CYP2A13

cytochrome P450 family 2 subfamily A member 13, the group of Cytochrome P450 family 2

Basic information

Region (hg38): 19:41088451-41096195

Links

ENSG00000197838 ∙ NCBI:1553 ∙ OMIM:608055 ∙ HGNC:2608 ∙ Uniprot:Q16696 ∙ 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 CYP2A13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP2A13 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				1		1
missense			58	3		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	4	0

Variants in CYP2A13

This is a list of pathogenic ClinVar variants found in the CYP2A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41088517-A-T		not specified	Uncertain significance (Sep 17, 2021)
19-41088563-G-A		not specified	Uncertain significance (Apr 06, 2023)
19-41088566-A-G		not specified	Uncertain significance (Feb 13, 2024)
19-41088643-C-T		not specified	Uncertain significance (Nov 09, 2022)
19-41088647-T-C		not specified	Uncertain significance (May 31, 2022)
19-41088938-C-A		not specified	Uncertain significance (Sep 03, 2024)
19-41088956-A-G		not specified	Uncertain significance (Mar 02, 2023)
19-41088995-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-41089039-G-T		not specified	Uncertain significance (Jun 29, 2023)
19-41089061-G-T		not specified	Uncertain significance (Jul 30, 2024)
19-41090049-G-T		not specified	Uncertain significance (Mar 06, 2023)
19-41090064-G-C		not specified	Uncertain significance (Aug 02, 2021)
19-41090097-A-G		not specified	Uncertain significance (Jan 09, 2024)
19-41090101-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-41090110-G-A		not specified	Uncertain significance (Jul 27, 2024)
19-41090124-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-41090146-G-A		not specified	Uncertain significance (Jul 29, 2022)
19-41090148-A-T		not specified	Uncertain significance (Jun 12, 2023)
19-41090164-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-41090194-A-G		not specified	Likely benign (Nov 08, 2022)
19-41090436-C-A		not specified	Uncertain significance (Dec 19, 2022)
19-41090449-A-G		not specified	Uncertain significance (Jun 02, 2023)
19-41090469-T-C		not specified	Uncertain significance (Mar 31, 2022)
19-41090494-A-G		not specified	Uncertain significance (Nov 09, 2023)
19-41090556-A-G		not specified	Uncertain significance (Feb 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYP2A13	protein_coding	protein_coding	ENST00000330436	9	7724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.65e-7	0.763	124247	8	1493	125748	0.00599

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.67	384	302	1.27	0.0000179	3256
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00760	0.00753
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.00185	0.00185
Finnish	0.00134	0.00134
European (Non-Finnish)	0.00966	0.00957
Middle Eastern	0.00185	0.00185
South Asian	0.00225	0.00226
Other	0.00637	0.00637

dbNSFP

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}.
• Pathway: Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Nicotine Pathway, Pharmacokinetics;Vitamin A Deficiency;Retinol Metabolism;Oxidation by Cytochrome P450;Tryptophan metabolism;Aflatoxin B1 metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Xenobiotics;Tyrosine metabolism;Fatty acids;Androgen and estrogen biosynthesis and metabolism;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;Tryptophan degradation;CYP2E1 reactions;Aflatoxin activation and detoxification;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.785
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.75

Haploinsufficiency Scores

• pHI: 0.0818
• hipred: N
• hipred_score: 0.194
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyp2a5
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: organic acid metabolic process;xenobiotic metabolic process;coumarin metabolic process;epoxygenase P450 pathway;exogenous drug catabolic process;oxidation-reduction process
• Cellular component: cytoplasm;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: monooxygenase activity;iron ion binding;coumarin 7-hydroxylase activity;arachidonic acid epoxygenase activity;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;aromatase activity