Primary hyperoxaluria: genes and variants
Explore variant evidence for Primary hyperoxaluria across 2 analyzed proteins (AGXT, AGT). Linked ClinVar records include 100 pathogenic or likely pathogenic variants, 62 variants of uncertain significance and 29 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-11. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Primary hyperoxaluria
AGXT: Alanine--glyoxylate aminotransferase
A peroxisomal enzyme that converts glyoxylate to glycine, helping prevent oxalate buildup. Biallelic variants cause primary hyperoxaluria type 1.
100 ClinVar pathogenic / likely pathogenic and 91 uncertain variants in AGXT have source records linked to Primary hyperoxaluria. Association strength is not clinical gene validity.
AGT: Angiotensinogen
It provides the precursor from which renin generates angiotensin I, placing it at the start of the renin-angiotensin system that regulates blood pressure and fluid balance. Rare variants can cause renal tubular dysgenesis, while common variation has been studied for effects on blood pressure.
0 ClinVar pathogenic / likely pathogenic and 0 uncertain variants in AGT have source records linked to Primary hyperoxaluria. Association strength is not clinical gene validity.
ClinVar pathogenic and likely pathogenic variants linked to Primary hyperoxaluria
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| AGXT S81L | 81 | Pathogenic / likely pathogenic (★★) | |
| AGXT G82R | 82 | Pathogenic / likely pathogenic (★★) | |
| AGXT G82E | 82 | Pathogenic / likely pathogenic (★★) | |
| AGXT W108R | 108 | Pathogenic / likely pathogenic (★★) | |
| AGXT G161C | 161 | Pathogenic / likely pathogenic (★★) | |
| AGXT G161D | 161 | Pathogenic / likely pathogenic (★★) | |
| AGXT C178Y | 178 | Pathogenic / likely pathogenic (★★) | |
| AGXT M195R | 195 | Pathogenic / likely pathogenic (★★) | |
| AGXT D201E | 201 | Pathogenic / likely pathogenic (★★) | |
| AGXT H261D | 261 | Pathogenic / likely pathogenic (★★) | |
| AGXT R360W | 360 | Pathogenic / likely pathogenic (★★) | |
| AGXT G116R | 116 | Pathogenic / likely pathogenic (★★) | |
| AGXT G161S | 161 | Pathogenic / likely pathogenic (★★) | |
| AGXT S205L | 205 | Pathogenic / likely pathogenic (★★) | |
| AGXT R360Q | 360 | Pathogenic / likely pathogenic (★★) | |
| AGXT M1N | 1 | Pathogenic / likely pathogenic (★★) | |
| AGXT A112D | 112 | Pathogenic / likely pathogenic (★★) | |
| AGXT S158L | 158 | Pathogenic / likely pathogenic (★★) | |
| AGXT G216R | 216 | Pathogenic / likely pathogenic (★★) | |
| AGXT I244T | 244 | Pathogenic / likely pathogenic (★★) | |
| AGXT L359P | 359 | Pathogenic / likely pathogenic (★★) | |
| AGXT M1T | 1 | Pathogenic / likely pathogenic (★★) | |
| AGXT R36H | 36 | Pathogenic / likely pathogenic (★★) | |
| AGXT R36C | 36 | Pathogenic / likely pathogenic (★★) | |
| AGXT G47R | 47 | Pathogenic / likely pathogenic (★★) | |
| AGXT F152I | 152 | Pathogenic / likely pathogenic (★★) | |
| AGXT G156R | 156 | Pathogenic / likely pathogenic (★★) | |
| AGXT S205P | 205 | Pathogenic / likely pathogenic (★★) | |
| AGXT S223R | 223 | Pathogenic / likely pathogenic (★★) | |
| AGXT R233H | 233 | Pathogenic / likely pathogenic (★★) | |
| AGXT R233C | 233 | Pathogenic / likely pathogenic (★★) | |
| AGXT G350D | 350 | Pathogenic / likely pathogenic (★★) | |
| AGXT N72I | 72 | Pathogenic / likely pathogenic (★★) | |
| AGXT G41R | 41 | Pathogenic / likely pathogenic (★★) | |
| AGXT G170R | 170 | Pathogenic / likely pathogenic (★★) | |
| AGXT S187F | 187 | Pathogenic / likely pathogenic (★★) | |
| AGXT G190R | 190 | Pathogenic / likely pathogenic (★★) | |
| AGXT S218L | 218 | Pathogenic / likely pathogenic (★★) | |
| AGXT V336D | 336 | Pathogenic / likely pathogenic (★★) | |
| AGXT G63R | 63 | Pathogenic / likely pathogenic (★★) | |
| AGXT R118S | 118 | Pathogenic / likely pathogenic (★) | |
| AGXT W108C | 108 | Pathogenic / likely pathogenic (★) | |
| AGXT G109E | 109 | Pathogenic / likely pathogenic (★) | |
| AGXT G116W | 116 | Pathogenic / likely pathogenic (★) | |
| AGXT R118H | 118 | Pathogenic / likely pathogenic (★) | |
| AGXT G161R | 161 | Pathogenic / likely pathogenic (★) | |
| AGXT M195L | 195 | Pathogenic / likely pathogenic (★) | |
| AGXT D201V | 201 | Pathogenic / likely pathogenic (★) | |
| AGXT S81W | 81 | Pathogenic / likely pathogenic (★) | |
| AGXT E157Q | 157 | Pathogenic / likely pathogenic (★) | |
| AGXT C173Y | 173 | Pathogenic / likely pathogenic (★) | |
| AGXT K209N | 209 | Pathogenic / likely pathogenic (★) | |
| AGXT I244N | 244 | Pathogenic / likely pathogenic (★) | |
| AGXT G350V | 350 | Pathogenic / likely pathogenic (★) | |
| AGXT G27W | 27 | Pathogenic / likely pathogenic (★) | |
| AGXT G47E | 47 | Pathogenic / likely pathogenic (★) | |
| AGXT H83R | 83 | Pathogenic / likely pathogenic (★) | |
| AGXT D98H | 98 | Pathogenic / likely pathogenic (★) | |
| AGXT C178W | 178 | Pathogenic / likely pathogenic (★) | |
| AGXT I202N | 202 | Pathogenic / likely pathogenic (★) |
Showing 60 of 100.
Uncertain variants prioritized for review in Primary hyperoxaluria
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| AGXT G63D | 63 | Conflicting reports (★) | +7: 2 other pathogenic changes within 3 positions; G63R at the same position is pathogenic; seen in 7.3e-07 of gnomAD DNA copies; REVEL 0.815 | |
| AGXT C173R | 173 | Conflicting reports (★) | +7: 2 other pathogenic changes within 3 positions; C173Y at the same position is pathogenic; seen in 0 of gnomAD DNA copies; REVEL 0.910 | |
| AGXT G41E | 41 | Conflicting reports (★) | +7: 2 other pathogenic changes within 3 positions; G41R at the same position is pathogenic; seen in 6.6e-06 of gnomAD DNA copies; REVEL 0.785 | |
| AGXT L276Q | 276 | Uncertain (★) | +7: 4 other pathogenic changes within 3 positions; L276E at the same position is pathogenic; seen in 6.8e-07 of gnomAD DNA copies; REVEL 0.929 | |
| AGXT M195V | 195 | Uncertain | +7: 3 other pathogenic changes within 3 positions; M195R at the same position is pathogenic; seen in 6.6e-06 of gnomAD DNA copies; REVEL 0.773 | |
| AGXT S187Y | 187 | Conflicting reports (★) | +6: 2 other pathogenic changes within 3 positions; S187F at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.83 | |
| AGXT D201N | 201 | Conflicting reports (★) | +6: 5 other pathogenic changes within 3 positions; D201V at the same position is pathogenic; REVEL 0.832 | |
| AGXT G350S | 350 | Conflicting reports (★) | +6: 2 other pathogenic changes within 3 positions; G350D at the same position is pathogenic; REVEL 0.826 | |
| AGXT R118C | 118 | Conflicting reports (★) | +6: 4 other pathogenic changes within 3 positions; R118H at the same position is pathogenic; REVEL 0.808 | |
| AGXT G41V | 41 | Conflicting reports (★) | +6: 2 other pathogenic changes within 3 positions; G41R at the same position is pathogenic; seen in 6.6e-06 of gnomAD DNA copies; REVEL 0.731 | |
| AGXT G27E | 27 | Uncertain (★) | +6: 3 other pathogenic changes within 3 positions; G27W at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.63 |
Which prediction tools work for Primary hyperoxaluria
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- CADD: 100 out of 100
- AlphaGenome (regulatory): 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- REVEL: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- AlphaMissense: 98 out of 100
- ESM1b (LLR): 98 out of 100
- SIFT: 97 out of 100
- phyloP: 94 out of 100
- AlphaGenome (splicing): 54 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- DMS / MaveDB: 26 out of 100
Diseases related to Primary hyperoxaluria
- Cardiac arrhythmia, also linked to AGXT
- Renal tubular dysgenesis, also linked to AGT
- Renal tubular dysgenesis of genetic origin, also linked to AGT
Frequently asked questions
Which genes have records linked to Primary hyperoxaluria?
This view contains 2 analyzed proteins: AGXT, AGT. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 100 pathogenic or likely pathogenic variants, 62 variants of uncertain significance and 29 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 11 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 243 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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