ALOX5AP
arachidonate 5-lipoxygenase activating protein
Basic information
Region (hg38): 13:30713478-30764426
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALOX5AP 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 | 4 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 3 | 1 |
Variants in ALOX5AP
This is a list of pathogenic ClinVar variants found in the ALOX5AP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-30713844-G-A | ALOX5AP-related disorder | Likely benign (Jul 03, 2019) | ||
| 13-30735566-T-C | ALOX5AP-related disorder | Likely benign (Dec 04, 2023) | ||
| 13-30735647-C-T | ALOX5AP-related disorder | Likely benign (Dec 04, 2023) | ||
| 13-30744085-C-T | Likely benign (Oct 25, 2018) | |||
| 13-30744112-C-T | Benign (Dec 31, 2019) | |||
| 13-30744153-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 13-30752086-G-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 13-30755984-G-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 13-30756019-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
| 13-30758476-T-C | not provided (-) | |||
| 13-30763949-C-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 13-30763972-A-G | not specified • ALOX5AP-related disorder | Uncertain significance (Oct 06, 2022) | ||
| 13-30764059-A-G | not specified | Uncertain significance (Oct 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ALOX5AP | protein_coding | protein_coding | ENST00000380490 | 5 | 28912 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0707 | 0.878 | 125742 | 0 | 5 | 125747 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 68 | 96.9 | 0.702 | 0.00000563 | 1056 |
| Missense in Polyphen | 24 | 40.29 | 0.59568 | 416 | ||
| Synonymous | 0.907 | 33 | 40.3 | 0.818 | 0.00000272 | 317 |
| Loss of Function | 1.65 | 3 | 8.05 | 0.373 | 3.43e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Required for leukotriene biosynthesis by ALOX5 (5- lipoxygenase). Anchors ALOX5 to the membrane. Binds arachidonic acid, and could play an essential role in the transfer of arachidonic acid to ALOX5. Binds to MK-886, a compound that blocks the biosynthesis of leukotrienes. {ECO:0000269|PubMed:2300173, ECO:0000269|PubMed:8440384}.;
- Disease
- DISEASE: Ischemic stroke (ISCHSTR) [MIM:601367]: A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=Genetic variations in ALOX5AP may be associated with susceptibility to myocardial infarction. Involvement in myocardial infarction is however unclear: according to some authors (PubMed:14770184), a 4-SNP haplotype in ALOX5AP confers risk of myocardial infarction, while according to other (PubMed:17304054) ALOX5AP is not implicated in this condition. {ECO:0000269|PubMed:14770184, ECO:0000269|PubMed:17304054}.;
- Pathway
- Fc epsilon RI signaling pathway - Homo sapiens (human);Leukotriene modifiers pathway, Pharmacodynamics;Selenium Micronutrient Network;Eicosanoid Synthesis;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;eicosanoid metabolism;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Synthesis of 5-eicosatetraenoic acids;Arachidonic acid metabolism;Synthesis of Lipoxins (LX);Metabolism;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.291
Intolerance Scores
- loftool
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.172
- hipred
- Y
- hipred_score
- 0.653
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.584
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Alox5ap
- Phenotype
- hematopoietic system phenotype; immune system phenotype; skeleton phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- alox5ap
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- leukotriene biosynthetic process;positive regulation of catalytic activity;protein homotrimerization;cellular response to calcium ion;cellular oxidant detoxification
- Cellular component
- nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;nuclear membrane
- Molecular function
- glutathione transferase activity;leukotriene-C4 synthase activity;glutathione peroxidase activity;protein binding;enzyme activator activity;protein N-terminus binding;arachidonic acid binding