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Aliases for CHAT Gene

Aliases for CHAT Gene

  • Choline O-Acetyltransferase 2 3 5
  • Choline Acetylase 3 4
  • EC 4 56
  • Acetyl CoA:Choline O-Acetyltransferase 3
  • Choline Acetyltransferase 2
  • EC 2.3.1 56
  • 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 Congenital Myasthenic Syndrome With Episodic Apnea. Among its related pathways are Circadian entrainment and Transmission across Chemical Synapses. Gene Ontology (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

Additional gene information for CHAT Gene

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

Genomics for CHAT Gene

GeneHancer (GH) Regulatory Elements for CHAT Gene

Promoters and enhancers for CHAT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I049612 Promoter/Enhancer 1 EPDnew ENCODE 550.8 +4.0 3957 0.1 CTCF KLF1 GLIS2 SP2 KLF9 EZH2 CHAT SLC18A3 GC10P049595 C10orf53
GH10I049610 Promoter 0.7 EPDnew 550.8 +1.2 1196 0.1 ZFHX2 EZH2 CHAT SLC18A3 GC10P049595
GH10I049608 Promoter 0.6 EPDnew 550.8 -0.1 -70 0.1 EZH2 CHAT SLC18A3 GC10P049595
GH10I049567 Enhancer 1.2 FANTOM5 Ensembl ENCODE 5.5 -40.2 -40189 2.2 MXI1 JUN MAX RFX5 RELA NFYB RCOR1 FOS RUNX3 NFE2L2 ERCC6 SLC18A3 CHAT PGBD3 HMGB1P50 GC10P049595
GH10I049690 Enhancer 0.5 ENCODE 10.4 +81.3 81275 0.2 SP1 POLR2A POU5F1 EZH2 OGDHL MAPK6PS6 CHAT SLC18A3 GC10M049685 C10orf53
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CHAT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHAT gene promoter:

Genomic Locations for CHAT Gene

Genomic Locations for CHAT Gene
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

Selected DME Specific Peptides for CHAT Gene


Post-translational modifications for CHAT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for CHAT Gene

Gene Families for CHAT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

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

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

Phenotypes From GWAS Catalog for CHAT Gene

Gene Ontology (GO) - Molecular Function for CHAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004102 choline O-acetyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups 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

Clone Products

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

Localization for CHAT Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHAT gene
Compartment Confidence
nucleus 5
cytosol 5
peroxisome 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CHAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10861222
GO:0005737 cytoplasm TAS 10861222
GO:0005829 cytosol TAS --
GO:0045202 synapse IEA --
GO:0098793 presynapse IEA --
genes like me logo Genes that share ontologies with CHAT: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) 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:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0007269 neurotransmitter secretion TAS --
GO:0042136 neurotransmitter biosynthetic process IEA --
genes like me logo Genes that share ontologies with CHAT: view

Drugs & Compounds for CHAT Gene

(60) 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 176
Donepezil Approved Pharma 295
Nicotine Approved Pharma Antagonist, Target 1188
Olanzapine Approved, Investigational Pharma Antagonist 408
Acetylcholine Approved Pharma Full agonist, Agonist 863

(47) 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Protein tissue co-expression partners for CHAT Gene

NURSA nuclear receptor signaling pathways regulating expression of CHAT Gene:


SOURCE GeneReport for Unigene cluster for CHAT Gene:


Evidence on tissue expression from TISSUES for CHAT Gene

  • Nervous system(4.7)
  • Blood(4.3)
  • Eye(2.3)
  • Intestine(2)
  • Muscle(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CHAT Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
  • chest wall
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
  • sternum
  • stomach
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with CHAT: view

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
(Pan troglodytes)
Mammalia CHAT 33 34
  • 99.1 (n)
(Bos Taurus)
Mammalia CHAT 33 34
  • 88.37 (n)
(Canis familiaris)
Mammalia CHAT 33 34
  • 87.58 (n)
(Rattus norvegicus)
Mammalia Chat 33
  • 86.14 (n)
(Mus musculus)
Mammalia Chat 33 16 34
  • 85.98 (n)
(Monodelphis domestica)
Mammalia CHAT 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CHAT 34
  • 79 (a)
(Gallus gallus)
Aves CHAT 33 34
  • 72.26 (n)
(Anolis carolinensis)
Reptilia CHAT 34
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia chat 33
  • 67.19 (n)
(Danio rerio)
Actinopterygii chat 33 34
  • 64.78 (n)
CHAT (2 of 2) 34
  • 58 (a)
zgc64220 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002370 33
  • 52.94 (n)
fruit fly
(Drosophila melanogaster)
Insecta Cha 35 33 34
  • 52.59 (n)
CG5122 35
  • 38 (a)
CG5265 35
  • 32 (a)
(Caenorhabditis elegans)
Secernentea cha-1 35 33 34
  • 45.84 (n)
B0395.3 35
  • 34 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAT2 34
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14198 33
Species where no ortholog for CHAT was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1057517665 pathogenic, Myasthenic syndrome, congenital, 21, presynaptic 49,611,297(+) G/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1057517666 pathogenic, Myasthenic syndrome, congenital, 21, presynaptic 49,611,932(+) G/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs113897064 likely-benign, benign, not specified, Familial infantile myasthenia 49,625,623(+) T/C coding_sequence_variant, synonymous_variant
rs114090981 benign, Familial infantile myasthenia 49,625,509(+) G/A/C coding_sequence_variant, synonymous_variant
rs115126024 benign, not specified, Familial infantile myasthenia 49,646,524(+) G/A coding_sequence_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
esv1348586 CNV insertion 17803354
nsv1042677 CNV loss 25217958
nsv1134007 CNV deletion 24896259
nsv1145454 CNV deletion 24896259
nsv510217 OTHER sequence alteration 20534489
nsv550819 CNV loss 21841781
nsv950954 CNV deletion 24416366

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)

Additional Variant Information for CHAT Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHAT Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
myasthenic syndrome, congenital, 6, presynaptic
  • cms6
congenital myasthenic syndrome with episodic apnea
  • myasthenic syndrome, presynaptic, congenital, associated with episodic apnea
congenital myasthenic syndrome
  • familial limb-girdle myasthenia
presynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, presynaptic
amnestic disorder
  • amnesia
- 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.

Additional Disease Information for CHAT

Genetic Association Database
Human Genome Epidemiology 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. 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 RM (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 22 44 58
  2. Alzheimer's disease: case-control association study of polymorphisms in ACHE, CHAT, and BCHE genes in a Sardinian sample. (PMID: 17503475) Piccardi M … Del Zompo M (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2007) 3 22 44 58
  3. Choline acetyltransferase variants and their influence in schizophrenia and olanzapine response. (PMID: 17503482) Mancama D … Arranz MJ (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2007) 3 22 44 58
  4. Substrate binding and catalytic mechanism of human choline acetyltransferase. (PMID: 17144655) Kim AR … Shilton BH (Biochemistry 2006) 3 4 22 58
  5. A single nucleotide polymorphism in CHAT influences response to acetylcholinesterase inhibitors in Alzheimer's disease. (PMID: 16424819) Harold D … Jones L (Pharmacogenetics and genomics 2006) 3 22 44 58

Products for CHAT Gene

Sources for CHAT Gene

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