AOX1
Basic information
Region (hg38): 2:200586014-200677064
Links
Phenotypes
GenCC
Source:
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 AOX1 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 | 10 | |||||
missense | 38 | 45 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | 2 | |||
non coding | 0 | |||||
Total | 0 | 0 | 39 | 9 | 8 |
Variants in AOX1
This is a list of pathogenic ClinVar variants found in the AOX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-200586118-G-C | not specified | Uncertain significance (Mar 28, 2022) | ||
2-200593146-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
2-200595281-C-T | not specified | Uncertain significance (May 26, 2022) | ||
2-200597423-T-C | not specified | Likely benign (Aug 13, 2021) | ||
2-200597428-A-G | not specified | Uncertain significance (Jan 03, 2024) | ||
2-200599660-G-A | not specified | Uncertain significance (May 16, 2023) | ||
2-200599687-A-G | not specified | Uncertain significance (Nov 09, 2021) | ||
2-200599700-G-A | Benign (Dec 31, 2019) | |||
2-200603291-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
2-200603314-T-A | not specified | Uncertain significance (Jul 30, 2023) | ||
2-200604024-C-T | not specified | Uncertain significance (Mar 22, 2023) | ||
2-200604062-C-G | not specified | Uncertain significance (Jun 07, 2023) | ||
2-200604743-G-A | Likely benign (Apr 19, 2018) | |||
2-200604790-T-G | not specified | Uncertain significance (Jan 25, 2023) | ||
2-200605551-T-A | not specified | Uncertain significance (Jan 31, 2024) | ||
2-200605631-G-A | Benign (Aug 17, 2018) | |||
2-200608996-G-A | not specified | Uncertain significance (Aug 23, 2021) | ||
2-200609017-A-G | Benign (May 16, 2018) | |||
2-200609355-A-T | not specified | Uncertain significance (Apr 17, 2023) | ||
2-200609396-C-T | not specified | Uncertain significance (Sep 09, 2024) | ||
2-200611393-G-A | not specified | Uncertain significance (Jan 10, 2022) | ||
2-200611396-A-T | not specified | Uncertain significance (Sep 03, 2024) | ||
2-200611410-G-A | not specified | Uncertain significance (May 21, 2024) | ||
2-200612648-G-T | not specified | Uncertain significance (Oct 06, 2020) | ||
2-200612651-A-G | not specified | Uncertain significance (Oct 17, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AOX1 | protein_coding | protein_coding | ENST00000374700 | 35 | 91197 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.17e-31 | 0.0719 | 125327 | 2 | 419 | 125748 | 0.00168 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.180 | 731 | 745 | 0.981 | 0.0000392 | 8774 |
Missense in Polyphen | 281 | 282.13 | 0.996 | 3379 | ||
Synonymous | -0.120 | 274 | 271 | 1.01 | 0.0000155 | 2555 |
Loss of Function | 2.02 | 59 | 78.3 | 0.753 | 0.00000442 | 910 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00339 | 0.00338 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00142 | 0.00141 |
Finnish | 0.000416 | 0.000416 |
European (Non-Finnish) | 0.00211 | 0.00209 |
Middle Eastern | 0.00142 | 0.00141 |
South Asian | 0.00180 | 0.00173 |
Other | 0.00213 | 0.00212 |
dbNSFP
Source:
- Function
- FUNCTION: Oxidase with broad substrate specificity, oxidizing aromatic azaheterocycles, such as N1-methylnicotinamide, N- methylphthalazinium and phthalazine, as well as aldehydes, such as benzaldehyde, retinal, pyridoxal, and vanillin. Plays a key role in the metabolism of xenobiotics and drugs containing aromatic azaheterocyclic substituents. Participates in the bioactivation of prodrugs such as famciclovir, catalyzing the oxidation step from 6-deoxypenciclovir to penciclovir, which is a potent antiviral agent. Is probably involved in the regulation of reactive oxygen species homeostasis. May be a prominent source of superoxide generation via the one-electron reduction of molecular oxygen. Also may catalyze nitric oxide (NO) production via the reduction of nitrite to NO with NADH or aldehyde as electron donor. May play a role in adipogenesis. {ECO:0000269|PubMed:20444863, ECO:0000269|PubMed:22031625, ECO:0000269|PubMed:22279051, ECO:0000269|PubMed:22522748, ECO:0000269|PubMed:22996261, ECO:0000269|PubMed:23857892, ECO:0000269|PubMed:26322824, ECO:0000269|PubMed:7786031, ECO:0000269|PubMed:9224775}.;
- Pathway
- Tryptophan metabolism - Homo sapiens (human);Retinol metabolism - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);nicotine degradation III;Drug metabolism - cytochrome P450 - Homo sapiens (human);Vitamin B6 metabolism - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);Nicotine Pathway, Pharmacokinetics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Citalopram Action Pathway;3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Nicotinate and Nicotinamide Metabolism;Hypophosphatasia;Citalopram Metabolism Pathway;Nicotine Metabolism Pathway;Nicotine Action Pathway;Thioguanine Action Pathway;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Maple Syrup Urine Disease;Vitamin B6 Metabolism;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Tryptophan Metabolism;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Methylmalonic Aciduria;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Mercaptopurine Metabolism Pathway;Beta-Ketothiolase Deficiency;Nicotine Metabolism;Effects of Nitric Oxide;Tryptophan metabolism;Metabolism;Vitamins B6 activation to pyridoxal phosphate;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Tryptophan degradation;Vitamin B6 metabolism;nicotine degradation IV
(Consensus)
Recessive Scores
- pRec
- 0.401
Intolerance Scores
- loftool
- 0.979
- rvis_EVS
- -1.23
- rvis_percentile_EVS
- 5.56
Haploinsufficiency Scores
- pHI
- 0.151
- hipred
- Y
- hipred_score
- 0.655
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Aox1
- Phenotype
Gene ontology
- Biological process
- xanthine catabolic process;drug metabolic process;electron transport chain;vitamin B6 metabolic process;oxidation-reduction process
- Cellular component
- cytosol;extracellular exosome
- Molecular function
- aldehyde oxidase activity;xanthine dehydrogenase activity;iron ion binding;electron transfer activity;identical protein binding;protein homodimerization activity;molybdopterin cofactor binding;flavin adenine dinucleotide binding;NAD binding;2 iron, 2 sulfur cluster binding;FAD binding;geranial:oxygen oxidoreductase activity;heptaldehyde:oxygen oxidoreductase activity