Skip to content
Use your HSA or FSA funds

Gene

GATM

glycine amidinotransferase

Summary

Cytogenetic location
15q21.1
Coordinates
Chromosome 15: 45,361,124–45,378,544 (GRCh38)
Exons
9 exons across 17.4 kb
Protein
423 amino acids
Also known as
AGAT
MANE Select transcript
ENST00000396659.8NM_001482.3
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 reports relevant to this gene

  • Cerebral Creatine Deficiency Syndromes

    • Cerebral Creatine Deficiency Syndrome

      Includes GAMT and AGAT deficiency (autosomal recessive) and creatine transporter deficiency (SLC6A8, X-linked), which can cause intellectual disability, speech delay, seizures and behavioural problems.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows creatine supplementation, with ornithine and dietary changes in GAMT deficiency, which can improve or prevent symptoms in the synthesis defects when started early.

  • Fanconi Renotubular Syndrome and Renal Glucosuria

    • Inherited Fanconi Renotubular Syndrome

      A group of inherited proximal tubule disorders, caused by genes such as GATM, EHHADH and HNF4A, in which many substances are lost in the urine, which can affect bones and kidney function.

      • ClinGen rates the link moderate
      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing allows monitoring of kidney function and bone health and replacement of lost minerals where needed.

How GATM is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 15, with a bracket where GATM sits. GATM and 14 genes near it on chromosome 15, from 44,869,834 to 45,869,833.Chromosome 1515q21.1p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q14q15.1q15.2q15.3q21.1q21.2q21.3q22.1q22.2q22.31q22.32q22.33q23q24.1q24.2q24.3q25.1q25.2q25.3q26.1q26.2q26.345 Mb45.2 Mb45.4 Mb45.6 Mb45.8 MbTERB2: 44,956,687–44,979,229, forward strandTERB2SORD: 45,023,116–45,077,185, forward strandSORDDUOX2: 45,092,650–45,114,185, reverse strandDUOX2DUOXA2: 45,114,325–45,118,421, forward strandDUOXA2DUOXA1: 45,117,364–45,130,611, reverse strandDUOXA1DUOX1: 45,129,450–45,165,576, forward strandDUOX1SHF: 45,165,572–45,201,175, reverse strandSHFSLC28A2: 45,252,227–45,277,846, forward strandSLC28A2GATM: 45,361,124–45,378,544, reverse strandGATMAFG2B: 45,402,325–45,421,415, forward strandAFG2BCOXFA4L3: 45,430,579–45,448,761, forward strandCOXFA4L3SLC30A4: 45,479,606–45,522,834, reverse strandSLC30A4BLOC1S6: 45,587,108–45,615,945, forward strandBLOC1S6: 45,587,351–45,676,314, forward strandSQOR: 45,631,148–45,691,299, forward strandSQORDiagram of GATM: 9 exons on the reverse strand of chromosome 15Exon 9: 2 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 7: 1 known disease-causing siteExon 6: 3 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 3 known disease-causing sitesExon 2: 7 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 9: 45,361,124–45,362,221, 1,098 bases. 2 variants with a page in exon 9. List themExon 8: 45,363,900–45,364,016, 117 bases. 1 variant with a page in exon 8. List themExon 7: 45,364,797–45,364,860, 64 basesExon 6: 45,366,046–45,366,210, 165 bases. 1 variant with a page in exon 6. List themExon 5: 45,366,371–45,366,508, 138 bases. 1 variant with a page in exon 5. List themExon 4: 45,368,070–45,368,260, 191 bases. 4 variants with a page in exon 4. List themExon 3: 45,369,326–45,369,521, 196 bases. 1 variant with a page in exon 3. List themExon 2: 45,376,601–45,376,819, 219 bases. 1 variant with a page in exon 2. List themExon 1: 45,378,385–45,378,544, 160 bases9876543215′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 2.3 kb of the gene's 17.4 kb; 1,272 of those bases code for the protein.

How a genome test reads GATM

34

positions in GATM 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 17.4 kb of GATM, introns included, not only the 2.3 kb of exons.

Variants with a page (12)

The GATM variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A185Pc.553G>CExon 445,368,192Likely pathogenic3 stars out of 4 reviewed by expert panel
c.484+1G>TIntron 345,369,325Pathogenic3 stars out of 4 reviewed by expert panel
M371Nfs*6c.1111dupExon 845,363,947Pathogenic3 stars out of 4 reviewed by expert panel
P320Lfs*41c.959delExon 645,366,064Likely pathogenic3 stars out of 4 reviewed by expert panel
R169Xc.505C>TExon 445,368,240Pathogenic3 stars out of 4 reviewed by expert panel
R260Xc.778C>TExon 545,366,406Likely pathogenic3 stars out of 4 reviewed by expert panel
R413Qc.1238G>AExon 945,362,143Likely pathogenic3 stars out of 4 reviewed by expert panel
R413Wc.1237C>TExon 945,362,144Likely pathogenic3 stars out of 4 reviewed by expert panel
W72Xc.216G>AExon 245,376,673Likely pathogenic3 stars out of 4 reviewed by expert panel
W149Xc.446G>AExon 345,369,364Pathogenic3 stars out of 4 reviewed by expert panel

See all 12 GATM variants →

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.). GATM gene: glycine amidinotransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/gatm

Vancouver

Dante Labs. GATM gene: glycine amidinotransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/gatm

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test