CYP2W1

protein-coding

cytochrome P450 family 2 subfamily W member 1, the group of Cytochrome P450 family 2

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. [provided by RefSeq, Jul 2008]

MANE transcript

NM_017781.3

Inheritance

—

ClinVar variants

U:118B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr7:983,181-989,640

External References & Databases

Ensembl (ENSG00000073067)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 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 CYP2W1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017781.3. 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 clinvar	4
missense			118 clinvar	7 clinvar	1 clinvar	126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	118	9	3	130

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017781.3	RefSeq	NP_060251.2	9	MANE Select
ENST00000308919.12	Ensembl	ENSP00000310149.7	9	MANE Select
ENST00000340150.10	Ensembl	ENSP00000344178.6	8	Standard
ENST00000340150.11	Ensembl	ENSP00000344178.6	8	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
Phase I - Functionalization of compounds
Xenobiotics
Miscellaneous substrates

Biological Process

organic acid metabolic process
xenobiotic metabolic process
exogenous drug catabolic process
aflatoxin B1 metabolic process
oxidation-reduction process

Molecular Function

monooxygenase activity
iron ion binding
steroid hydroxylase activity
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
heme binding

Cellular Component

cytoplasm
endoplasmic reticulum lumen
endoplasmic reticulum membrane
plasma membrane
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308919
Coding exons: 9
Length: 6442
Individuals with no LoFs: 125105
Homozygous LoFs: 0
Heterozygous LoFs: 67
Defined: 125172
p: 0.000268

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.173	306	315	0.973	0.0000224	3001
Missense (PolyPhen)		110	115.19	0.95494		1243
Synonymous	-1.31	174	153	1.13	0.0000110	1120
Loss of Function	1.24	13	18.8	0.691	9.71e-7	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0027	0.0027	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000047	0.000044	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to have broad catalytic activity towards several chemicals, including polycyclic aromatic hydrocarbon dihydrodiols and aromatic amines (PubMed:16551781, PubMed:24278521). Active also in the metabolism of indoline substrates and is able to activate aflatoxin B1 into cytotoxic products (PubMed:20805301). Furthermore, it seems to be involved in the oxydation of lysophospholipids and fatty acids (PubMed:22591743). {ECO:0000269|PubMed:16551781, ECO:0000269|PubMed:20805301, ECO:0000269|PubMed:22591743, ECO:0000269|PubMed:24278521}.;

Recessive Scores

pRec: 0.155

Intolerance Scores

LoFtool: 0.526
RVIS EVS: 0.53
RVIS percentile EVS: 81.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.127

Gene Damage Prediction

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