CYP2A13
Basic information
Region (hg38): 19:41088451-41096195
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (78 variants)
- not_provided (2 variants)
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. These statistics are base on transcript: NM_000000766.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 75 | 78 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 75 | 4 | 0 |
GnomAD
Source:
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:
- 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