CYP4Z1

cytochrome P450 family 4 subfamily Z member 1, the group of Cytochrome P450 family 4

Basic information

Region (hg38): 1:47067230-47118318

Links

ENSG00000186160 ∙ NCBI:199974 ∙ OMIM:618953 ∙ HGNC:20583 ∙ Uniprot:Q86W10 ∙ 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 CYP4Z1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP4Z1 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			27	3	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	27	3	1

Variants in CYP4Z1

This is a list of pathogenic ClinVar variants found in the CYP4Z1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47067501-C-G		not specified	Uncertain significance (Feb 15, 2023)
1-47067528-C-G		not specified	Uncertain significance (Mar 29, 2022)
1-47067554-A-C		not specified	Likely benign (Jan 26, 2022)
1-47067602-T-C		not specified	Likely benign (Jun 29, 2022)
1-47068656-A-G		not specified	Uncertain significance (Mar 15, 2024)
1-47068740-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-47082433-T-C		not specified	Uncertain significance (Nov 09, 2023)
1-47082451-G-A		not specified	Uncertain significance (Jun 30, 2022)
1-47084635-C-A		not specified	Uncertain significance (Oct 13, 2023)
1-47084636-A-C		not specified	Uncertain significance (Apr 01, 2024)
1-47084653-C-T		not specified	Likely benign (Jun 30, 2023)
1-47084659-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-47084685-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-47084702-T-C		not specified	Uncertain significance (Apr 12, 2024)
1-47084705-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-47084743-A-T		not specified	Uncertain significance (Mar 02, 2023)
1-47084879-C-A		not specified	Uncertain significance (Sep 21, 2023)
1-47084897-C-T		not specified	Uncertain significance (Feb 02, 2022)
1-47084952-T-C		not specified	Uncertain significance (Nov 08, 2021)
1-47094583-C-T		not specified	Uncertain significance (Dec 21, 2021)
1-47094634-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-47094635-G-A			Benign (Jul 20, 2018)
1-47094661-A-C		not specified	Uncertain significance (Aug 17, 2022)
1-47099096-C-T			Likely benign (Jul 01, 2023)
1-47099207-G-C		not specified	Uncertain significance (Jun 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP4Z1	protein_coding	protein_coding	ENST00000334194	12	50832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-17	0.00360	124323	32	1393	125748	0.00568

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	260	265	0.981	0.0000137	3370
Missense in Polyphen		85	90.105	0.94334		1022
Synonymous	1.11	80	93.6	0.855	0.00000463	913
Loss of Function	-0.219	25	23.8	1.05	0.00000114	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000775	0.000774
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00688	0.00687
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000429	0.000387
Middle Eastern	0.00688	0.00687
South Asian	0.0429	0.0402
Other	0.00379	0.00359

dbNSFP

Source: dbNSFP

• Pathway: Oxidation by Cytochrome P450;Metapathway biotransformation Phase I and II;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.797
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.354
• hipred: N
• hipred_score: 0.139
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0160

Gene Damage Prediction

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

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane
• Molecular function: iron ion binding;heme binding;aromatase activity