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Gene

AMT

aminomethyltransferase

Summary

Cytogenetic location
3p21.31
Coordinates
Chromosome 3: 49,416,778–49,422,473 (GRCh38)
Exons
9 exons across 5.7 kb
Protein
403 amino acids
Inheritance
Autosomal recessive
Also known as
GCST, NKH
MANE Select transcript
ENST00000273588.9NM_000481.4
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

  • Disorders of Glycine & Serine Metabolism

    • Glycine Encephalopathy (Non-Ketotic Hyperglycinemia)Autosomal recessive

      Caused by variants in GLDC, AMT or GCSH (and, in an atypical form, SLC6A9), which cause high glycine in the brain and can lead to seizures, low muscle tone and developmental problems.

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

      Knowing allows treatment with sodium benzoate and dextromethorphan, which can reduce seizures in some forms.

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 AMT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where AMT sits. AMT and 38 genes near it on chromosome 3, from 48,919,626 to 49,919,625.Chromosome 33p21.31p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2949 Mb49.2 Mb49.4 Mb49.6 Mb49.8 MbARIH2: 48,918,217–48,986,382, forward strandARIH2P4HTM: 48,989,858–49,007,153, forward strandWDR6: 49,007,062–49,015,953, forward strandDALRD3: 49,015,474–49,022,293, reverse strandNDUFAF3: 49,020,459–49,027,593, forward strandNDUFAF3IMPDH2: 49,024,315–49,029,452, reverse strandIMPDH2: 49,024,345–49,094,071, reverse strandQRICH1: 49,029,700–49,094,545, reverse strandQRICH1QARS1: 49,095,932–49,105,130, reverse strandQARS1USP19: 49,105,758–49,120,940, reverse strandUSP19LAMB2: 49,121,113–49,133,118, reverse strandLAMB2CCDC71: 49,161,063–49,166,357, reverse strandCCDC71KLHDC8B: 49,171,239–49,176,487, forward strandKLHDC8BCIMIP7: 49,177,634–49,191,858, reverse strandCIMIP7IHO1: 49,198,428–49,277,629, forward strandIHO1C3orf62: 49,268,596–49,277,236, reverse strandC3orf62USP4: 49,277,144–49,340,712, reverse strandUSP4GPX1: 49,357,174–49,358,605, reverse strandGPX1: 49,357,176–49,412,051, reverse strandRHOA: 49,359,136–49,412,998, reverse strandTCTA: 49,412,212–49,455,826, forward strandTCTA: 49,416,777–49,429,314, reverse strandAMT: 49,416,778–49,422,473, reverse strandAMTNICN1: 49,422,333–49,429,331, reverse strandNICN1DAG1: 49,468,649–49,535,624, forward strandDAG1BSN: 49,554,477–49,671,549, forward strandBSNAPEH: 49,673,818–49,683,973, forward strandAPEHMST1: 49,683,922–49,689,501, reverse strandMST1RNF123: 49,688,740–49,723,389, forward strandRNF123AMIGO3: 49,716,829–49,719,684, reverse strandAMIGO3GMPPB: 49,716,844–49,723,988, reverse strandIP6K1: 49,724,294–49,786,557, reverse strandIP6K1CDHR4: 49,790,732–49,799,879, reverse strandCDHR4INKA1: 49,803,228–49,805,237, forward strandINKA1UBA7: 49,805,205–49,814,151, reverse strandUBA7TRAIP: 49,828,595–49,856,597, reverse strandTRAIPCAMKV: 49,857,214–49,870,064, reverse strandCAMKVMST1R: 49,886,902–49,906,130, reverse strandMST1RMON1A: 49,907,160–49,930,173, reverse strandMON1ADiagram of AMT: 9 exons on the reverse strand of chromosome 3Exon 9: 15 known disease-causing sitesExon 8: 16 known disease-causing sitesExon 7: 14 known disease-causing sitesExon 6: 15 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 3: 6 known disease-causing sitesExon 2: 19 known disease-causing sitesExon 1: 11 known disease-causing sitesExon 9: 49,416,778–49,417,718, 941 basesExon 8: 49,417,818–49,417,973, 156 basesExon 7: 49,418,971–49,419,151, 181 basesExon 6: 49,419,260–49,419,405, 146 basesExon 5: 49,419,710–49,419,788, 79 basesExon 4: 49,420,211–49,420,342, 132 basesExon 3: 49,421,492–49,421,572, 81 basesExon 2: 49,422,104–49,422,271, 168 basesExon 1: 49,422,361–49,422,473, 113 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 kb of the gene's 5.7 kb; 1,212 of those bases code for the protein.

How a genome test reads AMT

130

positions in AMT 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 5.7 kb of AMT, introns included, not only the 2 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.). AMT gene: aminomethyltransferase. Retrieved 17 October 2026, from https://dantelabs.com/genes/amt

Vancouver

Dante Labs. AMT gene: aminomethyltransferase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/amt

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