Primary hyperoxaluria

disease
On this page

Also known as hyperoxaluria, primary

Summary

Primary hyperoxaluria (MONDO:0002474) is a disease with 4 cohort genes and 24 clinical trials. Top therapeutic interventions include lumasiran, nedosiran sodium, and stiripentol.

At a glance

  • Prevalence: 1-9 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Cohort genes: 4
  • ClinVar variants: 52
  • Phenotypes (HPO): 33
  • Clinical trials: 24

Clinical features

Epidemiology

Prevalence records

3 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Annual incidence<1 / 1 000 000WorldwideValidated
Point prevalence1-9 / 1 000 000WorldwideValidated
Point prevalence1-9 / 1 000 0000.2GermanyValidated

Signs & symptoms

Clinical features (HPO)

33 HPO clinical features (Orphanet curated; top 33 by frequency):

HPO IDTermFrequency
HP:0003159HyperoxaluriaVery frequent (80-99%)
HP:0008672Calcium oxalate nephrolithiasisVery frequent (80-99%)
HP:0000121NephrocalcinosisFrequent (30-79%)
HP:0000164Abnormality of the dentitionFrequent (30-79%)
HP:0000488RetinopathyFrequent (30-79%)
HP:0000543Optic disc pallorFrequent (30-79%)
HP:0000648Optic atrophyFrequent (30-79%)
HP:0000790HematuriaFrequent (30-79%)
HP:0001508Failure to thriveFrequent (30-79%)
HP:0001942Metabolic acidosisFrequent (30-79%)
HP:0002653Bone painFrequent (30-79%)
HP:0002757Recurrent fracturesFrequent (30-79%)
HP:0002910Elevated circulating hepatic transaminase concentrationFrequent (30-79%)
HP:0004417Intermittent claudicationFrequent (30-79%)
HP:0005789Generalized osteosclerosisFrequent (30-79%)
HP:0006479Abnormality of the dental pulpFrequent (30-79%)
HP:0007663Reduced visual acuityFrequent (30-79%)
HP:0009830Peripheral neuropathyFrequent (30-79%)
HP:0011072Rootless teethFrequent (30-79%)
HP:0011506Choroidal neovascularizationFrequent (30-79%)
HP:0012072AciduriaFrequent (30-79%)
HP:0012622Chronic kidney diseaseFrequent (30-79%)
HP:0012722Heart blockFrequent (30-79%)
HP:0025324Arterial occlusionFrequent (30-79%)
HP:0030880Raynaud phenomenonFrequent (30-79%)
HP:0031981Elevated urine glycolateFrequent (30-79%)
HP:0100758GangreneFrequent (30-79%)
HP:0001063AcrocyanosisOccasional (5-29%)
HP:0002150HypercalciuriaOccasional (5-29%)
HP:0003774Stage 5 chronic kidney diseaseOccasional (5-29%)
HP:0000965Cutis marmorataVery rare (<1-4%)
HP:0001638CardiomyopathyVery rare (<1-4%)
HP:0025520Calcinosis cutisVery rare (<1-4%)

Identifiers

Disease identifiers

FieldValue
Canonical nameprimary hyperoxaluria
Mondo IDMONDO:0002474
MeSHD006960
OMIM259900
Orphanet416
DOIDDOID:2977
ICD-10-CME72.53
NCITC123158
SNOMED CT17901006
UMLSC0020501
MedGen5697
GARD0016530
MedDRA10020703
NORD1608
Is cancer (heuristic)no

Also known as: hyperoxaluria, primary · primary hyperoxaluria

Data availability: 52 ClinVar variants · 1 GenCC gene-disease record.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseinborn errors of metabolisminborn carbohydrate metabolic disorderprimary hyperoxaluria

Related subtypes (17): GLUT1 deficiency syndrome, disorder of glycogen metabolism, G6PD deficiency, hyperinsulinemic hypoglycemia, multiple carboxylase deficiency, disorder of glycolysis, disorder of fructose metabolism, disorder of galactose metabolism, disorder of carbohydrate transmembrane transport and absorption, disorders of pentose/polyol metabolism, pyruvate dehydrogenase deficiency, disorder of gluconeogenesis, mucopolysaccharidosis, oligosaccharidosis, lactose intolerance, congenital disorder of deglycosylation 1, disorder of galactose and fructose metabolism

Subtypes (3): primary hyperoxaluria type 1, primary hyperoxaluria type 2, primary hyperoxaluria type 3

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

52 retrieved; paginated sample, class counts are floors:

26 pathogenic, 15 pathogenic/likely pathogenic, 6 likely pathogenic, 4 conflicting classifications of pathogenicity, 1 uncertain significance

ClinVarVariant (HGVS)GeneClassificationReview
140583NM_000030.3(AGXT):c.33dup (p.Lys12fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
140584NM_000030.3(AGXT):c.560C>T (p.Ser187Phe)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
188774NM_000030.3(AGXT):c.777-1G>CAGXTPathogeniccriteria provided, multiple submitters, no conflicts
188775NM_000030.3(AGXT):c.33del (p.Lys12fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
188986NM_000030.3(AGXT):c.1049G>A (p.Gly350Asp)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189161NM_000030.3(AGXT):c.976del (p.Val326fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204065NM_000030.3(AGXT):c.2T>C (p.Met1Thr)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204069NM_000030.3(AGXT):c.32C>G (p.Pro11Arg)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204072NM_000030.3(AGXT):c.107G>A (p.Arg36His)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204079NM_000030.3(AGXT):c.187G>C (p.Gly63Arg)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204083NM_000030.3(AGXT):c.242C>T (p.Ser81Leu)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204091NM_000030.3(AGXT):c.331C>T (p.Arg111Ter)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204093NM_000030.3(AGXT):c.335C>A (p.Ala112Asp)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204105NM_000030.3(AGXT):c.481G>A (p.Gly161Ser)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204109NM_000030.3(AGXT):c.519C>A (p.Cys173Ter)AGXTPathogeniccriteria provided, single submitter
204118NM_000030.3(AGXT):c.614C>T (p.Ser205Leu)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204128NM_000030.3(AGXT):c.806T>C (p.Leu269Pro)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204154NM_000030.3(AGXT):c.680+1G>AAGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204159NM_000030.3(AGXT):c.846+1G>TAGXTPathogeniccriteria provided, multiple submitters, no conflicts
204168NM_000030.3(AGXT):c.847-1G>CAGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204175NM_000030.3(AGXT):c.116_117dup (p.Ala40fs)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204176NM_000030.3(AGXT):c.126del (p.Leu43fs)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
204185NM_000030.3(AGXT):c.447_454del (p.Leu151fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204190NM_000030.3(AGXT):c.570del (p.Thr191fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204191NM_000030.3(AGXT):c.577del (p.Leu193fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204192NM_000030.3(AGXT):c.577dup (p.Leu193fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
204201NM_000030.3(AGXT):c.823_824dup (p.Ser275fs)AGXTPathogeniccriteria provided, multiple submitters, no conflicts
2577088NM_000030.3(AGXT):c.568G>C (p.Gly190Arg)AGXTPathogeniccriteria provided, single submitter
2681157NM_000030.3(AGXT):c.244G>A (p.Gly82Arg)AGXTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2681179NM_000030.3(AGXT):c.622C>T (p.Gln208Ter)AGXTPathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 1 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
SLC26A6LimitedAutosomal dominantprimary hyperoxaluria

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
MOCOSOrphanet:93602Xanthinuria type II
AGXTOrphanet:93598Primary hyperoxaluria type 1
GRHPROrphanet:93599Primary hyperoxaluria type 2

Cohort genes → proteins

4 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SLC26A6HGNC:14472ENSG00000225697Q9BXS9Solute carrier family 26 member 6gencc
MOCOSHGNC:18234ENSG00000075643Q96EN8Molybdenum cofactor sulfuraseclinvar
AGXTHGNC:341ENSG00000172482P21549Alanine–glyoxylate aminotransferaseclinvar
GRHPRHGNC:4570ENSG00000137106Q9UBQ7Glyoxylate reductase/hydroxypyruvate reductaseclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SLC26A6Solute carrier family 26 member 6Apical membrane anion-exchanger with wide epithelial distribution that plays a role as a component of the pH buffering system for maintaining acid-base homeostasis.
MOCOSMolybdenum cofactor sulfuraseSulfurates the molybdenum cofactor.
AGXTAlanine–glyoxylate aminotransferasePeroxisomal aminotransferase that catalyzes the transamination of glyoxylate to glycine and contributes to the glyoxylate detoxification.
GRHPRGlyoxylate reductase/hydroxypyruvate reductaseEnzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities.

Protein-family classification

Druggable: 3 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.75

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Transporter119.4×0.076
Enzyme (other)26.0×0.076
Other/Unknown10.5×0.962

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SLC26A6TransporteryesSLC26A/SulP_fam, STAS_dom, SLC26A/SulP_dom
MOCOSOther/UnknownnoAminotrans_V_dom, MoCF_Sase_C, MOCOS_middle
AGXTEnzyme (other)yes2.6.1.44Aminotrans_V_dom, PyrdxlP-dep_Trfase_major, PyrdxlP-dep_Trfase_small
GRHPREnzyme (other)yes1.1.1.26D-isomer_2_OHA_DH_cat_dom, D-isomer_DH_NAD-bd, D-isomer_DH_CS

Expression context

Cohort genes with no expression data: 0.

4 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)4
unknown0

Top tissues across cohort

TissueCohort genes
liver3
right lobe of liver3
descending thoracic aorta1
mucosa of transverse colon1
popliteal artery1
secondary oocyte1
endometrium epithelium1
right adrenal gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SLC26A6180ubiquitousmarkermucosa of transverse colon, descending thoracic aorta, popliteal artery
MOCOS193ubiquitousmarkersecondary oocyte, right lobe of liver, liver
AGXT125tissue_specificmarkerright lobe of liver, liver, endometrium epithelium
GRHPR292ubiquitousmarkerright lobe of liver, liver, right adrenal gland

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
GRHPR2,785
AGXT2,648
MOCOS1,785
SLC26A61,442

Intra-cohort edges

ABSources
AGXTGRHPRstring_interaction

Structural data

PDB: 3 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
AGXTP2154917
GRHPRQ9UBQ74
SLC26A6Q9BXS91

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MOCOSQ96EN880.88

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 12. Enrichment computed across 4 evidence-associated genes (4 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Glyoxylate metabolism and glycine degradation2380.7×1e-04AGXT, GRHPR
Molybdenum cofactor biosynthesis1407.9×0.013MOCOS
Inorganic anion exchange by SLC26 transporters1317.2×0.013SLC26A6
Protein localization147.6×0.046AGXT
Metabolism of water-soluble vitamins and cofactors145.3×0.046MOCOS
Peroxisomal protein import143.3×0.046AGXT
R-HSA-425393132.4×0.051SLC26A6
Metabolism of vitamins and cofactors129.1×0.051MOCOS
Metabolism25.8×0.053MOCOS, AGXT
Metabolism of amino acids and derivatives116.9×0.069AGXT
SLC-mediated transmembrane transport114.8×0.072SLC26A6
Transport of small molecules16.3×0.150SLC26A6

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
oxalic acid secretion22808.7×5e-06SLC26A6, AGXT
glyoxylate metabolic process21404.3×1e-05AGXT, GRHPR
formate transport14213.0×0.002SLC26A6
mannitol transmembrane transport14213.0×0.002SLC26A6
molybdopterin cofactor metabolic process12106.5×0.002MOCOS
dicarboxylic acid metabolic process12106.5×0.002GRHPR
positive regulation of dipeptide transmembrane transport12106.5×0.002SLC26A6
obsolete glycine biosynthetic process, by transamination of glyoxylate11404.3×0.002AGXT
molybdopterin cofactor biosynthetic process11404.3×0.002MOCOS
intracellular pH elevation11404.3×0.002SLC26A6
glyoxylate catabolic process11053.2×0.002AGXT
L-cysteine catabolic process11053.2×0.002AGXT
L-alanine catabolic process11053.2×0.002AGXT
protein kinase C signaling11053.2×0.002SLC26A6
cellular response to fructose stimulus11053.2×0.002SLC26A6
carboxylic acid metabolic process1702.2×0.003GRHPR
Mo-molybdopterin cofactor biosynthetic process1601.9×0.003MOCOS
oxalate transport1601.9×0.003SLC26A6
epithelial fluid transport1526.6×0.004SLC26A6
transepithelial chloride transport1468.1×0.004SLC26A6
L-serine metabolic process1421.3×0.004AGXT
angiotensin-activated signaling pathway1383.0×0.004SLC26A6
estrous cycle1351.1×0.004SLC26A6
intestinal absorption1300.9×0.005SLC26A6
transepithelial transport1300.9×0.005SLC26A6
sulfate transmembrane transport1300.9×0.005SLC26A6
bicarbonate transport1200.6×0.007SLC26A6
sperm capacitation1168.5×0.008SLC26A6
regulation of intracellular pH1150.5×0.008SLC26A6
chloride transport1113.9×0.011SLC26A6

Therapeutics

Drugs indicated for this disease

1 approved, 4 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
Nedosiran SodiumApproved (phase 4)
Lisinopril AnhydrousPhase 3 (in late-stage trials)
LosartanPhase 3 (in late-stage trials)
LumasiranPhase 3 (in late-stage trials)
ReloxaliasePhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Betaine, Stiripentol.

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 4

Druggability breadth: 3 of 4 evidence-associated genes (75%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SLC26A600
MOCOS00
AGXT00
GRHPR00

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
AGXT8Binding:8
SLC26A65Binding:5
GRHPR2Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
AGXT2.6.1.44, 2.6.1.51alanine-glyoxylate transaminase, serine-pyruvate transaminase
GRHPR1.1.1.26, 1.1.1.79, 1.1.1.81glyoxylate reductase, glyoxylate reductase (NADP+), hydroxypyruvate reductase

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug3SLC26A6, AGXT, GRHPR
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1MOCOS

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
SLC26A65
MOCOS0
AGXT8
GRHPR2

Clinical trials & evidence

Clinical trials

Clinical trials: 24.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified11
PHASE25
PHASE34
PHASE2/PHASE32
PHASE1/PHASE21
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT00638703PHASE2/PHASE3COMPLETEDStudy to Evaluate the Efficacy and Safety of OxabactTM on Reduction of Urinary Oxalate in Primary Hyperoxaluria Patients
NCT01037231PHASE2/PHASE3COMPLETEDPhase 2/3 Oxabact Study
NCT03116685PHASE3COMPLETEDA Study to Evaluate the Efficacy and Safety of Oxabact in Patients With Primary Hyperoxaluria
NCT03905694PHASE3COMPLETEDA Study of Lumasiran in Infants and Young Children With Primary Hyperoxaluria Type 1
NCT03938272PHASE3TERMINATEDAn Extension Study to Evaluate the Long-term Efficacy and Safety of Oxabact in Patients With Primary Hyperoxaluria
NCT04152200PHASE3COMPLETEDA Study to Evaluate Lumasiran in Patients With Advanced Primary Hyperoxaluria Type 1
NCT02000219PHASE2COMPLETEDStudy to Evaluate the Efficacy and Safety of Oxabact (OC5) in Primary Hyperoxaluria Patients Who Are on Dialysis
NCT02012985PHASE1/PHASE2COMPLETEDStudy to Evaluate the Efficacy and Safety of Oxabact (OC5) in Patients With Primary Hyperoxaluria
NCT03350451PHASE2COMPLETEDAn Extension Study of an Investigational Drug, Lumasiran (ALN-GO1), in Participants With Primary Hyperoxaluria Type 1
NCT03391804PHASE2COMPLETEDStudy of ALLN-177 in Patients Aged 12 Years or Older With Enteric or Primary Hyperoxaluria and Hyperoxalemia
NCT03819647PHASE2COMPLETEDEvaluation of the Efficacy of Stiripentol (Diacomit) as Monotherapy for the Treatment of Primary Hyperoxaluria
NCT05001269PHASE2COMPLETEDNedosiran in Pediatric Patients From Birth to 11 Years of Age With PH and Relatively Intact Renal Function
NCT03392896PHASE1COMPLETEDStudy of DCR-PHXC-101 in Normal Healthy Volunteers and Patients With Primary Hyperoxaluria
NCT00588562Not specifiedRECRUITINGRare Kidney Stone Consortium Patient Registry
NCT02026388Not specifiedRECRUITINGRare Kidney Stone Consortium Biobank
NCT05843851Not specifiedRECRUITINGGenetic Newborn Screening for Cystinosis and Primary Hyperoxaluria
NCT06065852Not specifiedRECRUITINGNational Registry of Rare Kidney Diseases
NCT00589225Not specifiedCOMPLETEDPrimary Hyperoxaluria Mutation Genotyping
NCT00875823Not specifiedWITHDRAWNInternational Registry for Primary Hyperoxaluria
NCT02124395Not specifiedCOMPLETEDHealth-related Quality of Life in Rare Kidney Stone
NCT02340689Not specifiedCOMPLETEDPrimary Hyperoxaluria Mutation Genotyping/Phenotyping
NCT04125472Not specifiedAPPROVED_FOR_MARKETINGExpanded Access Protocol to Provide Lumasiran to Patients With Primary Hyperoxaluria Type 1
NCT05107830Not specifiedUNKNOWNPhenotyping of Primary Hyperoxaluria
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
LUMASIRAN44
NEDOSIRAN SODIUM41
STIRIPENTOL41
RELOXALIASE31
NEDOSIRAN21