CHAT choline O-acetyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHATprovided by HGNC
Official Full Name: choline O-acetyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:1912
See related: Ensembl:ENSG00000070748 MIM:118490; AllianceGenome:HGNC:1912
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CMS6; CMS1A; CMS1A2; CHOACTASE
Summary: 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]
Expression: Biased expression in placenta (RPKM 2.7), small intestine (RPKM 0.2) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 10q11.23

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (49609095..49667942)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (50457901..50516753)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (50817141..50875988)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Choline-acetyltransferase (ChAT) and acetylcholinesterase (AChE) in the human infant dorsal motor nucleus of the Vagus (DMNV), and alterations according to sudden infant death syndrome (SIDS) category.
Title: Choline-acetyltransferase (ChAT) and acetylcholinesterase (AChE) in the human infant dorsal motor nucleus of the Vagus (DMNV), and alterations according to sudden infant death syndrome (SIDS) category.
Genetic associations in CHAT and COL11A1 with primary angle-closure glaucoma susceptibility: A systematic review and meta-analysis.
Title: Genetic associations in CHAT and COL11A1 with primary angle-closure glaucoma susceptibility: A systematic review and meta-analysis.
Immunohistochemical Expression of Choline Acetyltransferase and Catecholamine-Synthesizing Enzymes in Head-and-Neck and Thoracoabdominal Paragangliomas and Pheochromocytomas.
Title: Immunohistochemical Expression of Choline Acetyltransferase and Catecholamine-Synthesizing Enzymes in Head-and-Neck and Thoracoabdominal Paragangliomas and Pheochromocytomas.
Coronary vasodilation mediated by T cells expressing choline acetyltransferase.
Title: Coronary vasodilation mediated by T cells expressing choline acetyltransferase.
The SNP rs3753841 in COL11A1, rs1258267 in CHAT and rs736893 in GLIS3 are associated with PACG in northern Chinese people, and the association of genetic markers manifests a tendency of ethnic diversity. Larger population-based studies are warranted to reveal additional primary angle-closure glaucoma loci and ethnic aspects of primary angle-closure glaucoma.
Title: Genotype-ocular biometry correlation analysis of eight primary angle closure glaucoma susceptibility loci in a cohort from Northern China.
CHAT SNP rs12246528 had the strongest association with parahippocampal structure, with the A allele being linked to smaller volume, surface area, and thickness. SNP rs1917814 had the strongest association with hippocampal volume, with the T allele being linked to larger hippocampal volume. CHAT rs3729496 had the strongest association with memory span, with the T allele being associated with a greater memory span.
Title: The Choline Acetyltransferase (CHAT) Gene is Associated with Parahippocampal and Hippocampal Structure and Short-term Memory Span.
CHAT may contribute to Tourette syndrome susceptibility in the Han Chinese population.
Title: Choline acetyltransferase may contribute to the risk of Tourette syndrome: Combination of family-based analysis and case-control study.
the AA genotype of CHAT was associated with a 1.25 times higher risk of Alzheimer's disease (AD) thus demonstrating that the rs3810950 polymorphism can have a modest but statistically significant effect on the risk of AD in the Czech population
Title: CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer's disease in the Czech population.
Compared with the control group, the densitometric quantification and mean density of GPR43 and ChAT proteins, and expression of GPR43 and CHAT genes, were significantly decreased in the patients with mixed refractory constipation.
Title: Function and clinical implications of short-chain fatty acids in patients with mixed refractory constipation.
meta-analysis suggested that rs1880670G/A, and rs2177369 G/A polymorphisms were not risk factors for Alzheimer's Disease. However, rs3810950G/A, or rs868750G/A genetic polymorphism was a genetic risk factor for the development of Alzheimer's Disease.
Title: Association of Choline Acetyltransferase Gene Polymorphisms (SNPs rs868750G/A, rs1880676G/A, rs2177369G/A and rs3810950G/A) with Alzheimer's Disease Risk: A Meta-Analysis.

Submit: New GeneRIF Correction See all GeneRIFs (70)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Familial infantile myasthenia MedGen: C0393929 OMIM: 254210 GeneReviews: Congenital Myasthenic Syndromes Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S1607 (e-PCR)
- UniSTS:38965

fc03d10.x1 (e-PCR)
- UniSTS:192112

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables choline O-acetyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables choline O-acetyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in acetylcholine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuromuscular synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in neurotransmitter transport	TAS Traceable Author Statement more info
involved_in phosphatidylcholine biosynthetic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: choline O-acetyltransferase

Names: acetyl CoA:choline O-acetyltransferase; choline acetylase

NP_001136401.2

EC 2.3.1.6

NP_001136405.2

EC 2.3.1.6

NP_001136406.2

EC 2.3.1.6

NP_065574.4

EC 2.3.1.6

NP_066264.4

EC 2.3.1.6

NP_066265.4

EC 2.3.1.6

NP_066266.4

EC 2.3.1.6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011797.2 RefSeqGene

Range

9944..63849

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001142929.2 → NP_001136401.2 choline O-acetyltransferase isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (M) contains alternate 5' exon M (PMID 7616604) but uses a downstream start codon and encodes isoform 1. Transcript variants R, N1, N2, M and S encode isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS7233.1

UniProtKB/TrEMBL

B4DJJ6

Conserved Domains (1) summary

pfam00755
Location:13 → 601

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_001142933.2 → NP_001136405.2 choline O-acetyltransferase isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (S) contains alternate 5' exons M and S in the 5' coding region, and uses an upstream start codon (PMID 11172068). The resulting protein (isoform 3) has a longer N-terminus compared to isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS44389.1

UniProtKB/TrEMBL

B4DJJ6

Related

ENSP00000378929.2, ENST00000395562.2

Conserved Domains (1) summary

pfam00755
Location:49 → 637

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_001142934.2 → NP_001136406.2 choline O-acetyltransferase isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (S) contains alternate 5' exons M and S in the 5' coding region but uses a downstream start codon and encodes isoform 1 (PMID 11172068). Transcript variants R, N1, N2, M and S encode isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS7233.1

UniProtKB/TrEMBL

B4DJJ6

Conserved Domains (1) summary

pfam00755
Location:13 → 601

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_020549.5 → NP_065574.4 choline O-acetyltransferase isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (M) contains alternate 5' exon M (PMID 7616604) and uses an upstream start codon. The resulting protein (isoform 2) has a longer N-terminus compared to isoform 1

Source sequence(s)

AC073366

Consensus CDS

CCDS7232.1

UniProtKB/Swiss-Prot

A2BDF4, A2BDF5, P28329, Q16488, Q9BQ23, Q9BQ35, Q9BQE1

Related

ENSP00000337103.2, ENST00000337653.7

Conserved Domains (2) summary

PHA03247
Location:27 → 138

PHA03247; large tegument protein UL36; Provisional

pfam00755
Location:131 → 719

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_020984.4 → NP_066264.4 choline O-acetyltransferase isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (R) contains alternate 5' exon R (PMID 7616604) and encodes isoform 1. Transcript variants R, N1, N2, M and S encode isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS7233.1

UniProtKB/TrEMBL

B4DJJ6

Related

ENSP00000343486.1, ENST00000339797.5

Conserved Domains (1) summary

pfam00755
Location:13 → 601

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_020985.4 → NP_066265.4 choline O-acetyltransferase isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (N1) contains alternate 5' exon N and uses an alternate splice site within alternate exon M, and encodes isoform 1 (PMID 9073174). Transcript variants R, N1, N2, M and S encode isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS7233.1

UniProtKB/TrEMBL

B4DJJ6

Related

ENSP00000345878.3, ENST00000351556.7

Conserved Domains (1) summary

pfam00755
Location:13 → 601

Carn_acyltransf; Choline/Carnitine o-acyltransferase
NM_020986.4 → NP_066266.4 choline O-acetyltransferase isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (N2) contains alternate 5' exon N and encodes isoform 1 (PMID 9073174). Transcript variants R, N1, N2, M and S encode isoform 1.

Source sequence(s)

AC073366

Consensus CDS

CCDS7233.1

UniProtKB/TrEMBL

B4DJJ6

Related

ENSP00000378926.2, ENST00000395559.6

Conserved Domains (1) summary

pfam00755
Location:13 → 601

Carn_acyltransf; Choline/Carnitine o-acyltransferase