CYP4Z1

protein-coding

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

Gene summary

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 gene is part of a cluster of cytochrome P450 genes on chromosome 1p33. [provided by RefSeq, Jul 2008]

MANE transcript

NM_178134.3

Inheritance

—

ClinVar variants

U:73B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr1:47,067,231-47,118,318

External References & Databases

Ensembl (ENSG00000186160)

Transcript & Mutation Effects

hg38 • Region Span ~51.1 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 CYP4Z1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178134.3. 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				2 clinvar		2
missense			71 clinvar	6 clinvar	1 clinvar	78
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	73	8	1	82

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178134.3	RefSeq	NP_835235.1	12	MANE Select
ENST00000334194.4	Ensembl	ENSP00000334246.3	12	MANE Select
XM_024453856.2	RefSeq	XP_024309624.1	12	Standard

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
Tyrosine metabolism
Androgen and estrogen biosynthesis and metabolism
Leukotriene metabolism

Biological Process

oxidation-reduction process

Molecular Function

iron ion binding
heme binding
aromatase activity

Cellular Component

endoplasmic reticulum membrane
integral component of membrane
organelle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334194
Coding exons: 12
Length: 50832
Individuals with no LoFs: 124323
Homozygous LoFs: 32
Heterozygous LoFs: 1393
Defined: 125748
p: 0.00568

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.111	260	265	0.981	0.0000137	3370
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00053	0.00052	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0069	0.0069	notable
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00043	0.00039	rare
South Asian	0.043	0.040	notable
Other	0.0038	0.0036	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.797
RVIS EVS: 0.31
RVIS percentile EVS: 72.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0160

Gene Damage Prediction

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