CYP4X1

protein-coding

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

Gene summary

This gene encodes a member of the cytochrome P450 superfamily of enzymes and is located within a cluster of genes belonging to this superfamily on chromosome 1. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The expression pattern of a similar rat protein suggests that this protein may be involved in neurovascular function in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

MANE transcript

NM_178033.2

Inheritance

—

ClinVar variants

U:75B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr1:47,023,669-47,050,751

External References & Databases

Ensembl (ENSG00000186377)

Transcript & Mutation Effects

hg38 • Region Span ~27.1 kb

Loading mutation effect viewer...

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 CYP4X1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178033.2. 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			72 clinvar	5 clinvar		77
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	75	5	0	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178033.2	RefSeq	NP_828847.1	12	MANE Select
ENST00000371901.4	Ensembl	ENSP00000360968.3	12	MANE Select
NM_001320289.2	RefSeq	NP_001307218.1	12	Standard
NM_001320290.2	RefSeq	NP_001307219.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Serotonergic synapse - Homo sapiens (human)
nicotine degradation III
Oxidation by Cytochrome P450
Metapathway biotransformation Phase I and II
bupropion degradation

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: ENST00000371901
Coding exons: 12
Length: 89388
Individuals with no LoFs: 125651
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	220	281	0.784	0.0000139	3365
Missense (PolyPhen)		77	95.523	0.80609		1247
Synonymous	0.283	103	107	0.965	0.00000550	948
Loss of Function	1.12	21	27.3	0.769	0.00000133	312

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0020	0.0020	notable
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00085	0.00085	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.896
RVIS EVS: -0.56
RVIS percentile EVS: 19.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.134

Gene Damage Prediction

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