CYP2A13

protein-coding

cytochrome P450 family 2 subfamily A member 13, 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. This protein localizes to the endoplasmic reticulum. Although its endogenous substrate has not been determined, it is known to metabolize 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, a major nitrosamine specific to tobacco. This gene is part of a large cluster of cytochrome P450 genes from the CYP2A, CYP2B and CYP2F subfamilies on chromosome 19q. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000766.5

Inheritance

—

ClinVar variants

U:86B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr19:41,088,451-41,096,195

External References & Databases

Ensembl (ENSG00000197838)

Transcript & Mutation Effects

hg38 • Region Span ~7.7 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 CYP2A13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000766.5. 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			1 clinvar	1 clinvar		2
missense			84 clinvar	4 clinvar		88
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	5	0	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000766.5	RefSeq	NP_000757.2	9	MANE Select
ENST00000330436.4	Ensembl	ENSP00000332679.1	9	MANE Select
ENST00000874269.1	Ensembl	ENSP00000544328.1	9	Standard
ENST00000874269.2	Ensembl	ENSP00000544328.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human)
Chemical carcinogenesis - Homo sapiens (human)
Nicotine Pathway, Pharmacokinetics
Vitamin A Deficiency
Retinol Metabolism

Biological Process

organic acid metabolic process
xenobiotic metabolic process
coumarin metabolic process
epoxygenase P450 pathway
exogenous drug catabolic process

Molecular Function

monooxygenase activity
iron ion binding
coumarin 7-hydroxylase activity
arachidonic acid epoxygenase activity
steroid hydroxylase activity

Cellular Component

cytoplasm
endoplasmic reticulum membrane
organelle membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330436
Coding exons: 9
Length: 7724
Individuals with no LoFs: 124247
Homozygous LoFs: 8
Heterozygous LoFs: 1493
Defined: 125748
p: 0.00599

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.67	384	302	1.27	0.0000179	3256
Missense (PolyPhen)		145	120.51	1.2033		1295
Synonymous	-1.85	149	123	1.21	0.00000723	972
Loss of Function	1.28	12	17.9	0.672	7.55e-7	222

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0060	0.0060	notable
Ashkenazi Jewish	0.0015	0.0015	notable
East Asian	0.0018	0.0019	notable
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.0097	0.0096	notable
South Asian	0.0023	0.0023	notable
Other	0.0064	0.0064	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N- dimethylaniline, 2'-methoxyacetophenone, N- nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4- (methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity. {ECO:0000269|PubMed:18779312}.;

Recessive Scores

pRec: 0.169

Intolerance Scores

LoFtool: 0.785
RVIS EVS: 0.31
RVIS percentile EVS: 72.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.830

Gene Damage Prediction

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