HAO1
Basic information
Region (hg38): 20:7882985-7940458
Previous symbols: [ "GOX1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
- not_provided (1 variants)
- glycolate_oxidase_deficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017545.3. 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 | 0 | |||||
| missense | 49 | 51 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 0 | 50 | 1 | 0 |
Highest pathogenic variant AF is 0.0000210669
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HAO1 | protein_coding | protein_coding | ENST00000378789 | 8 | 57494 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.46e-7 | 0.623 | 125694 | 0 | 46 | 125740 | 0.000183 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.497 | 239 | 218 | 1.09 | 0.0000123 | 2387 |
| Missense in Polyphen | 111 | 95.431 | 1.1631 | 990 | ||
| Synonymous | 0.182 | 81 | 83.1 | 0.975 | 0.00000477 | 749 |
| Loss of Function | 1.10 | 13 | 18.0 | 0.720 | 9.14e-7 | 213 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000473 | 0.000471 |
| Ashkenazi Jewish | 0.000298 | 0.000298 |
| East Asian | 0.000329 | 0.000326 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000150 | 0.000149 |
| Middle Eastern | 0.000329 | 0.000326 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Has 2-hydroxyacid oxidase activity. Most active on the 2-carbon substrate glycolate, but is also active on 2-hydroxy fatty acids, with high activity towards 2-hydroxy palmitate and 2- hydroxy octanoate. {ECO:0000269|PubMed:18215067}.;
- Pathway
- Peroxisome - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism;Peroxisomal protein import;Glyoxylate metabolism and glycine degradation;Glycine, serine, alanine and threonine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.302
Intolerance Scores
- loftool
- 0.818
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.38
Haploinsufficiency Scores
- pHI
- 0.156
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.405
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.950
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hao1
- Phenotype
Gene ontology
- Biological process
- fatty acid alpha-oxidation;protein targeting to peroxisome;response to oxidative stress;cellular nitrogen compound metabolic process;glycolate catabolic process
- Cellular component
- peroxisome;peroxisomal matrix;cytosol
- Molecular function
- (S)-2-hydroxy-acid oxidase activity;signaling receptor binding;glycolate oxidase activity;FMN binding;glyoxylate oxidase activity;very-long-chain-(S)-2-hydroxy-acid oxidase activity;long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity;medium-chain-(S)-2-hydroxy-acid oxidase activity