HAO2

hydroxyacid oxidase 2

Basic information

Region (hg38): 1:119368779-119394130

Links

ENSG00000116882 ∙ NCBI:51179 ∙ OMIM:605176 ∙ HGNC:4810 ∙ Uniprot:Q9NYQ3 ∙ 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 HAO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAO2 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in HAO2

This is a list of pathogenic ClinVar variants found in the HAO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-119381117-C-T		not specified	Uncertain significance (Dec 03, 2024)
1-119381119-C-T		not specified	Uncertain significance (Nov 07, 2024)
1-119381150-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-119382926-G-A		not specified	Uncertain significance (Jun 13, 2023)
1-119382929-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-119382931-C-T		not specified	Uncertain significance (Apr 04, 2024)
1-119382989-T-G		not specified	Uncertain significance (Oct 04, 2022)
1-119383019-G-C		not specified	Uncertain significance (Oct 01, 2024)
1-119383030-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-119384785-C-A		not specified	Uncertain significance (Sep 27, 2024)
1-119384803-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-119384827-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-119384829-C-G		not specified	Uncertain significance (Aug 12, 2021)
1-119384917-T-A		not specified	Uncertain significance (Oct 02, 2023)
1-119384921-G-C		not specified	Uncertain significance (Nov 07, 2023)
1-119384973-G-C		not specified	Uncertain significance (Jan 09, 2024)
1-119385001-G-A		not specified	Likely benign (May 01, 2024)
1-119385006-C-A		not specified	Uncertain significance (Oct 29, 2021)
1-119386650-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-119386671-G-A		not specified	Uncertain significance (May 05, 2023)
1-119386697-A-G		not specified	Uncertain significance (Nov 08, 2022)
1-119386760-G-A		not specified	Uncertain significance (May 23, 2023)
1-119386776-A-T		not specified	Uncertain significance (Dec 13, 2022)
1-119386781-A-G		not specified	Uncertain significance (Jun 28, 2024)
1-119392111-T-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAO2	protein_coding	protein_coding	ENST00000325945	7	25352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.00e-10	0.234	125384	2	336	125722	0.00135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0690	202	199	1.01	0.0000108	2281
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00767	0.00767
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000926	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000926	0.000925
South Asian	0.00105	0.00101
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.
• Pathway: Peroxisome - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism of proteins;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.949
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.0589
• hipred: N
• hipred_score: 0.264
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hao2

Gene ontology

• Biological process: protein targeting to peroxisome;fatty acid catabolic process;fatty acid oxidation
• Cellular component: peroxisome;peroxisomal matrix;cytosol
• 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;medium-chain-(S)-2-hydroxy-acid oxidase activity