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Gene

CHAT

choline O-acetyltransferase

Summary

Cytogenetic location
10q11.23
Coordinates
Chromosome 10: 49,614,037–49,667,942 (GRCh38)
Exons
15 exons across 53.9 kb
Protein
748 amino acids
Inheritance
Autosomal recessive
Also known as
CHOACTase
MANE Select transcript
ENST00000337653.7NM_020549.5
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

  • Congenital Myasthenic Syndrome

    • Congenital Myasthenic Syndrome 6Autosomal recessive

      Congenital myasthenic syndrome caused by mutation(s) in the CHAT gene, encoding choline O-acetyltransferase. It is inherited in an autosomal recessive manner.

      • ClinGen rates the link definitive
      • 3 GenCC submitters rate it definitive or strong
    • Congenital Myasthenic Syndrome (All Types)

      Umbrella term covering all congenital myasthenic syndromes, including the common CHRNE, RAPSN, DOK7 and MUSK forms.

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

      Many forms respond to specific medications such as pyridostigmine, salbutamol or ephedrine, and the right choice depends on the gene involved.

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 CHAT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 10, with a bracket where CHAT sits. CHAT and 12 genes near it on chromosome 10, from 49,140,990 to 50,140,989.Chromosome 1010q11.23p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.349.2 Mb49.4 Mb49.6 Mb49.8 Mb50 MbTMEM273: 49,153,753–49,188,585, reverse strandTMEM273C10orf71: 49,299,137–49,329,924, forward strandC10orf71DRGX: 49,364,065–49,398,484, reverse strandDRGXERCC6: 49,454,168–49,539,538, reverse strandERCC6SLC18A3: 49,610,310–49,612,720, forward strandSLC18A3CHAT: 49,614,037–49,667,942, forward strandCHATC10orf53: 49,679,638–49,710,261, forward strandC10orf53OGDHL: 49,721,386–49,762,392, reverse strandOGDHLPARG: 49,815,132–49,970,203, reverse strandPARGTIMM23B: 49,942,031–49,977,625, forward strandTIMM23BTIMM23B-AGAP6: 49,942,056–50,011,654, forward strandTIMM23B-AGAP6AGAP6: 49,982,190–50,011,654, forward strandAGAP6WASHC2A: 50,067,881–50,136,578, forward strandWASHC2ADiagram of CHAT: 15 exons on the forward strand of chromosome 10Exon 1: 3 known disease-causing sitesExon 3: 12 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 1 known disease-causing siteExon 6: 4 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 8: 7 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 10: 13 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 12: 11 known disease-causing sitesExon 14: 8 known disease-causing sitesExon 15: 2 known disease-causing sitesExon 1: 49,614,037–49,614,475, 439 basesExon 2: 49,616,502–49,616,602, 101 basesExon 3: 49,619,725–49,619,916, 192 basesExon 4: 49,620,495–49,620,613, 119 basesExon 5: 49,622,097–49,622,150, 54 basesExon 6: 49,625,473–49,625,653, 181 basesExon 7: 49,627,608–49,627,785, 178 basesExon 8: 49,646,505–49,646,674, 170 basesExon 9: 49,648,507–49,648,607, 101 basesExon 10: 49,649,508–49,649,636, 129 basesExon 11: 49,651,884–49,652,006, 123 basesExon 12: 49,655,095–49,655,236, 142 basesExon 13: 49,655,386–49,655,448, 63 basesExon 14: 49,662,645–49,662,782, 138 basesExon 15: 49,664,777–49,667,942, 3,166 bases12468101214155′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 5.3 kb of the gene's 53.9 kb; 2,247 of those bases code for the protein.

How a genome test reads CHAT

101

positions in CHAT 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 53.9 kb of CHAT, introns included, not only the 5.3 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.). CHAT gene: choline O-acetyltransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/chat

Vancouver

Dante Labs. CHAT gene: choline O-acetyltransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/chat

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