYP20A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-203239133-C-A		not specified	Uncertain significance (Jul 12, 2022)
2-203245892-A-C		not specified	Uncertain significance (Nov 21, 2022)
2-203246800-G-T		not specified	Uncertain significance (Feb 28, 2023)
2-203246805-T-A		not specified	Uncertain significance (Jun 07, 2023)
2-203246815-G-T		not specified	Uncertain significance (Sep 20, 2023)
2-203246825-T-G		not specified	Uncertain significance (Oct 03, 2022)
2-203246832-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-203246858-C-T		not specified	Uncertain significance (Aug 30, 2022)
2-203246907-A-G		not specified	Uncertain significance (Jul 06, 2021)
2-203252041-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-203266631-A-C		not specified	Uncertain significance (Jun 10, 2022)
2-203272692-G-C		not specified	Uncertain significance (Feb 23, 2023)
2-203272727-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-203278629-A-G		not specified	Uncertain significance (Oct 06, 2022)
2-203278642-A-G		not specified	Uncertain significance (Dec 28, 2022)
2-203278682-C-A		not specified	Uncertain significance (Apr 04, 2024)
2-203280101-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-203285687-T-C		not specified	Uncertain significance (Jan 04, 2022)
2-203285729-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-203289791-C-G		not specified	Uncertain significance (Jun 04, 2024)
2-203289835-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-203289852-T-G			Benign (Apr 19, 2018)
2-203292271-C-T		not specified	Uncertain significance (May 31, 2024)
2-203292283-G-T		not specified	Uncertain significance (Aug 28, 2023)
2-203292284-G-A		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP20A1	protein_coding	protein_coding	ENST00000356079	13	59347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.89e-17	0.00900	125647	0	100	125747	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.375	215	231	0.931	0.0000109	3011
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000761	0.000682
Ashkenazi Jewish	0.00	0.00
East Asian	0.000388	0.000381
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000440	0.000422
Middle Eastern	0.000388	0.000381
South Asian	0.000849	0.000817
Other	0.000547	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.865
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.216
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp20a1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: cyp20a1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased behavioural activity

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: membrane;integral component of membrane
• Molecular function: monooxygenase activity;iron ion binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;heme binding