Primary Hyperoxaluria Type 3

Metabolic Disorder MONDO:0013327 Pathograph 7 Show in embeddings browser Inborn Error of Metabolism Primary Hyperoxaluria Genetic Kidney Disease

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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1
Inheritance
5
Pathophys.
3
Phenotypes
1
Gaps
7
Pathograph
2
Genes
1
Medical Actions
1
References
1
Deep Research
🏷

Classifications

ICIMD (Inherited Metabolic Disorders)
glyoxylate and oxalate
👪

Inheritance

1
Autosomal recessive inheritance HP:0000007
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.
Autosomal recessive inheritance
Show evidence (2 references)
PMID:20797690 SUPPORT Human Clinical
"Primary hyperoxaluria (PH) is an autosomal-recessive disorder of endogenous"
States the autosomal recessive mode of inheritance of primary hyperoxaluria.
PMID:26401545 SUPPORT Other
"PH3 is inherited in an autosomal recessive manner."
GeneReviews establishes autosomal recessive inheritance for PH3.
?

Discussions and Knowledge Gaps

1
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?
KNOWLEDGE GAP OPEN gap_ph3_oxalate_overproduction_mechanism
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.

Pathophysiology

5
HOGA1 4-Hydroxy-2-Oxoglutarate Aldolase Deficiency
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.
hepatocyte CL:0000182 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves hepatocyte (CL:0000182). CL:0000182 is a cell type from the Cell Ontology.
HOGA1 hgnc:25155 HUGO Gene Nomenclature Committee (hgnc) Relation: this pathophysiological event involves this gene This pathophysiological event involves HOGA1 (hgnc:25155). hgnc:25155 is a gene from the HUGO Gene Nomenclature Committee.
glyoxylate metabolic process GO:0046487 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves dysregulated glyoxylate metabolic process (GO:0046487). GO:0046487 is a biological process from the Gene Ontology. ↕ DYSREGULATED
4-hydroxy-2-oxoglutarate aldolase activity GO:0106009 Gene Ontology (GO) Relation: this pathophysiological event involves this molecular function This pathophysiological event involves decreased 4-hydroxy-2-oxoglutarate aldolase activity, annotated with (4S)-4-hydroxy-2-oxoglutarate aldolase activity (GO:0106009). GO:0106009 is a molecular function from the Gene Ontology. ↓ DECREASED
Show evidence (3 references)
PMID:22391140 SUPPORT Human Clinical
"definitive proof that PH Type 3 is due to deficiency of the"
Demonstrates via loss-of-function nonsense variants that PH3 results from deficiency of the 4-hydroxy-2-oxoglutarate aldolase enzyme.
PMID:22729392 SUPPORT Human Clinical
"HOGA1 is a mitochondrial"
Establishes HOGA1 as the mitochondrial 4-hydroxy-2-oxoglutarate aldolase acting in the hydroxyproline pathway.
PMID:20797690 SUPPORT Human Clinical
"aldolase, catalyzing the final step in the metabolic pathway of hydroxyproline."
Identifies the HOGA1 gene product as the aldolase catalyzing the final step of hydroxyproline metabolism.
Hydroxyproline-Pathway Metabolite Accumulation
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.
glyoxylate metabolic process GO:0046487 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves dysregulated glyoxylate metabolic process (GO:0046487). GO:0046487 is a biological process from the Gene Ontology. ↕ DYSREGULATED
Show evidence (1 reference)
PMID:22729392 SUPPORT Human Clinical
"Significant increases in concentrations of"
Human urine GC-MS shows significant increases of 4-hydroxy-2-oxoglutarate and related metabolites in all PH3 patients versus carriers and controls.
Cytosolic Glyoxylate-to-Oxalate Overproduction
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.
oxalate biosynthetic process GO:0033610 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased oxalate biosynthetic process (GO:0033610). GO:0033610 is a biological process from the Gene Ontology. ↑ INCREASED
Show evidence (2 references)
PMID:22729392 SUPPORT Human Clinical
"its transport into the cytosol where it is converted to"
Proposes cytosolic conversion of accumulated 4-hydroxy-2-oxoglutarate to glyoxylate as the route to increased oxalate.
PMID:26428388 SUPPORT In Vitro
"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"
Alternative/contributing mechanism in which accumulated HOG inhibits glyoxylate reductase, based on in vitro assays with purified enzyme.
Urinary Calcium Oxalate Supersaturation
Increased urinary oxalate raises calcium oxalate crystallization burden in PH3, specializing the nephrolithiasis supersaturation module to HOGA1 deficiency.
Renal Excretion of Oxalate GO:0007588 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased Renal Excretion of Oxalate, annotated with excretion (GO:0007588). GO:0007588 is a biological process from the Gene Ontology. ↑ INCREASED
Show evidence (1 reference)
PMID:20797690 SUPPORT Human Clinical
"characterized by accumulation of calcium oxalate primarily in"
Primary hyperoxaluria is characterized by endogenous oxalate synthesis and calcium oxalate accumulation in the kidney.
Calcium Oxalate Nephrolithiasis
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.
kidney UBERON:0002113 Uberon multi-species anatomy ontology (UBERON) Relation: this pathophysiological event occurs in this anatomical location This pathophysiological event occurs in kidney (UBERON:0002113). UBERON:0002113 is an anatomical location from the Uberon multi-species anatomy ontology.
Show evidence (2 references)
PMID:20797690 SUPPORT Human Clinical
"patients from eight unrelated"
The PH3-defining cohort was selected from patients with calcium oxalate nephrolithiasis.
PMID:22781098 SUPPORT Human Clinical
"point to a favorable outcome of type III in the context of PH despite incomplete or"
Supports the generally favorable renal outcome of PH3.

Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence and cross-linked metadata.
Pathograph: causal mechanism network for Primary Hyperoxaluria Type 3 Interactive directed graph showing how pathophysiology mechanisms, phenotypes, genetic factors and variants, experimental models, environmental triggers, and treatments relate through causal and linked edges.

Phenotypes

3
Hyperoxaluria Biochemical HP:0003159 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Hyperoxaluria (HP:0003159). HP:0003159 is a phenotype from the Human Phenotype Ontology.
Show evidence (1 reference)
PMID:26428388 SUPPORT Human Clinical
"Affected individuals have increased excretions of oxalate, 4-OH-Glu, HOG and DHG in their urine"
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.
Calcium oxalate nephrolithiasis Clinical HP:0008672 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Calcium oxalate nephrolithiasis (HP:0008672). HP:0008672 is a phenotype from the Human Phenotype Ontology.
Show evidence (2 references)
PMID:22729392 SUPPORT Human Clinical
"recessive disorders characterized by kidney"
Primary hyperoxalurias are characterized by kidney stone disease.
PMID:26401545 SUPPORT Other
"recurring calcium oxalate stones beginning in childhood or adolescence"
GeneReviews describes recurrent calcium oxalate stones as the core PH3 presentation.
Context-specific annotations (1)
Onset: CHILDHOOD
PH3 most often presents in early childhood, although adolescent and adult presentations occur.
Show evidence (1 reference)
PMID:26401545 SUPPORT Other
"PH3 most often presents in childhood (median age 2 to 3 years)"
GeneReviews supports childhood onset for the typical PH3 stone phenotype.
Nephrocalcinosis OCCASIONAL Clinical HP:0000121 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Nephrocalcinosis (HP:0000121). HP:0000121 is a phenotype from the Human Phenotype Ontology.
Show evidence (1 reference)
PMID:26401545 SUPPORT Other
"on occasion, nephrocalcinosis or reduced kidney function"
GeneReviews reports nephrocalcinosis as an occasional PH3 feature.
🧬

Genetic Associations

2
HOGA1
Gene: HOGA1 hgnc:25155 HUGO Gene Nomenclature Committee (hgnc) Relation: this disease-associated gene is this gene This disease-associated gene is HOGA1 (hgnc:25155). hgnc:25155 is a gene from the HUGO Gene Nomenclature Committee. relationship_type: CAUSATIVE
Show evidence (2 references)
PMID:22391140 SUPPORT Human Clinical
"The recurrent c.700 + 5G > T splice site mutation in intron 5 was most common with a frequency of 67%."
Reports the recurrent c.700+5G>T HOGA1 splice-site variant as the most common PH3 allele.
PMID:20797690 SUPPORT Human Clinical
"an allelic fragment shared by all patients of Ashkenazi Jewish descent and"
Identifies an Ashkenazi Jewish founder allele bearing a 3 bp deletion in HOGA1 (DHDPSL).
AGXT
Gene: AGXT hgnc:341 HUGO Gene Nomenclature Committee (hgnc) Relation: this disease-associated gene is this gene This disease-associated gene is AGXT (hgnc:341). hgnc:341 is a gene from the HUGO Gene Nomenclature Committee. relationship_type: MODIFIER
Show evidence (1 reference)
PMID:22781098 SUPPORT Human Clinical
"The two girls exhibiting triallelic inheritance presented a more severe phenotype"
Supports AGXT as a potential modifier of PH3 severity in one triallelic family.
💊

Medical Actions

1
High Fluid Intake and Crystallization Inhibitors
Action: supportive careNCI Thesaurus (NCIT) Relation: this treatment is this clinical intervention This treatment is supportive care (NCIT:C15747). NCIT:C15747 is a clinical intervention from the NCI Thesaurus. Ontology label: Supportive Care NCIT:C15747
Agent: potassium citrate CHEBI:64733 Chemical Entities of Biological Interest (CHEBI) Relation: this treatment uses this therapeutic agent This treatment uses potassium citrate, annotated with potassium citrate (anhydrous) (CHEBI:64733). CHEBI:64733 is a therapeutic agent from Chemical Entities of Biological Interest.
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.
Show evidence (1 reference)
PMID:26401545 SUPPORT Other
"potassium and/or sodium citrate"
GeneReviews supports citrate crystallization inhibitors as part of PH3 supportive management.
🔬

Biochemical Markers

1
Urinary hydroxyproline-pathway metabolite elevation (INCREASED)
Pathograph Readouts
Readout Of Hydroxyproline-Pathway Metabolite Accumulation Positive Diagnostic
Increased urinary HOG and related hydroxyproline-pathway metabolites report the HOGA1 metabolic block and are used diagnostically for PH3.
Show evidence (1 reference)
PMID:22729392 SUPPORT Human Clinical
"These studies provide a diagnostic tool for primary hyperoxaluria type"
The metabolite profiling study presents HOG-related elevations as a PH3 diagnostic tool.
Show evidence (1 reference)
PMID:22729392 SUPPORT Human Clinical
"4-hydroxy-2-oxoglutarate and its precursor and derivative 4-hydroxyglutamate and 2,4-dihydroxyglutarate, respectively, were found in all patients"
The human urine GC-MS study identifies elevated HOG, 4-hydroxyglutamate, and DHG in PH3 patients.
📊

Prevalence

1
Worldwide
Unknown Rare
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.
Show evidence (1 reference)
PMID:22781098 SUPPORT Human Clinical
"the pathophysiology and prevalence of type"
States that the prevalence of PH3 is largely unknown.
{ }

Source YAML

click to show
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.
📚

References & Deep Research

References

1
Primary Hyperoxaluria Type 3.
No top-level findings curated for this source.

Deep Research

1
Claude Code
1. Disease Information
claude-haiku-4-5-20251001, claude-opus-4-8 16 citations 2026-07-07T02:57:54.893269

1. Disease Information

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) 613597HOGA1
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.


2. Etiology

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).


3. Phenotypes

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).


4. Genetic / Molecular Information

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).


5. Environmental Information

  • Environmental/toxic factors: No infectious or toxic environmental cause; PH3 is purely genetic. Relevant exogenous modifiers are dietary oxalate, dietary hydroxyproline (collagen/gelatin), and high-dose ascorbic acid (oxalate precursor).
  • Lifestyle factors: Fluid intake (low volume worsens supersaturation), and dietary patterns affecting urinary citrate/calcium. Adequate hydration is protective (see §13).
  • Infectious agents: Not applicable as a cause; however, urinary tract infections are a frequent secondary complication of stone disease.

6. Mechanism / Pathophysiology

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:

  1. HOG-mediated inhibition of glyoxylate reductase (GRHPR) — the leading biochemical model. Accumulated HOG specifically inhibits GR, phenocopying PH2: "GR was inhibited by HOG but not by 2-hydroxyglutarate or 2-oxoglutarate" (Riedel et al., PMID:22771891). With GR inhibited, glyoxylate is not efficiently reduced to glycolate and is instead shunted to oxalate via LDH.
  2. Ectopic/cytosolic cleavage of accumulated HOG, liberating glyoxylate outside the mitochondrion where detoxification capacity is limited, feeding oxalate synthesis.

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).


7. Anatomical Structures Affected

  • Primary organ affected clinically: Kidney / urinary tract (UBERON:0002113 kidney; UBERON:0000056 ureter; UBERON:0001255 urinary bladder) — recurrent calcium oxalate stones, occasional nephrocalcinosis.
  • Primary organ of the metabolic defect: Liver (UBERON:0002107) — hepatic mitochondria are the site of HOGA1 expression and oxalate overproduction.
  • Body systems: Renal/urinary system (primary); hepatic/metabolic (biochemical origin).
  • Tissue/cell level: Renal tubular epithelium (crystal-associated injury), hepatocytes (CL:0000182).
  • Subcellular level: Mitochondrion (GO:0005739) — HOGA1 localization and HOG cleavage; cytosol — glyoxylate/oxalate handling.
  • Localization/laterality: Stones/nephrocalcinosis are typically bilateral but can be unilateral; distribution follows the collecting system.

8. Temporal Development

  • Onset: Early childhood, earliest of the three PH types — median symptomatic onset ~2.7 years; stones usually begin before age 5. Some patients are diagnosed only in adulthood (PMID:33543760; GeneReviews PMID:26401545).
  • Onset pattern: Insidious biochemically (lifelong hyperoxaluria) with episodic clinical stone events.
  • Course: Chronic, recurrent, relapsing stone disease that can continue into the sixth decade; kidney function is usually stable.
  • Stages/progression: Most patients remain in early CKD stages; a minority progress to CKD 3–5. A 2024 single-cohort report described one patient reaching CKD stage 5 and two others at CKD stage 2 at last follow-up (Pediatric Nephrology 2024, doi:10.1007/s00467-024-06536-w).
  • Critical windows: Early diagnosis and initiation of hydration/citrate before repeated obstructive/infectious insults; closer monitoring for children <4 years and those with reduced kidney function.

9. Inheritance and Population

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..


10. Diagnostics

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).


11. Outcome / Prognosis

  • Kidney survival is favorable — the defining prognostic feature. ESKD by age 40 is only ~2.9% in PH3, versus ~63.8% in PH1 and ~34.2% in PH2 (PMID:33543760).
  • eGFR at diagnosis is highest among PH types (~96 mL/min/1.73 m²).
  • Systemic oxalosis has not been reported in PH3.
  • Kidney failure is possible but rare: individual cases are documented — "Primary Hyperoxaluria Type 3 Can Also Result in Kidney Failure: A Case Report" (PMID:34245816) — and a 2024 cohort reported one CKD-5 patient (doi:10.1007/s00467-024-06536-w). Reported ESKD cases often have contributing factors.
  • Morbidity is driven by recurrent stones, colic, obstructive events, urologic procedures, and UTIs rather than progressive kidney failure.
  • Prognostic factors: degree of hyperoxaluria, stone/nephrocalcinosis burden, hydration/citrate adherence, and baseline kidney function. Life expectancy is essentially normal in most patients.

Sources: (PMID:33543760); (PMID:34245816); GeneReviews (PMID:26401545).


12. Treatment

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).


13. Prevention

  • Primary prevention: Not preventable (genetic); genetic counseling and reproductive options (carrier testing, prenatal/preimplantation genetic testing once familial variants known) — MAXO genetic counseling (MAXO:0000079).
  • Secondary prevention (early detection): Cascade/carrier screening of relatives; targeted screening in founder populations (Ashkenazi Jewish); early biochemical/genetic diagnosis in children with early stones.
  • Tertiary prevention (complication avoidance): Lifelong hydration + citrate, dietary control, avoidance of volume contraction, high-dose vitamin C, and nephrotoxins; prompt treatment of obstruction/UTI; regular surveillance (annual clinical assessment, kidney imaging, serum creatinine/eGFR, 24-h urine oxalate/supersaturation; more frequent for young children and impaired kidney function).
  • Immunization / public-health / environmental interventions: Not applicable.

Sources: GeneReviews (PMID:26401545); ERKNet/OxalEurope consensus (Nat Rev Nephrol 2023).


14. Other Species / Natural Disease

  • Taxonomy: Human disease (Homo sapiens, NCBITaxon:9606). No naturally occurring HOGA1-deficiency disease is well described in companion animals or wildlife (OMIA has no established PH3 entry analogous to human PH3). Calcium oxalate urolithiasis occurs naturally in dogs/cats but is not attributed to HOGA1 loss.
  • Orthology: HOGA1 is evolutionarily conserved across vertebrates (mouse Hoga1, NCBI Gene present; conserved in the hydroxyproline-degradation pathway), enabling model-organism study.
  • Comparative biology: The hydroxyproline→HOG→glyoxylate pathway is conserved; however (see §15) the mouse phenotype does not fully recapitulate human hyperoxaluria, an important interspecies difference.
  • Zoonotic potential / transmission: None (non-communicable genetic disease).

15. Model Organisms

  • Mouse (Hoga1 knockout): The principal PH3 model. Key finding & human–model mismatch: Hoga1-null mice did not develop hyperoxaluria on a hydroxyproline-free diet, in marked contrast to PH3 patients, although urine/plasma HOG and DHG and hepatic DHG were significantly elevated — Li et al., "Hydroxyproline metabolism in a mouse model of Primary Hyperoxaluria Type 3" (PMID:26428388, PMC4615548), extended by "4-hydroxy-2-oxoglutarate metabolism in a mouse model of Primary Hyperoxaluria Type 3" (Mol Genet Metab Rep 2024, ScienceDirect S2405580824001298). This mismatch (suggests HUMAN_MODEL_MISMATCH rather than a clean phenotype recapitulation) indicates additional/diet-dependent factors in human oxalate overproduction.
  • In vitro / biochemical models: Recombinant human HOGA1 expression for enzyme kinetics, stability, and structural studies (crystal structures; Type I aldolase mechanism) — used to demonstrate variant instability/inactivity and HOG-mediated GRHPR inhibition (PMID:21998747; PMID:22771891; PMID:31696211).
  • Model utility: Study of HOG/DHG metabolism, the reduction of HOG→DHG as a possible oxalate-limiting shunt, and metabolic perturbations of glyoxylate handling (PMID:22729392).
  • Limitations: Mouse does not reproduce spontaneous hyperoxaluria; heavy reliance on dietary hydroxyproline loading; no robust stone-forming small-animal model of PH3.

Sources: Hydroxyproline metabolism in Hoga1-KO mouse (PMID:26428388); HOG metabolism in PH3 mouse (2024); PH3 as a model for glyoxylate perturbations (PMID:22729392).


Consolidated Ontology-Term Suggestions (for KB population)

  • MONDO: MONDO:0013327 (primary hyperoxaluria type 3)
  • Gene (HGNC): hgnc:25155 (HOGA1)
  • Phenotypes (HP): HP:0000787 Nephrolithiasis; HP:0003159 Hyperoxaluria; HP:0000790 Hematuria; HP:0000121 Nephrocalcinosis; HP:0002150 Hypercalciuria; HP:0000010 Recurrent UTI; HP:0012622 CKD; HP:0000007 Autosomal recessive inheritance
  • Biological process (GO): GO:0019471 4-hydroxyproline catabolic process; GO:0006979/oxidative response context; oxalate biosynthetic/metabolic process
  • Cellular component (GO): GO:0005739 mitochondrion
  • Cell types (CL): CL:0000182 hepatocyte; renal tubular epithelial cell
  • Anatomy (UBERON): UBERON:0002113 kidney; UBERON:0002107 liver; UBERON:0000056 ureter; UBERON:0001255 urinary bladder
  • Chemicals (CHEBI): CHEBI:30623 oxalate; CHEBI:16891 glyoxylate; CHEBI:18095 4-hydroxyproline; CHEBI:16810 2-oxoglutarate; CHEBI:15361 pyruvate; CHEBI:17497 glycolate; CHEBI:30769 citrate
  • Treatments (MAXO): MAXO:0000950 supportive care; MAXO:0000088 dietary intervention; MAXO:0000079 genetic counseling; MAXO:0000004 surgical procedure

Key Citations (verify PMIDs/snippets before KB entry)

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.