AGXT

Chr 2AR

alanine--glyoxylate aminotransferase

Also known as: AGT, AGT1, AGXT1, PH1, SPAT, SPT, Ser-PyrAT, TLH6

NCBI Gene: 189ENSG00000172482UniProt: P21549OMIM: 604285

This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Hyperoxaluria, primary, type 1MIM #259900
AR
UniProtHyperoxaluria primary 1

Clinical highlights

Gene-disease validity (ClinGen)
alanine glyoxylate aminotransferase deficiency · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
7
Active trials
54
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
1.03
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — AGXT
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
1.03LOEUF
pLI 0.000
Z-score 1.46
OE 0.66 (0.43–1.03)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-0.27Z-score
OE missense 1.05 (0.95–1.16)
263 obs / 251.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.66 (0.43–1.03)
0≤0.351.4
Missense OE?1.05 (0.95–1.16)
0≤0.61.4
Synonymous OE?1.08
0≤1.21.6
LoF obs/exp: 14 / 21.3Missense obs/exp: 263 / 251.1Syn Z: -0.64

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

AGXT · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Kidney StoneUrolithiasis, Calcium Oxalate

Heterozygous Individuals for AGXT and Kidney Stones

ENROLLING BY INVITATION
NCT04430426Phase NAUniversity of Alabama at BirminghamStarted 2027-07-01
Controlled Diet
Type 1 Primary Hyperoxaluria

Clinical Exploration Study of YOLT-203 in the Treatment of Type 1 Primary Hyperoxaluria (PH1)

RECRUITING
NCT06511349Phase EARLY_PHASE1RenJi HospitalStarted 2024-07-15
YOLT-203
Primary Hyperoxaluria Type 1 (PH1)

Phase 1/2 Study of ABO-101 in Primary Hyperoxaluria Type 1 (redePHine)

RECRUITING
NCT06839235Phase PHASE1, PHASE2Arbor BiotechnologiesStarted 2025-06-16
ABO-101
Patients With PH1 Treated With Lumasiran in France

Retrospective and Prospective Follow-up of Patients With Primary Hyperoxaluria Type 1 Treated With Lumasiran in France.

RECRUITING
NCT06225882Hospices Civils de LyonStarted 2023-01-01
Oxaluria evolution.
Primary Hyperoxaluria Type 1PH1

Study of YOLT-203 in Children and Adults With Primary Hyperoxaluria Type 1 (PH1)

RECRUITING
NCT07587021Phase PHASE2YolTech Therapeutics Co., LtdStarted 2026-09
YOLT-203Placebo
Type 1 Primary Hyperoxaluria

Clinical Exploration Study of YOLT-203 in the Treatment of Type 1 Primary Hyperoxaluria (PH1)

ACTIVE NOT RECRUITING
NCT06892301Phase EARLY_PHASE1Guangzhou Women and Children's Medical CenterStarted 2025-02-27
YOLT-203
Primary Hyperoxaluria Type 1PH1

Phase I Exploratory Study of YOLT-203 in Patients With Primary Hyperoxaluria Type 1 (PH1)

RECRUITING
NCT07776626Phase PHASE1YolTech Therapeutics Co., LtdStarted 2026-08
YOLT-203

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients