HAO1

hydroxyacid oxidase 1

Basic information

Region (hg38): 20:7882984-7940458

Previous symbols: [ "GOX1" ]

Links

ENSG00000101323 ∙ NCBI:54363 ∙ OMIM:605023 ∙ HGNC:4809 ∙ Uniprot:Q9UJM8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HAO1 gene.

• Inborn genetic diseases (14 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.

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						0
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in HAO1

This is a list of pathogenic ClinVar variants found in the HAO1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-7883607-C-T		not specified	Uncertain significance (Mar 29, 2023)
20-7885726-C-T		not specified	Likely benign (Sep 14, 2022)
20-7885795-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-7885852-G-A		not specified	Uncertain significance (Jun 03, 2022)
20-7885861-C-T		not specified	Uncertain significance (Oct 12, 2021)
20-7885865-C-G			Uncertain significance (Jul 17, 2020)
20-7888809-T-C		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7890075-C-T		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7895158-C-T		not specified	Uncertain significance (Jan 03, 2024)
20-7895173-G-A		not specified	Uncertain significance (Aug 02, 2021)
20-7904537-C-G		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7906244-T-C		not specified	Uncertain significance (Jul 09, 2021)
20-7906322-T-A		not specified	Uncertain significance (Nov 08, 2021)
20-7912993-A-G		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7914194-C-T		not specified	Uncertain significance (Nov 30, 2021)
20-7914210-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-7914231-C-G		not specified	Uncertain significance (May 31, 2022)
20-7914299-C-T		not specified	Uncertain significance (Oct 03, 2023)
20-7914317-A-G		not specified	Uncertain significance (Apr 26, 2023)
20-7914330-G-A		not specified	Uncertain significance (Jan 31, 2024)
20-7914414-G-C		not specified	Uncertain significance (Sep 14, 2022)
20-7916402-C-T		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7919281-T-C		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7926296-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
20-7928519-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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