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Gene

AGXT

alanine--glyoxylate aminotransferase

Summary

Cytogenetic location
2q37.3
Coordinates
Chromosome 2: 240,868,824–240,880,500 (GRCh38)
Exons
11 exons across 11.7 kb
Protein
392 amino acids
Inheritance
Autosomal recessive
Also known as
AGXT1, PH1, AGT, SPT, AGT1, TLH6, Ser-PyrAT
Previous symbols
SPAT
MANE Select transcript
ENST00000307503.4NM_000030.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Primary Hyperoxaluria

    • Alanine Glyoxylate Aminotransferase Deficiency

      Any disorder of plasmalogen biosynthesis in which the cause of the disease is a mutation in the AGXT gene.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
    • Autosomal recessive

      A hereditary disorder characterized by excessive oxalate production, leading to hyperoxaluria.

      • 6 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How AGXT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 2, with a bracket where AGXT sits. AGXT and 19 genes near it on chromosome 2, from 240,374,662 to 241,374,661.Chromosome 22q37.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3240.4 Mb240.6 Mb240.8 Mb241 Mb241.2 MbGPC1: 240,435,434–240,468,115, forward strandGPC1ANKMY1: 240,479,422–240,569,209, reverse strandANKMY1DUSP28: 240,560,054–240,565,256, forward strandDUSP28RNPEPL1: 240,565,804–240,581,372, forward strandRNPEPL1CAPN10: 240,586,366–240,618,845, forward strandCAPN10GPR35: 240,605,404–240,633,159, forward strandGPR35AQP12B: 240,676,418–240,682,906, reverse strandAQP12BAQP12A: 240,691,866–240,698,483, forward strandAQP12AKIF1A: 240,713,761–240,824,320, reverse strandKIF1AAGXT: 240,868,824–240,880,500, forward strandAGXTMAB21L4: 240,886,048–240,896,894, reverse strandMAB21L4CROCC2: 240,906,330–240,993,311, forward strandCROCC2SNED1: 240,998,612–241,095,579, forward strandSNED1MTERF4: 241,072,169–241,102,332, reverse strandMTERF4PASK: 241,106,094–241,150,852, reverse strandPASKPPP1R7: 241,149,549–241,183,652, forward strandPPP1R7ANO7: 241,188,509–241,227,338, forward strandANO7HDLBP: 241,227,264–241,317,061, reverse strandHDLBPSEPTIN2: 241,314,923–241,354,030, forward strandSEPTIN2FARP2: 241,356,244–241,494,847, forward strandFARP2Diagram of AGXT: 11 exons on the forward strand of chromosome 2Exon 1: 19 known disease-causing sitesExon 2: 37 known disease-causing sitesExon 3: 9 known disease-causing sitesExon 4: 17 known disease-causing sitesExon 5: 16 known disease-causing sitesExon 6: 20 known disease-causing sitesExon 7: 15 known disease-causing sitesExon 8: 11 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 10: 11 known disease-causing sitesExon 11: 9 known disease-causing sitesExon 1: 240,868,824–240,869,030, 207 basesExon 2: 240,869,170–240,869,362, 193 basesExon 3: 240,870,644–240,870,708, 65 basesExon 4: 240,871,349–240,871,449, 101 basesExon 5: 240,872,979–240,873,049, 71 basesExon 6: 240,873,978–240,874,062, 85 basesExon 7: 240,875,109–240,875,204, 96 basesExon 8: 240,875,935–240,876,004, 70 basesExon 9: 240,877,537–240,877,632, 96 basesExon 10: 240,878,022–240,878,150, 129 basesExon 11: 240,878,714–240,880,500, 1,787 bases12345678910115′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.9 kb of the gene's 11.7 kb; 1,179 of those bases code for the protein.

How a genome test reads AGXT

201

positions in AGXT where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 11.7 kb of AGXT, introns included, not only the 2.9 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). AGXT gene: alanine--glyoxylate aminotransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/agxt

Vancouver

Dante Labs. AGXT gene: alanine--glyoxylate aminotransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/agxt

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