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Aliases for CHAT Gene

Aliases for CHAT Gene

  • Choline O-Acetyltransferase 2 3 5
  • Choline Acetylase 3 4
  • EC 4 63
  • Acetyl CoA:Choline O-Acetyltransferase 3
  • Choline Acetyltransferase 2
  • EC 2.3.1 63
  • CMS1A2 3
  • CMS1A 3
  • CMS6 3
  • ChAT 4

External Ids for CHAT Gene

Previous GeneCards Identifiers for CHAT Gene

  • GC10P049721
  • GC10P050709
  • GC10P050161
  • GC10P050487
  • GC10P050817
  • GC10P045081

Summaries for CHAT Gene

Entrez Gene Summary for CHAT Gene

  • This gene encodes an enzyme which catalyzes the biosynthesis of the neurotransmitter acetylcholine. This gene product is a characteristic feature of cholinergic neurons, and changes in these neurons may explain some of the symptoms of Alzheimer's disease. Polymorphisms in this gene have been associated with Alzheimer's disease and mild cognitive impairment. Mutations in this gene are associated with congenital myasthenic syndrome associated with episodic apnea. Multiple transcript variants encoding different isoforms have been found for this gene, and some of these variants have been shown to encode more than one isoform. [provided by RefSeq, May 2010]

GeneCards Summary for CHAT Gene

CHAT (Choline O-Acetyltransferase) is a Protein Coding gene. Diseases associated with CHAT include Myasthenic Syndrome, Congenital, 6, Presynaptic and Myasthenic Syndrome, Congenital, 1A, Slow-Channel. Among its related pathways are Sympathetic Nerve Pathway (Pre- and Post- Ganglionic Junction) and Glycerophospholipid biosynthesis. GO annotations related to this gene include transferase activity, transferring acyl groups and choline O-acetyltransferase activity. An important paralog of this gene is CRAT.

UniProtKB/Swiss-Prot for CHAT Gene

  • Catalyzes the reversible synthesis of acetylcholine (ACh) from acetyl CoA and choline at cholinergic synapses.

Gene Wiki entry for CHAT Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHAT Gene

Genomics for CHAT Gene

Regulatory Elements for CHAT Gene

Enhancers for CHAT Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CHAT on UCSC Golden Path with GeneCards custom track

Genomic Location for CHAT Gene

49,609,095 bp from pter
49,665,104 bp from pter
56,010 bases
Plus strand

Genomic View for CHAT Gene

Genes around CHAT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHAT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHAT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHAT Gene

Proteins for CHAT Gene

  • Protein details for CHAT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Choline O-acetyltransferase
    Protein Accession:
    Secondary Accessions:
    • A2BDF4
    • A2BDF5
    • Q16488
    • Q9BQ23
    • Q9BQ35
    • Q9BQE1

    Protein attributes for CHAT Gene

    748 amino acids
    Molecular mass:
    82536 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CHAT Gene

    Alternative splice isoforms for CHAT Gene


neXtProt entry for CHAT Gene

Proteomics data for CHAT Gene at MOPED

Post-translational modifications for CHAT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for CHAT (Choline Acetyltransferase/ChAT)

Domains & Families for CHAT Gene

Protein Domains for CHAT Gene

Suggested Antigen Peptide Sequences for CHAT Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the carnitine/choline acetyltransferase family.
  • Belongs to the carnitine/choline acetyltransferase family.
genes like me logo Genes that share domains with CHAT: view

No data available for Gene Families for CHAT Gene

Function for CHAT Gene

Molecular function for CHAT Gene

GENATLAS Biochemistry:
choline acetyltransferase neurotransmitter acetylcholine catalyzing enzyme synthesis,expressed in the brain and spinal cord
UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + choline = CoA + O-acetylcholine.
UniProtKB/Swiss-Prot Function:
Catalyzes the reversible synthesis of acetylcholine (ACh) from acetyl CoA and choline at cholinergic synapses.

Enzyme Numbers (IUBMB) for CHAT Gene

Gene Ontology (GO) - Molecular Function for CHAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0033265 choline binding IEA --
genes like me logo Genes that share ontologies with CHAT: view
genes like me logo Genes that share phenotypes with CHAT: view

Human Phenotype Ontology for CHAT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CHAT Gene

MGI Knock Outs for CHAT:

Animal Model Products

miRNA for CHAT Gene

miRTarBase miRNAs that target CHAT

No data available for Transcription Factor Targets and HOMER Transcription for CHAT Gene

Localization for CHAT Gene

Subcellular locations from

Jensen Localization Image for CHAT Gene COMPARTMENTS Subcellular localization image for CHAT gene
Compartment Confidence
cytosol 5
nucleus 5
mitochondrion 3
peroxisome 3
cytoskeleton 2
extracellular 2
plasma membrane 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for CHAT Gene

Pathways & Interactions for CHAT Gene

genes like me logo Genes that share pathways with CHAT: view

SIGNOR curated interactions for CHAT Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CHAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006644 phospholipid metabolic process TAS --
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0007269 neurotransmitter secretion TAS --
GO:0007584 response to nutrient IEA --
GO:0007613 memory IEA --
genes like me logo Genes that share ontologies with CHAT: view

Drugs & Compounds for CHAT Gene

(57) Drugs for CHAT Gene - From: DrugBank, PharmGKB, ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Enzyme, substrate 139
Donepezil Approved Pharma 273
Nicotine Approved Pharma Antagonist, Target 990
Olanzapine Approved, Investigational Pharma Antagonist 380
Galantamine Approved Pharma 103

(50) Additional Compounds for CHAT Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
genes like me logo Genes that share compounds with CHAT: view

Transcripts for CHAT Gene

Unigene Clusters for CHAT Gene

Choline O-acetyltransferase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CHAT Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15 ^ 16 ^ 17 ^ 18a · 18b
SP1: - - -
SP2: - - - - -
SP3: - - - -
SP5: -

Relevant External Links for CHAT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CHAT Gene

mRNA expression in normal human tissues for CHAT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CHAT Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x16.6), Brain - Caudate (basal ganglia) (x15.3), and Brain - Nucleus accumbens (basal ganglia) (x6.1).

Protein differential expression in normal tissues from HIPED for CHAT Gene

This gene is overexpressed in Monocytes (34.9), Tlymphocyte (20.1), and Placenta (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CHAT Gene

SOURCE GeneReport for Unigene cluster for CHAT Gene Hs.302002

genes like me logo Genes that share expression patterns with CHAT: view

Protein tissue co-expression partners for CHAT Gene

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for CHAT Gene

Orthologs for CHAT Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CHAT Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CHAT 35
  • 88.37 (n)
  • 90.3 (a)
  • 89 (a)
(Canis familiaris)
Mammalia CHAT 35
  • 87.58 (n)
  • 89.83 (a)
  • 84 (a)
(Mus musculus)
Mammalia Chat 35
  • 85.98 (n)
  • 88.19 (a)
Chat 16
Chat 36
  • 87 (a)
(Pan troglodytes)
Mammalia CHAT 35
  • 99.1 (n)
  • 98.19 (a)
  • 98 (a)
(Rattus norvegicus)
Mammalia Chat 35
  • 86.14 (n)
  • 88.5 (a)
(Monodelphis domestica)
Mammalia CHAT 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CHAT 36
  • 79 (a)
(Gallus gallus)
Aves CHAT 35
  • 72.26 (n)
  • 78.01 (a)
  • 78 (a)
(Anolis carolinensis)
Reptilia CHAT 36
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia chat 35
  • 67.19 (n)
  • 74.02 (a)
(Danio rerio)
Actinopterygii chat 35
  • 64.78 (n)
  • 67.42 (a)
zgc64220 35
chat 36
  • 65 (a)
CHAT (2 of 2) 36
  • 58 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG5122 37
  • 38 (a)
CG5265 37
  • 32 (a)
Cha 37
  • 38 (a)
Cha 35
  • 52.59 (n)
  • 41.58 (a)
Cha 36
  • 35 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002370 35
  • 52.94 (n)
  • 41.35 (a)
(Caenorhabditis elegans)
Secernentea B0395.3 37
  • 34 (a)
cha-1 37
  • 34 (a)
cha-1 35
  • 45.84 (n)
  • 37.52 (a)
cha-1 36
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAT2 36
  • 28 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14198 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 47 (a)
Species with no ortholog for CHAT:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CHAT Gene

Gene Tree for CHAT (if available)
Gene Tree for CHAT (if available)

Paralogs for CHAT Gene

Paralogs for CHAT Gene

(4) SIMAP similar genes for CHAT Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CHAT: view

Variants for CHAT Gene

Sequence variations from dbSNP and Humsavar for CHAT Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_011666 Myasthenic syndrome, congenital, 6, presynaptic (CMS6)
VAR_011667 Myasthenic syndrome, congenital, 6, presynaptic (CMS6)
VAR_011668 Myasthenic syndrome, congenital, 6, presynaptic (CMS6)
VAR_011669 Myasthenic syndrome, congenital, 6, presynaptic (CMS6)
VAR_011670 Myasthenic syndrome, congenital, 6, presynaptic (CMS6)

Structural Variations from Database of Genomic Variants (DGV) for CHAT Gene

Variant ID Type Subtype PubMed ID
nsv7203 OTHER Inversion 18451855
nsv895365 CNV Loss 21882294
nsv895369 CNV Gain 21882294
nsv895375 CNV Gain 21882294
nsv895378 CNV Gain 21882294
esv1348586 CNV Insertion 17803354
nsv510217 CNV Loss 20534489

Variation tolerance for CHAT Gene

Residual Variation Intolerance Score: 97.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.10; 87.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHAT Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHAT Gene

Disorders for CHAT Gene

MalaCards: The human disease database

(27) MalaCards diseases for CHAT Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CHAT in MalaCards View complete list of genes associated with diseases


  • Myasthenic syndrome, congenital, 6, presynaptic (CMS6) [MIM:254210]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. CMS6 affected individuals have myasthenic symptoms since birth or early infancy, negative tests for anti-AChR antibodies, and abrupt episodic crises with increased weakness, bulbar paralysis, and apnea precipitated by undue exertion, fever, or excitement. CMS6 inheritance is autosomal recessive. {ECO:0000269 PubMed:11172068, ECO:0000269 PubMed:12756141}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CHAT

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CHAT: view

No data available for Genatlas for CHAT Gene

Publications for CHAT Gene

  1. A complementary DNA for human choline acetyltransferase induces two forms of enzyme with different molecular weights in cultured cells. (PMID: 1337937) Oda Y. … Deguchi T. (Brain Res. Mol. Brain Res. 1992) 3 4 23 67
  2. Substrate binding and catalytic mechanism of human choline acetyltransferase. (PMID: 17144655) Kim A.-R. … Shilton B.H. (Biochemistry 2006) 3 23 25
  3. Variability of AChE, BChE, and ChAT genes in the late-onset form of Alzheimer's disease and relationships with response to treatment with Donepezil and Rivastigmine. (PMID: 18780301) Scacchi R. … Corbo R.M. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009) 3 23
  4. ChAT and NOS in human myenteric neurons: co-existence and co-absence. (PMID: 19711100) Beck M. … Brehmer A. (Cell Tissue Res. 2009) 3 23
  5. Choline acetyltransferase activity in vascular dementia and stroke. (PMID: 19776575) Sharp S.I. … Ballard C.G. (Dement Geriatr Cogn Disord 2009) 3 23

Products for CHAT Gene

Sources for CHAT Gene