IEMbase 0096: AGXT-related alanine-glyoxylate aminotransferase deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 96 |
| Nosology | 13.1.04.01 |
| Gene | AGXT |
| External IDs | OMIM:259900 |
| Generated mapping | UNMAPPED; best fuzzy candidate ornithine_aminotransferase_deficiency.yaml |
| Candidate DisMech targets | Primary_Hyperoxaluria_Type_1.yaml; Disorders_of_Glyoxylate_and_Oxalate_Metabolism.yaml |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents this as autosomal recessive peroxisomal alanine-glyoxylate aminotransferase deficiency, with alternate labels primary hyperoxaluria type 1, AGT, and PH1. Treatability is marked unknown, and prevalence is listed near 1:500,000.
The characteristic biochemical rows are plasma and urinary oxalic acid and plasma and urinary glycolic acid. The wider panel also includes plasma creatinine and urea.
The characteristic clinical rows include failure to thrive, growth retardation, nephrocalcinosis, nephrolithiasis, radiolucent metaphyseal bands, renal colic, and chronic renal failure.
Treatment rows include lumasiran, kidney transplantation, liver transplantation, hyperhydration, potassium citrate, and pyridoxine.
DisMech phenotype coverage
The generated UNMAPPED status is a false negative. The best local disease target
is Primary_Hyperoxaluria_Type_1.yaml, with
Disorders_of_Glyoxylate_and_Oxalate_Metabolism.yaml as grouping context.
DisMech models PH1 as biallelic AGXT deficiency of hepatic peroxisomal alanine-glyoxylate aminotransferase, impaired glyoxylate-to-glycine conversion, glyoxylate diversion to oxalate, urinary calcium oxalate supersaturation, nephrolithiasis, nephrocalcinosis, chronic kidney disease, and systemic oxalosis after kidney failure. The grouping explicitly distinguishes the AGXT mechanism from GRHPR/PH2 and other glyoxylate-oxalate pathway members.
ornithine_aminotransferase_deficiency.yaml is an aminotransferase-name false
positive and should not be used for this IEMbase record.
Concordance and completeness
Judgement: false-negative mapping with high local mechanistic coverage.
DisMech currently lacks much of the IEMbase treatment list for PH1 and does not separately capture glycolic acid, creatinine, urea, renal colic, growth failure, or radiolucent metaphyseal bands in the disease entry. IEMbase is therefore useful as a treatment and phenotype-gap checklist.
Curation actions
- Update the mapping logic or manual crosswalk to resolve this record to
Primary_Hyperoxaluria_Type_1.yaml. - Keep
Disorders_of_Glyoxylate_and_Oxalate_Metabolism.yamlas grouping context, not the primary disease target. - Consider adding PH1 treatment coverage for lumasiran, pyridoxine, hyperhydration/citrate, and liver/kidney transplantation with evidence.