AGXT

Chr 2AR

alanine--glyoxylate aminotransferase

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

NCBI Gene: 189ENSG00000172482UniProt: P21549

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]

Primary Disease Associations & Inheritance

Hyperoxaluria, primary, type 1MIM #259900
AR
UniProtHyperoxaluria primary 1
598
ClinVar variants
154
Pathogenic / LP
0.00
pLI score
6
Active trials
Clinical Summary— AGXT
🧬
Gene-Disease Validity (ClinGen)
alanine glyoxylate aminotransferase deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
154 Pathogenic / Likely Pathogenic· 122 VUS of 598 total submissions
💊
Clinical Trials
6 active or recruiting trials — potential therapeutic options may be available
Some data sources returned errors (1)

pubmed: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.27Z-score
OE missense 1.05 (0.95–1.16)
263 obs / 251.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.66 (0.43–1.03)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.05 (0.95–1.16)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.08
0≤1.21.6
LoF obs/exp: 14 / 21.3Missense obs/exp: 263 / 251.1Syn Z: -0.64

ClinVar Variant Classifications

598 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic79
Likely Pathogenic75
VUS122
Likely Benign286
Benign27
Conflicting9
79
Pathogenic
75
Likely Pathogenic
122
VUS
286
Likely Benign
27
Benign
9
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
29
6
44
0
79
Likely Pathogenic
28
39
8
0
75
VUS
0
95
18
9
122
Likely Benign
0
3
136
147
286
Benign
0
0
27
0
27
Conflicting
—9
Total57143233156598

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in 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.

Gene2Phenotype Curations

AGXT-related hyperoxaluria, primary

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersEyeSkin
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Hyperoxaluria, primary, type 1

MIM #259900

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — AGXT
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Kidney Stone

Heterozygous Individuals for AGXT and Kidney Stones

NOT YET RECRUITING
NCT04430426Phase NAUniversity of Alabama at BirminghamStarted 2026-07-01
Controlled DietGlycolate Administration
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
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
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
Hyperoxaluria (Disorder)

Oxalate Excretion Profile in Patients with a Heterozygous Mutation of the AGXT (alanine-glyoxylate Aminotransferase) Gene

RECRUITING
NCT06283082Phase NAHospices Civils de LyonStarted 2024-12-11
Lithiasis assessment
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.

External Resources

Links to major genomics databases and tools