Primary hyperoxaluria type 3 (PH3) is an autosomal recessive disorder of glyoxylate metabolism caused by biallelic HOGA1 pathogenic variants. HOGA1 encodes the mitochondrial enzyme 4-hydroxy-2-oxoglutarate aldolase, which catalyzes the final step of the hepatic hydroxyproline degradation pathway, cleaving 4-hydroxy-2-oxoglutarate (HOG) into pyruvate and glyoxylate. Loss of HOGA1 activity causes accumulation of HOG and related hydroxyproline metabolites and, paradoxically, increased endogenous oxalate production (proposed to arise from cytosolic conversion of accumulated HOG to glyoxylate and/or inhibition of glyoxylate reductase). The resulting hyperoxaluria drives calcium oxalate supersaturation and recurrent calcium oxalate nephrolithiasis, typically presenting in early childhood. PH3 is generally the mildest of the primary hyperoxalurias, with progression to kidney failure uncommon.
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name: Primary Hyperoxaluria Type 3
creation_date: "2026-07-07T12:00:00Z"
description: >-
Primary hyperoxaluria type 3 (PH3) is an autosomal recessive disorder of
glyoxylate metabolism caused by biallelic HOGA1 pathogenic variants. HOGA1
encodes the mitochondrial enzyme 4-hydroxy-2-oxoglutarate aldolase, which
catalyzes the final step of the hepatic hydroxyproline degradation pathway,
cleaving 4-hydroxy-2-oxoglutarate (HOG) into pyruvate and glyoxylate. Loss of
HOGA1 activity causes accumulation of HOG and related hydroxyproline
metabolites and, paradoxically, increased endogenous oxalate production
(proposed to arise from cytosolic conversion of accumulated HOG to glyoxylate
and/or inhibition of glyoxylate reductase). The resulting hyperoxaluria drives
calcium oxalate supersaturation and recurrent calcium oxalate nephrolithiasis,
typically presenting in early childhood. PH3 is generally the mildest of the
primary hyperoxalurias, with progression to kidney failure uncommon.
category: Metabolic Disorder
parents:
- Inborn Error of Metabolism
- Primary Hyperoxaluria
- Genetic Kidney Disease
synonyms:
- PH3
- HOGA1 deficiency
- 4-hydroxy-2-oxoglutarate aldolase deficiency
- HOGA1 primary hyperoxaluria
classifications:
icimd_category:
- classification_value: glyoxylate_and_oxalate
notes: >-
ICIMD category 13.1, disorders of glyoxylate and oxalate metabolism.
PH3 is the HOGA1 / 4-hydroxy-2-oxoglutarate aldolase defect in the
hepatic hydroxyproline pathway.
disease_term:
preferred_term: primary hyperoxaluria type 3
term:
id: MONDO:0013327
label: primary hyperoxaluria type 3
references:
- reference: PMID:26401545
title: "Primary Hyperoxaluria Type 3."
tags:
- GeneReviews
inheritance:
- name: Autosomal recessive inheritance
inheritance_term:
preferred_term: Autosomal recessive inheritance
term:
id: HP:0000007
label: Autosomal recessive inheritance
description: >-
PH3 is caused by biallelic HOGA1 variants. A recurrent intron 5 splice-site
variant (c.700+5G>T) is a common founder allele in European patients, and a
3 bp deletion is a founder allele in individuals of Ashkenazi Jewish descent.
evidence:
- reference: PMID:20797690
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "Primary hyperoxaluria (PH) is an autosomal-recessive disorder of endogenous"
explanation: States the autosomal recessive mode of inheritance of primary hyperoxaluria.
reference_title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III
- reference: PMID:26401545
reference_title: "Primary Hyperoxaluria Type 3."
supports: SUPPORT
evidence_source: OTHER
snippet: "PH3 is inherited in an autosomal recessive manner."
explanation: GeneReviews establishes autosomal recessive inheritance for PH3.
pathophysiology:
- name: HOGA1 4-Hydroxy-2-Oxoglutarate Aldolase Deficiency
description: >-
Biallelic loss-of-function HOGA1 variants abolish mitochondrial
4-hydroxy-2-oxoglutarate aldolase activity, the fourth and final enzymatic
step of the hepatic hydroxyproline degradation pathway that cleaves
4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate.
role: trigger
genes:
- preferred_term: HOGA1
term:
id: hgnc:25155
label: HOGA1
molecular_functions:
- preferred_term: 4-hydroxy-2-oxoglutarate aldolase activity
term:
id: GO:0106009
label: (4S)-4-hydroxy-2-oxoglutarate aldolase activity
modifier: DECREASED
biological_processes:
- preferred_term: glyoxylate metabolic process
term:
id: GO:0046487
label: glyoxylate metabolic process
modifier: DYSREGULATED
cell_types:
- preferred_term: hepatocyte
term:
id: CL:0000182
label: hepatocyte
evidence:
- reference: PMID:22391140
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "definitive proof that PH Type 3 is due to deficiency of the"
explanation: >-
Demonstrates via loss-of-function nonsense variants that PH3 results from
deficiency of the 4-hydroxy-2-oxoglutarate aldolase enzyme.
reference_title: The enzyme 4-hydroxy-2-oxoglutarate aldolase is deficient in primary hyperoxaluria type 3
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "HOGA1 is a mitochondrial"
explanation: >-
Establishes HOGA1 as the mitochondrial 4-hydroxy-2-oxoglutarate aldolase
acting in the hydroxyproline pathway.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
- reference: PMID:20797690
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "aldolase, catalyzing the final step in the metabolic pathway of hydroxyproline."
explanation: >-
Identifies the HOGA1 gene product as the aldolase catalyzing the final
step of hydroxyproline metabolism.
reference_title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III
downstream:
- target: Hydroxyproline-Pathway Metabolite Accumulation
causal_link_type: DIRECT
description: >-
Loss of the aldolase step causes accumulation of its substrate
4-hydroxy-2-oxoglutarate and related hydroxyproline metabolites.
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "HOGA1 deficiency results in the accumulation of 4-hydroxy-2-oxoglutarate in the"
explanation: Directly links HOGA1 deficiency to accumulation of 4-hydroxy-2-oxoglutarate.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
- name: Hydroxyproline-Pathway Metabolite Accumulation
description: >-
HOGA1 deficiency causes accumulation of 4-hydroxy-2-oxoglutarate together
with its precursor 4-hydroxyglutamate and derivative 2,4-dihydroxyglutarate,
detectable as increased urinary excretion of these hydroxyproline
metabolites and used diagnostically.
role: amplifier
biological_processes:
- preferred_term: glyoxylate metabolic process
term:
id: GO:0046487
label: glyoxylate metabolic process
modifier: DYSREGULATED
chemical_entities:
- preferred_term: 4-hydroxy-2-oxoglutarate
term:
id: CHEBI:30923
label: 4-hydroxy-2-oxoglutaric acid
modifier: INCREASED
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "Significant increases in concentrations of"
explanation: >-
Human urine GC-MS shows significant increases of 4-hydroxy-2-oxoglutarate
and related metabolites in all PH3 patients versus carriers and controls.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
downstream:
- target: Cytosolic Glyoxylate-to-Oxalate Overproduction
causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
description: >-
Accumulated 4-hydroxy-2-oxoglutarate is proposed to be exported to the
cytosol and converted to glyoxylate, which is oxidized to oxalate.
- name: Cytosolic Glyoxylate-to-Oxalate Overproduction
description: >-
Despite a block in the mitochondrial conversion of hydroxyproline to
glyoxylate, endogenous oxalate production increases in PH3. The leading
proposed mechanism is that accumulated 4-hydroxy-2-oxoglutarate is exported
to the cytosol and cleaved by a non-HOGA1 cytosolic aldolase to glyoxylate,
which is oxidized to oxalate; accumulated substrate may additionally inhibit
glyoxylate reductase. The precise pathomechanism remains uncertain.
role: central_effector
biological_processes:
- preferred_term: oxalate biosynthetic process
term:
id: GO:0033610
label: oxalate biosynthetic process
modifier: INCREASED
chemical_entities:
- preferred_term: glyoxylate
term:
id: CHEBI:36655
label: glyoxylate
modifier: INCREASED
- preferred_term: oxalate
term:
id: CHEBI:132952
label: oxalate
modifier: INCREASED
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "its transport into the cytosol where it is converted to"
explanation: >-
Proposes cytosolic conversion of accumulated 4-hydroxy-2-oxoglutarate to
glyoxylate as the route to increased oxalate.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
- reference: PMID:26428388
supports: SUPPORT
evidence_source: IN_VITRO
snippet: "a buildup of HOG due to HOGA deficiency may result in an inhibition of GR activity based on results observed in vitro with the purified enzyme"
explanation: >-
Alternative/contributing mechanism in which accumulated HOG inhibits
glyoxylate reductase, based on in vitro assays with purified enzyme.
reference_title: Hydroxyproline metabolism in a mouse model of Primary Hyperoxaluria Type 3
downstream:
- target: Urinary Calcium Oxalate Supersaturation
causal_link_type: DIRECT
description: Increased endogenous oxalate raises urinary calcium oxalate supersaturation.
- name: Urinary Calcium Oxalate Supersaturation
conforms_to: "nephrolithiasis_crystal_nucleation#Urinary Supersaturation"
description: >-
Increased urinary oxalate raises calcium oxalate crystallization burden in
PH3, specializing the nephrolithiasis supersaturation module to HOGA1
deficiency.
role: central_effector
biological_processes:
- preferred_term: Renal Excretion of Oxalate
term:
id: GO:0007588
label: excretion
modifier: INCREASED
chemical_entities:
- preferred_term: oxalate
term:
id: CHEBI:132952
label: oxalate
modifier: INCREASED
- preferred_term: calcium oxalate
term:
id: CHEBI:60579
label: calcium oxalate
modifier: INCREASED
evidence:
- reference: PMID:20797690
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "characterized by accumulation of calcium oxalate primarily in"
explanation: >-
Primary hyperoxaluria is characterized by endogenous oxalate synthesis and
calcium oxalate accumulation in the kidney.
reference_title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III
downstream:
- target: Calcium Oxalate Nephrolithiasis
causal_link_type: DIRECT
description: Calcium oxalate supersaturation leads to recurrent kidney stones.
- name: Calcium Oxalate Nephrolithiasis
conforms_to: "nephrolithiasis_crystal_nucleation#Symptomatic Kidney Stones"
description: >-
PH3 typically presents in early childhood with recurrent calcium oxalate
nephrolithiasis. In contrast to PH1 and PH2, the outcome is generally
favorable and progression to end-stage kidney disease is uncommon.
role: consequence
locations:
- preferred_term: kidney
term:
id: UBERON:0002113
label: kidney
evidence:
- reference: PMID:20797690
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "patients from eight unrelated"
explanation: >-
The PH3-defining cohort was selected from patients with calcium oxalate
nephrolithiasis.
reference_title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III
- reference: PMID:22781098
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "point to a favorable outcome of type III in the context of PH despite incomplete or"
explanation: Supports the generally favorable renal outcome of PH3.
reference_title: Novel findings in patients with primary hyperoxaluria type III and implications for advanced molecular testing strategies
phenotypes:
- category: Biochemical
name: Hyperoxaluria
description: PH3 is characterized by increased endogenous oxalate synthesis and urinary oxalate excretion.
phenotype_term:
preferred_term: Hyperoxaluria
term:
id: HP:0003159
label: Hyperoxaluria
evidence:
- reference: PMID:26428388
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "Affected individuals have increased excretions of oxalate, 4-OH-Glu, HOG and DHG in their urine"
explanation: >-
Affected individuals with HOGA1 deficiency have increased urinary oxalate
excretion; this sentence in the mouse-model paper summarizes human PH3
biochemical observations from prior clinical reports.
reference_title: Hydroxyproline metabolism in a mouse model of Primary Hyperoxaluria Type 3
- category: Clinical
name: Calcium oxalate nephrolithiasis
description: Recurrent calcium oxalate stones, often from early childhood, are the core PH3 manifestation.
phenotype_term:
preferred_term: Calcium oxalate nephrolithiasis
term:
id: HP:0008672
label: Calcium oxalate nephrolithiasis
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "recessive disorders characterized by kidney"
explanation: Primary hyperoxalurias are characterized by kidney stone disease.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
- reference: PMID:26401545
reference_title: "Primary Hyperoxaluria Type 3."
supports: SUPPORT
evidence_source: OTHER
snippet: "recurring calcium oxalate stones beginning in childhood or adolescence"
explanation: GeneReviews describes recurrent calcium oxalate stones as the core PH3 presentation.
phenotype_contexts:
- onset:
onset_category: CHILDHOOD
notes: PH3 most often presents in early childhood, although adolescent and adult presentations occur.
evidence:
- reference: PMID:26401545
reference_title: "Primary Hyperoxaluria Type 3."
supports: SUPPORT
evidence_source: OTHER
snippet: "PH3 most often presents in childhood (median age 2 to 3 years)"
explanation: GeneReviews supports childhood onset for the typical PH3 stone phenotype.
- category: Clinical
name: Nephrocalcinosis
description: Nephrocalcinosis is reported occasionally in PH3 and may contribute to reduced kidney function.
frequency: OCCASIONAL
phenotype_term:
preferred_term: Nephrocalcinosis
term:
id: HP:0000121
label: Nephrocalcinosis
evidence:
- reference: PMID:26401545
reference_title: "Primary Hyperoxaluria Type 3."
supports: SUPPORT
evidence_source: OTHER
snippet: "on occasion, nephrocalcinosis or reduced kidney function"
explanation: GeneReviews reports nephrocalcinosis as an occasional PH3 feature.
biochemical:
- name: Urinary hydroxyproline-pathway metabolite elevation
presence: INCREASED
notes: >-
Urinary 4-hydroxy-2-oxoglutarate (HOG), 4-hydroxyglutamate, and
2,4-dihydroxyglutarate elevations provide a diagnostic biochemical profile
for PH3.
biomarker_term:
preferred_term: 4-hydroxy-2-oxoglutarate
term:
id: CHEBI:30923
label: 4-hydroxy-2-oxoglutaric acid
readouts:
- target: Hydroxyproline-Pathway Metabolite Accumulation
relationship: READOUT_OF
direction: POSITIVE
endpoint_context: DIAGNOSTIC
interpretation: >-
Increased urinary HOG and related hydroxyproline-pathway metabolites
report the HOGA1 metabolic block and are used diagnostically for PH3.
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "These studies provide a diagnostic tool for primary hyperoxaluria type"
explanation: The metabolite profiling study presents HOG-related elevations as a PH3 diagnostic tool.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
evidence:
- reference: PMID:22729392
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "4-hydroxy-2-oxoglutarate and its precursor and derivative 4-hydroxyglutamate and 2,4-dihydroxyglutarate, respectively, were found in all patients"
explanation: The human urine GC-MS study identifies elevated HOG, 4-hydroxyglutamate, and DHG in PH3 patients.
reference_title: Primary hyperoxaluria type III--a model for studying perturbations in glyoxylate metabolism
genetic:
- name: HOGA1
gene_term:
preferred_term: HOGA1
term:
id: hgnc:25155
label: HOGA1
relationship_type: CAUSATIVE
notes: >-
Biallelic HOGA1 loss-of-function variants cause PH3. The intron 5
c.700+5G>T splice-site variant is the most common allele and a probable
European founder mutation; a 3 bp deletion is an Ashkenazi Jewish founder
allele.
evidence:
- reference: PMID:22391140
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "The recurrent c.700 + 5G > T splice site mutation in intron 5 was most common with a frequency of 67%."
explanation: Reports the recurrent c.700+5G>T HOGA1 splice-site variant as the most common PH3 allele.
reference_title: The enzyme 4-hydroxy-2-oxoglutarate aldolase is deficient in primary hyperoxaluria type 3
- reference: PMID:20797690
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "an allelic fragment shared by all patients of Ashkenazi Jewish descent and"
explanation: Identifies an Ashkenazi Jewish founder allele bearing a 3 bp deletion in HOGA1 (DHDPSL).
reference_title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III
- name: AGXT
gene_term:
preferred_term: AGXT
term:
id: hgnc:341
label: AGXT
relationship_type: MODIFIER
notes: >-
AGXT is not the primary PH3 disease gene, but a reported family with
homozygous HOGA1 p.P190L plus heterozygous AGXT p.D201E had a more severe
phenotype than HOGA1 p.P190L alone, suggesting a possible oligogenic
modifier effect in selected families. Note this entry does NOT bind an
oligogenic inheritance term (HP:0010983) and is not a member of the Digenic
and Oligogenic Disorders grouping: biallelic HOGA1 causes PH3 by itself,
and the quoted "triallelic inheritance" describes a severity difference in
two sisters, not a third allele the disease requires.
evidence:
- reference: PMID:22781098
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "The two girls exhibiting triallelic inheritance presented a more severe phenotype"
explanation: Supports AGXT as a potential modifier of PH3 severity in one triallelic family.
reference_title: Novel findings in patients with primary hyperoxaluria type III and implications for advanced molecular testing strategies
prevalence:
- population: Worldwide
measure_type: UNKNOWN
prevalence_class: RARE
notes: >-
PH3 is a rare disorder; its true prevalence is not well established. It
accounts for a minority of primary hyperoxaluria cases, with founder alleles
in European and Ashkenazi Jewish populations.
evidence:
- reference: PMID:22781098
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: "the pathophysiology and prevalence of type"
explanation: States that the prevalence of PH3 is largely unknown.
reference_title: Novel findings in patients with primary hyperoxaluria type III and implications for advanced molecular testing strategies
treatments:
- name: High Fluid Intake and Crystallization Inhibitors
description: >-
Supportive management aims to reduce urinary calcium oxalate supersaturation
through high fluid intake and urinary crystallization inhibitors (e.g.,
potassium citrate), with dietary measures to limit stone formation. There is
no HOGA1-specific targeted therapy approved for PH3.
treatment_term:
preferred_term: supportive care
term:
id: NCIT:C15747
label: Supportive Care
therapeutic_agent:
- preferred_term: potassium citrate
term:
id: CHEBI:64733
label: potassium citrate (anhydrous)
evidence:
- reference: PMID:26401545
reference_title: "Primary Hyperoxaluria Type 3."
supports: SUPPORT
evidence_source: OTHER
snippet: "potassium and/or sodium citrate"
explanation: GeneReviews supports citrate crystallization inhibitors as part of PH3 supportive management.
discussions:
- discussion_id: gap_ph3_oxalate_overproduction_mechanism
prompt: >-
Given that HOGA1 deficiency blocks the mitochondrial conversion of
4-hydroxy-2-oxoglutarate to glyoxylate, by what route does endogenous
oxalate production nonetheless increase in PH3 — cytosolic cleavage of
accumulated 4-hydroxy-2-oxoglutarate by a non-HOGA1 aldolase, substrate
inhibition of glyoxylate reductase, or another mechanism — and why do only a
minority of biallelic HOGA1 carriers develop clinical hyperoxaluria?
kind: KNOWLEDGE_GAP
status: OPEN
rationale: >-
The paradox of increased oxalate despite a functional block upstream of
glyoxylate is unresolved; competing cytosolic-aldolase models and
glyoxylate-reductase-inhibition models are proposed but not established, and the
incomplete penetrance of the HOGA1 genotype is unexplained.
attaches_to:
- pathophysiology#Cytosolic Glyoxylate-to-Oxalate Overproduction
notes: >-
IEMbase package seed WP-003, classification code 1.7.02.02
(HOGA1-related mitochondrial 4-hydroxy-2-oxoglutarate aldolase 1 deficiency);
OMIM:613616; ORPHA:93600. MONDO provides an exact disease term
(MONDO:0013327), so PH3 is curated as a separate Disease entry and added to
the Disorders of Glyoxylate and Oxalate Metabolism grouping alongside PH1 and
PH2. The gene was originally reported as DHDPSL before being renamed HOGA1.
Overview. Primary hyperoxaluria type 3 (PH3) is an autosomal recessive inborn error of glyoxylate/4-hydroxyproline metabolism caused by biallelic loss-of-function variants in HOGA1, encoding the mitochondrial enzyme 4-hydroxy-2-oxoglutarate aldolase. Loss of this enzyme results in excessive endogenous oxalate synthesis and recurrent calcium oxalate nephrolithiasis, typically beginning in early childhood. It is the most recently described and generally the least severe of the three classic primary hyperoxalurias, with kidney function preserved in most patients and (to date) no reported systemic oxalosis.
Key identifiers:
| Resource | Identifier |
|---|---|
| OMIM (disease) | 613616 — HYPEROXALURIA, PRIMARY, TYPE III; HP3 |
| OMIM (gene) | 613597 — HOGA1 |
| MONDO | MONDO:0013327 (primary hyperoxaluria type 3) |
| Orphanet | ORPHA:93600 (primary hyperoxaluria type 3) |
| ICD-10 | E72.53 (primary hyperoxaluria) |
| ICD-11 | 5C51.20 (primary hyperoxaluria) |
| MeSH | Hyperoxaluria, Primary (D006960) |
| Gene (NCBI) | 112817; HGNC:25155; cytoband 10q24.2 |
Synonyms / alternative names: PH3; PH III; HP3; hyperoxaluria, primary, type III; HOGA1-related hyperoxaluria; historically associated with the gene name DHDPSL (dihydrodipicolinate synthase-like), the original name of HOGA1 at discovery.
Sources: OMIM 613616; GeneReviews: PH3, NBK316514 (PMID:26401545); MedlinePlus: HOGA1.
Primary causal factor (genetic). PH3 is caused by homozygous or compound heterozygous pathogenic variants in HOGA1 (10q24.2). The disease was first defined by Belostotsky et al., who mapped it to DHDPSL/HOGA1 — "Mutations in DHDPSL Are Responsible for Primary Hyperoxaluria Type III" (Belostotsky R et al., Am J Hum Genet 2010; PMID:20797690 — verify). The gene product is a mitochondrial aldolase; its loss increases endogenous oxalate production (OMIM 613616; GeneReviews PMID:26401545).
Genetic risk factors. - Biallelic HOGA1 pathogenic variants are necessary and sufficient to cause the Mendelian disease. - Carrier / heterozygous state as a stone risk modifier: Monico et al. proposed that HOGA1 may be a risk factor for idiopathic calcium oxalate urolithiasis even in heterozygotes — "Primary Hyperoxaluria Type III Gene HOGA1 (Formerly DHDPSL) as a Possible Risk Factor for Idiopathic Calcium Oxalate Urolithiasis" (PMID:21896830). - Consanguinity / founder effects increase homozygote frequency in specific populations (see §9).
Environmental / lifestyle contributors (disease-modifying, not causal). - Dietary oxalate and hydroxyproline load (collagen-rich foods, gelatin) can raise the substrate pool feeding oxalate synthesis. - Dehydration / low fluid intake and low urinary citrate promote calcium oxalate supersaturation and stone formation. - High-dose vitamin C (ascorbate) is a precursor to oxalate and is discouraged.
Gene–environment interaction. The genotype sets excess endogenous oxalate production, but clinical stone burden is modulated by urine volume, citrate, calcium, and dietary oxalate/hydroxyproline — hence the mainstays of management are hydration and citrate rather than gene-directed therapy (GeneReviews PMID:26401545).
PH3 is dominated by stone-related urologic phenotypes and biochemical (laboratory) abnormalities, with kidney-function decline in a minority.
| Phenotype | Type | Onset / course | Frequency in PH3 | Suggested HPO term |
|---|---|---|---|---|
| Recurrent calcium oxalate nephrolithiasis (kidney stones) | Clinical sign | Median onset 2–3 y; recurrent through adulthood | Near-universal in symptomatic patients (~89% have stones at first evaluation) | HP:0000787 Nephrolithiasis / HP:0008672 CaOx nephrolithiasis |
| Hyperoxaluria (elevated urinary oxalate) | Lab abnormality | From infancy | Defining; median ~1.1 mmol/1.73 m²/day (lowest of the three PH types) | HP:0003159 Hyperoxaluria |
| Hematuria | Clinical sign | With stone episodes | Common | HP:0000790 Hematuria |
| Dysuria / urinary frequency | Symptom | With stones/UTI | Common | HP:0100518 Dysuria; HP:0100515 Urinary frequency |
| Renal/ureteral colic (flank pain) | Symptom | Episodic with stones | Common | HP:0012622 (Chronic kidney disease context) / stone pain |
| Urinary tract infection | Clinical sign | Recurrent with stones | Frequent | HP:0000010 Recurrent UTI |
| Nephrocalcinosis | Imaging/lab sign | Childhood | ~7% at diagnosis (vs 26% PH1, 16% PH2) | HP:0000121 Nephrocalcinosis |
| Hypercalciuria | Lab abnormality | — | ~10% (vs ~2% PH1) | HP:0002150 Hypercalciuria |
| Elevated urinary 4-hydroxy-2-oxoglutarate (HOG) | Lab biomarker | From onset; declines with age | Highly characteristic (see §10) | (no specific HP term; use HP:0003159 parent) |
| Elevated urinary 2,4-dihydroxyglutarate (DHG) | Lab biomarker | — | Characteristic | (no specific HP term) |
| Chronic kidney disease / reduced eGFR | Clinical sign | Later, minority | ~2.9% reach ESKD by age 40 | HP:0012622 Chronic kidney disease; HP:0003774 Stage 5 CKD |
Phenotype characteristics. - Age of onset: Earliest of the three PH types. Median symptomatic onset ~2.7 years; some patients present only in adulthood (PMID:33543760). - Severity: Generally mild-to-moderate; recurrent stones dominate. "Compared to hyperoxaluria type I and type II, HP3 appears to be the least severe, with good preservation of kidney function in most patients" (OMIM 613616). - Progression: Recurrent/episodic stone events that can persist into the sixth decade; kidney function usually stable, but CKD (including rare kidney failure) does occur. - Quality-of-life impact: Driven by recurrent painful stone episodes, procedures, and infections; formal QoL instrument data specific to PH3 are limited/not available.
Sources: Clinical characterization of PH3 vs PH1/PH2 (PMID:33543760); GeneReviews (PMID:26401545).
Causal gene: HOGA1 (4-hydroxy-2-oxoglutarate aldolase 1; formerly DHDPSL), HGNC:25155, OMIM 613597, chromosome 10q24.2, NCBI Gene 112817. It has 7 coding exons encoding the mitochondrial aldolase (UniProt Q86XE5; suggested GO:0008700-related aldolase activity; see §6).
Pathogenic variant spectrum. - >50 disease-associated variants reported to date; the majority are missense variants, with a loss-of-function mechanism (unstable, aggregation-prone, catalytically inactive protein). "All nine examined PH3 variants were found to be unstable, aggregation-prone, and enzymatically inactive" (Riedel et al., PMID:22771891). A dominant-negative contribution has also been proposed for some alleles (Abid et al., Hum Mutat 2022, PMID:36259736). - Common/recurrent alleles: - c.700+5G>T — a splice-site variant; the most common allele in European/non-Ashkenazi populations (reported allelic frequencies ~35–46%; potential founder mutation) (PMID:22781098; PMID:33948853). - c.944_946delAGG (p.Glu315del) — the predominant Ashkenazi Jewish founder allele (~66% of Ashkenazi PH3 alleles per GeneReviews). - c.107C>T (p.Ala36Val) — second common Ashkenazi allele (~22%). - Variant classification: ACMG/AMP classifications (pathogenic/likely pathogenic vs VUS) are curated in ClinVar; OMIM lists ≥24 disease-causing variants. - Origin: Germline; autosomal recessive. No somatic mechanism. - Functional consequence: Loss of function (protein instability + loss of aldolase activity), possibly with dominant-negative effects on the tetramer.
Modifier genes. Not formally established. Because accumulated HOG inhibits GRHPR (the PH2 enzyme), GRHPR activity/variation is a plausible mechanistic modifier of oxalate output (see §6).
Epigenetics / chromosomal abnormalities. No disease-specific DNA-methylation, histone-modification, aneuploidy, or structural-rearrangement associations are described for PH3. Diagnosis relies on sequencing, not cytogenetics.
Sources: Abid et al. 2022, Hum Mutat; Beck et al. — novel findings/molecular testing; Ethnic associations of HOGA1 variants; GeneReviews (PMID:26401545).
Normal pathway (mitochondrial hydroxyproline degradation). Dietary and endogenous collagen turnover supplies 4-hydroxyproline (~300–450 mg/day from endogenous collagen turnover). In the mitochondrion, hydroxyproline is metabolized through several steps to 4-hydroxy-2-oxoglutarate (HOG). HOGA1 catalyzes the final step — a retro-aldol cleavage of HOG into glyoxylate + pyruvate (suggested biological process GO:0019471 4-hydroxyproline catabolic process; molecular function: aldolase/lyase activity). Glyoxylate is normally detoxified by: - AGT (AGXT, peroxisomal, PLP-dependent alanine–glyoxylate aminotransferase) → glycine (defective in PH1), and - GR/GRHPR (glyoxylate reductase/hydroxypyruvate reductase, cytosolic) → glycolate (defective in PH2). Any glyoxylate escaping detoxification is oxidized by LDH (lactate dehydrogenase) to oxalate.
PH3 mechanism (loss of HOGA1). Loss of HOGA1 aldolase activity causes accumulation of HOG in urine, serum, and liver. Two complementary, still-debated mechanisms convert this into oxalate overproduction:
Enzyme structure/function. HOGA1 is a mitochondrial homotetramer ("dimer of dimers"); each monomer has an (α/β)₈ TIM-barrel catalytic domain plus a C-terminal three-helix bundle. It uses a Type I aldolase mechanism with a Schiff-base–forming catalytic Lys196 (proton relay via Tyr168/Ser77); no metal cofactor is required. Disease variants disrupt either the active site or tetramer assembly, and are unstable/aggregation-prone (Riedel et al., PMID:21998747; PLOS One PMC3188589). HOGA activity is additionally regulated by pyruvate and α-ketoglutarate (product/substrate feedback), relevant to PH3 (PMID:31696211).
Protein dysfunction: Loss of function via misfolding/aggregation and loss of catalytic activity (possible dominant-negative on the tetramer).
Metabolic changes: Elevated HOG and its reduction product 2,4-dihydroxyglutarate (DHG); increased net oxalate synthesis; urinary glycolate/glycerate typically normal (distinguishing from PH1/PH2).
Tissue damage mechanism: Calcium oxalate crystal deposition → crystal nucleation/aggregation → mechanical/inflammatory tubular injury, stone formation, occasional nephrocalcinosis, and — over time in a minority — chronic kidney injury. (Notably, systemic oxalosis has not been reported in PH3, unlike PH1.)
Cell types & anatomy involved: Hepatic mitochondria (site of HOGA1 expression and oxalate overproduction; suggested CL:0000182 hepatocyte, GO:0005739 mitochondrion) and renal tubular epithelium (site of crystal-related injury; suggested CL:1000507/renal tubule epithelial cells, UBERON:0002113 kidney).
Molecular profiling: No large-scale disease-specific transcriptomic/proteomic/single-cell datasets for PH3; the field is characterized by targeted metabolomics (urine/plasma HOG, DHG, oxalate quantitation by LC-MS/MS) and enzyme kinetics.
Chemical entities (CHEBI suggestions): oxalate (CHEBI:30623), glyoxylate (CHEBI:16891), 4-hydroxyproline (CHEBI:18095), 4-hydroxy-2-oxoglutarate/HOG, 2-oxoglutarate (CHEBI:16810), pyruvate (CHEBI:15361), glycolate (CHEBI:17497), citrate (CHEBI:30769).
Sources: Structural/biochemical HOGA (PLOS One) (PMID:21998747); HOGA inactivity & GR inhibition (PMID:22771891); Regulation of HOGA by pyruvate/α-KG (PMID:31696211).
Inheritance: Autosomal recessive (25% recurrence risk per pregnancy for carrier couples). Suggested HPO mode-of-inheritance term: HP:0000007 Autosomal recessive inheritance.
Penetrance / expressivity: Biochemical penetrance (hyperoxaluria) is essentially complete in biallelic carriers; clinical expressivity is variable (stone burden and kidney outcomes differ widely, even within genotype). No genetic anticipation (not a repeat-expansion disorder).
Epidemiology: - Overall primary hyperoxaluria prevalence: ~1–3 per 1,000,000. - PH3 constitutes ~7–12% of all primary hyperoxaluria cases (~10% commonly cited). - Estimated PH3 prevalence: ~1 per 136,000 (GeneReviews). - Carrier frequency: ~1 in 185 general population; ~1 in 55 in Ashkenazi Jews (GeneReviews; PMID:33948853).
Founder effects / population genetics: - Ashkenazi Jewish founder alleles: c.944_946delAGG (p.Glu315del) and c.107C>T (p.Ala36Val). - European/non-Ashkenazi: c.700+5G>T splice variant predominates (potential founder; ~35–46% of alleles). - Consanguinity increases homozygous disease in some populations; genetically homogeneous founder cohorts have been described.
Demographics: No strong sex predilection reported; onset in early childhood; enrichment in populations carrying founder alleles (Ashkenazi Jewish; specific European and Middle Eastern groups).
Sources: GeneReviews (PMID:26401545); Ethnic associations of HOGA1 variants; Beck et al..
Biochemical (urine/blood): - 24-hour urinary oxalate: Elevated (>0.7 mmol/1.73 m²/day); PH3 shows the lowest oxalate of the three types (median ~1.1 mmol/1.73 m²/day). LOINC-type analyte: urine oxalate. - Urinary HOG (4-hydroxy-2-oxoglutarate): The key discriminating biomarker — markedly elevated in PH3 (median ~110 mg/g creatinine, normal <10) and essentially absent in PH1/PH2; described as "an excellent biomarker for PH3 diagnosis" and decreases with age (PMID:33543760). - Urinary 2,4-dihydroxyglutarate (DHG): Elevated; complementary PH3 marker (LC-MS/MS). - Urinary glycolate (PH1) and glycerate (PH2): typically normal in PH3 — helps differentiate. - Urine citrate: normal (contrasts with PH1); urine calcium: normal-to-mildly high (hypercalciuria ~10%). - Plasma oxalate: mildly elevated only with reduced GFR.
Imaging: Renal ultrasound / CT for stones and nephrocalcinosis; stone analysis shows calcium oxalate (often mixed mono-/dihydrate — ~36% mixed in PH3).
Genetic testing (confirmatory / gold standard): - Single-gene HOGA1 sequencing and deletion/duplication analysis, or a primary hyperoxaluria multigene panel (AGXT, GRHPR, HOGA1), or WES/WGS. Testing is available (e.g., GTR-listed labs; PreventionGenetics). - Chromosomal microarray/karyotype/FISH/mtDNA testing are not indicated.
Clinical criteria / differential diagnosis: Diagnosis rests on hyperoxaluria + elevated HOG/DHG + biallelic HOGA1 variants. Differentiate from: - PH1 (AGXT): higher oxalate, high glycolate, ~64% ESKD by 40, systemic oxalosis. - PH2 (GRHPR): elevated urinary glycerate, ~34% ESKD by 40. - Idiopathic calcium oxalate stones / secondary (enteric, dietary, medication) hyperoxaluria.
Screening: Carrier / cascade testing for relatives once familial variants are known; targeted screening in founder populations (Ashkenazi Jewish).
Sources: Clinical characterization PH1/2/3 (PMID:33543760); GeneReviews (PMID:26401545).
Sources: (PMID:33543760); (PMID:34245816); GeneReviews (PMID:26401545).
There is no PH3-specific approved disease-modifying drug; management is conservative/supportive and stone-directed.
Conservative (mainstay) — suggested MAXO terms noted: - High fluid intake (>2.5 L/m²/day) to lower supersaturation — MAXO: increased fluid intake / supportive care (MAXO:0000950). - Alkali citrate supplementation (potassium/sodium citrate, ~1–3 mEq/kg/day) to inhibit CaOx crystallization — pharmacotherapy (NCIT:C15986; therapeutic agent citrate, CHEBI:30769). - Dietary modification — limit oxalate/high-hydroxyproline foods, avoid high-dose ascorbate — MAXO dietary intervention (MAXO:0000088). - Thiazide diuretics for hypercalciuria (selected patients).
Stone/urologic management (interventional): - Extracorporeal shock wave lithotripsy, ureteroscopy, percutaneous nephrolithotomy as needed; prompt relief of obstruction; treat UTIs — surgical/therapeutic procedure (MAXO:0000004 / NCIT:C15329).
RNAi / advanced therapeutics — important caveat for PH3: - Lumasiran (anti-HAO1/glycolate oxidase siRNA) and nedosiran (anti-LDHA siRNA) are approved/developed primarily for PH1. Lumasiran ILLUMINATE-A: "84% of patients had 24-hour urinary oxalate excretion no higher than 1.5 times the upper limit of the normal range at month 6, as compared with 0% in the placebo group" (Garrelfs et al., NEJM 2021, PMID:33356090 — verify). - Mechanistic limitation in PH3: glycolate-oxidase inhibition (lumasiran) is not expected to reduce hepatic oxalate to the same extent in HOGA1 deficiency; more PH2/PH3 patients need testing. Nedosiran (LDH-directed) is being studied across PH types but PH3 efficacy data remain limited. - Transplantation: Rarely needed in PH3 (kidney failure is uncommon); combined liver–kidney transplantation (standard in severe PH1) is generally not required.
Pharmacogenomics: Not established for PH3.
Sources: RNAi for PH systematic review; Nedosiran design/development; ERKNet/OxalEurope expert consensus, Nat Rev Nephrol 2023 (s41581-022-00661-1).
Sources: GeneReviews (PMID:26401545); ERKNet/OxalEurope consensus (Nat Rev Nephrol 2023).
HUMAN_MODEL_MISMATCH rather than a clean phenotype recapitulation) indicates additional/diet-dependent factors in human oxalate overproduction.Sources: Hydroxyproline metabolism in Hoga1-KO mouse (PMID:26428388); HOG metabolism in PH3 mouse (2024); PH3 as a model for glyoxylate perturbations (PMID:22729392).
| PMID / ID | Content | Verified in-search? |
|---|---|---|
| 26401545 | GeneReviews: Primary Hyperoxaluria Type 3 (clinical, genetics, management) | Yes |
| 33543760 | Clinical characterization of PH3 vs PH1/PH2 (HOG biomarker, ESKD rates) | Yes |
| 21998747 | Structural/biochemical HOGA1; TIM-barrel, Type I aldolase | Yes |
| 22771891 | HOGA1 inactivity + HOG-mediated GR/GRHPR inhibition | Yes |
| 31696211 | Regulation of HOGA1 by pyruvate/α-ketoglutarate | Yes |
| 21896830 | HOGA1 (DHDPSL) as risk factor for idiopathic CaOx urolithiasis | Yes |
| 22781098 | Novel findings / molecular testing (c.700+5G>T) | Yes |
| 36259736 | Abid et al. 2022 Hum Mutat variant spectrum + dominant-negative | Yes |
| 33948853 | Ethnic associations of HOGA1 variants | Yes |
| 34245816 | PH3 can result in kidney failure (case report) | Yes |
| 26428388 | Hydroxyproline metabolism in Hoga1-KO mouse (human–model mismatch) | Yes |
| 22729392 | PH3 as model for glyoxylate metabolism perturbations | Yes |
| doi:10.1007/s00467-024-06536-w | 2024 PH3 cohort (16 patients, CKD outcomes) | Yes (search) |
| 20797690 | Belostotsky et al. 2010 — original DHDPSL/HOGA1 discovery | Recalled — verify |
| 33356090 | Garrelfs et al. NEJM 2021 — lumasiran ILLUMINATE-A (PH1) | Recalled — verify |
| Nat Rev Nephrol 2023 (s41581-022-00661-1) | ERKNet/OxalEurope PH clinical practice consensus | Yes (search) |
Bottom line for the KB entry: PH3 is an autosomal-recessive, HOGA1-driven inborn error of hydroxyproline/glyoxylate metabolism. Loss of mitochondrial 4-hydroxy-2-oxoglutarate aldolase causes HOG accumulation, which (chiefly via HOG-mediated GRHPR inhibition) shunts glyoxylate to oxalate, producing early-childhood-onset recurrent calcium oxalate nephrolithiasis. It is the mildest primary hyperoxaluria (low ESKD, no systemic oxalosis), diagnosed by elevated urinary HOG/DHG plus biallelic HOGA1 variants (founder alleles c.700+5G>T in Europeans; p.Glu315del/p.Ala36Val in Ashkenazi Jews), and managed conservatively with hydration and citrate — RNAi therapies validated in PH1 have uncertain benefit in PH3.