HOGA1

4-hydroxy-2-oxoglutarate aldolase 1

Basic information

Region (hg38): 10:97584323-97612802

Previous symbols: [ "C10orf65", "DHDPSL" ]

Links

ENSG00000241935

∙ NCBI:112817 ∙ OMIM:613597 ∙ HGNC:25155 ∙ Uniprot:Q86XE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

primary hyperoxaluria type 3 (Definitive), mode of inheritance: AR
primary hyperoxaluria type 3 (Supportive), mode of inheritance: AR
primary hyperoxaluria type 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperoxaluria, primary, type III	AD/AR	Renal	Increased fluid intake in order to promote hydration as well as medical therapy (eg, neutral phosphate therapy, citrate medications, thiazides) may be beneficial	Biochemical; Renal	20797690; 21896830; 22781098; 22688746; 22391140

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HOGA1 gene.

not_provided (345 variants)
Primary_hyperoxaluria_type_3 (248 variants)
Inborn_genetic_diseases (44 variants)
not_specified (12 variants)
HOGA1-related_disorder (7 variants)
Primary_hyperoxaluria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOGA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138413.4. 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	1 clinvar	1 clinvar	7 clinvar	133 clinvar	1 clinvar	143
missense	9 clinvar	59 clinvar	116 clinvar	10 clinvar		194
nonsense	11 clinvar	10 clinvar				21
start loss	3					3
frameshift	17 clinvar	15 clinvar				32
splice donor/acceptor (+/-2bp)	2 clinvar	18 clinvar				20
Total	43	103	123	143	1

Highest pathogenic variant AF is 0.00226545

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOGA1	protein_coding	protein_coding	ENST00000370646	7	28480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.58e-14	0.00373	125677	1	70	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.279	217	206	1.05	0.0000128	2115
Missense in Polyphen		81	77.025	1.0516		787
Synonymous	0.710	75	83.2	0.901	0.00000538	686
Loss of Function	-0.874	19	15.3	1.24	8.32e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000518
Ashkenazi Jewish	0.00	0.00
East Asian	0.000943	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000943	0.000925
South Asian	0.000429	0.000392
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the final step in the metabolic pathway of hydroxyproline. {ECO:0000269|PubMed:20797690, ECO:0000269|PubMed:21998747}.;
Disease: DISEASE: Hyperoxaluria primary 3 (HP3) [MIM:613616]: A disorder phenotypically similar to hyperoxaluria type 1 and type 2. It is characterized by increase in urinary oxalate excretion and mild glycolic aciduria. Clinical manifestations include calcium oxalate urolithiasis, hematuria, pain, and/or urinary tract infection. {ECO:0000269|PubMed:20797690}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Arginine and proline metabolism - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Metabolism of amino acids and derivatives;Metabolism;4-hydroxyproline degradation;Glyoxylate metabolism and glycine degradation (Consensus)

Recessive Scores

pRec: 0.146

Intolerance Scores

loftool
rvis_EVS: -1
rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

pHI: 0.0918
hipred: N
hipred_score: 0.251
ghis: 0.516

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hoga1
Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype; liver/biliary system phenotype;

Gene ontology

Biological process: glyoxylate catabolic process;4-hydroxyproline catabolic process;oxalate metabolic process;pyruvate biosynthetic process;glyoxylate metabolic process
Cellular component: mitochondrion;mitochondrial matrix
Molecular function: protein binding;4-hydroxy-2-oxoglutarate aldolase activity;protein homodimerization activity