HAO2
protein-codinghydroxyacid oxidase 2
Gene summary
This gene is one of three related genes that have 2-hydroxyacid oxidase activity. The encoded protein localizes to the peroxisome has the highest activity toward the substrate 2-hydroxypalmitate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HAO2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016527.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 50 | 5 | 55 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 51 | 5 | 0 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057611.1 | 7 | MANE Select | |
| Ensembl | ENSP00000316339.3 | 7 | MANE Select | |
| RefSeq | NP_001005783.2 | 8 | Standard | |
| RefSeq | NP_001364401.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Glyoxylate and dicarboxylate metabolism - Homo sapiens (human)
- Metabolism of lipids
- Metabolism of proteins
- Peroxisomal lipid metabolism
Biological Process
- protein targeting to peroxisome
- fatty acid catabolic process
- fatty acid oxidation
Molecular Function
- (S)-2-hydroxy-acid oxidase activity
- signaling receptor binding
- FMN binding
- very-long-chain-(S)-2-hydroxy-acid oxidase activity
- long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity
Cellular Component
- peroxisome
- peroxisomal matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000325945
- Coding exons
- 7
- Length
- 25352
- Individuals with no LoFs
- 125384
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 336
- Defined
- 125722
- p
- 0.00135
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0690 | 202 | 199 | 1.01 | 0.0000108 | 2281 |
| Missense (PolyPhen) | 60 | 75.022 | 0.79976 | 846 | ||
| Synonymous | -0.834 | 86 | 76.7 | 1.12 | 0.00000405 | 714 |
| Loss of Function | 0.678 | 16 | 19.2 | 0.833 | 0.00000129 | 180 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00055 | 0.00055 | rare |
| Latino/Admixed American | 0.0071 | 0.0071 | notable |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00093 | 0.00092 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.0010 | 0.0010 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.949
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 38.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.919
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |