Gene
GAMT
guanidinoacetate N-methyltransferase
- HGNC 4136(opens in a new tab)
- Ensembl gene ENSG00000130005(opens in a new tab)
- NCBI Gene 2593(opens in a new tab)
Summary
- Cytogenetic location
- 19p13.3
- Coordinates
- Chromosome 19: 1,397,026–1,401,542 (GRCh38)
- Exons
- 6 exons across 4.5 kb
- Protein
- 236 amino acids
- Also known as
- PIG2, TP53I2
- MANE Select transcript
- ENST00000252288.8NM_000156.6
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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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
- 6 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.
How GAMT is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Variants with a page
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 1.1 kb of the gene's 4.5 kb; 711 of those bases code for the protein.
How a genome test reads GAMT
126
positions in GAMT 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 4.5 kb of GAMT, introns included, not only the 1.1 kb of exons.
Variants with a page (69)
The GAMT variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| A22Gfs*63 | c.64dup | Exon 1 | 1,401,412 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| A54P | c.160G>C | Exon 1 | 1,401,317 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| A74P | c.220G>C | Exon 2 | 1,399,900 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| A75V | c.224C>T | Exon 2 | 1,399,896 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| A156D | c.467C>A | Exon 5 | 1,399,019 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.1A>G | Exon 1 | 1,401,476 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel | |
| c.114C>T | Exon 1 | 1,401,363 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel | |
| c.158_181+7del | Intron 1 | 1,401,288 | Pathogenic | 3 stars out of 4 reviewed by expert panel | |
| c.327+43G>A | Intron 2 | 1,399,750 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel | |
| c.327G>A | Exon 2 | 1,399,793 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
Traits linked to GAMT
The Human Phenotype Ontology lists these as features of the rare conditions GAMT can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Delayed speech and language development
- Elevated brain guanidinoacetate level by MRS
- Intellectual disability, severe
- Severe global developmental delay
- Epilepsy
- Abnormality of extrapyramidal motor function
- Abnormality of movement
- Absent speech development
Show 25 more traits
- Aggressive behavior
- Ataxia
- Behavioral abnormality
- Poor speech
- Progressive extrapyramidal movement disorder
- Sudden loss of muscle tone
- Abnormal head movements
- Autism
- Chorea
- Dystonia
- Febrile seizure (within the age range of 3 months to 6 years)
- Focal impaired awareness seizure
- Generalized myoclonic seizure
- Grand mal seizures
- Involuntary writhing movements in fingers, hands, toes, and feet
- Loss of developmental milestones
- More active than typical
- Partial paralysis of legs
- Self-injurious behavior
- Tremor
- Global developmental delay
- Increased reflexes
- Intellectual disability
- Jerking
- Reduced brain creatine level by MRS
External links
Gene records
Transcript
Protein
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
Dante Labs. (n.d.). GAMT gene: guanidinoacetate N-methyltransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/gamt
Dante Labs. GAMT gene: guanidinoacetate N-methyltransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/gamt
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