Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1103
Gene name	Choline O-acetyltransferase
Gene symbol	CHAT
Synonyms (NCBI Gene)	CHOACTASECMS1ACMS1A2CMS6
Chromosome	10
Chromosome location	10q11.23
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.

Show/Hide all (28)

SNP ID	Visualize variation	Clinical significance	Consequence
rs75466054	T>C,G	Pathogenic	Missense variant, coding sequence variant
rs76570508	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, synonymous variant
rs116071049	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs121912815	C>G	Pathogenic	Missense variant, coding sequence variant
rs121912816	G>A,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs121912817	G>A,T	Pathogenic	Missense variant, coding sequence variant
rs121912819	G>A	Pathogenic	Missense variant, coding sequence variant
rs121912820	T>C	Pathogenic	Missense variant, coding sequence variant
rs121912821	C>T	Pathogenic	Missense variant, coding sequence variant
rs121912822	C>T	Pathogenic	Missense variant, coding sequence variant
rs121912823	T>C	Pathogenic	Missense variant, coding sequence variant
rs201439531	C>G	Pathogenic	Coding sequence variant, missense variant
rs201479289	G>A	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Coding sequence variant, missense variant
rs369251527	C>T	Pathogenic	Coding sequence variant, stop gained
rs376808313	T>C,G	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs560648873	CCT>-	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion
rs753652169	C>A,G,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs760936252	C>G,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs764497513	G>A,C	Conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, missense variant
rs769234940	C>T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs772025588	A>C,T	Pathogenic, likely-benign	Stop gained, synonymous variant, intron variant, 5 prime UTR variant, coding sequence variant
rs794727516	C>T	Pathogenic	Stop gained, coding sequence variant
rs1198717023	C>-	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant
rs1272947184	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1279554995	A>G	Likely-pathogenic, uncertain-significance	Intron variant
rs1554802792	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1554802808	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1590576560	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017364	hsa-miR-335-5p	Microarray	18185580
MIRT046123	hsa-miR-30b-5p	CLASH	23622248

Show/Hide all (3)

Transcription factor	Regulation	Reference
ESR1	Unknown	10037443
ESR2	Unknown	10037443
STAT1	Unknown	12425940

Show/Hide all (16)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004102	Function	Choline O-acetyltransferase activity	IBA
GO:0004102	Function	Choline O-acetyltransferase activity	IEA
GO:0004102	Function	Choline O-acetyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	TAS	10861222
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	TAS	10861222
GO:0005829	Component	Cytosol	TAS
GO:0006656	Process	Phosphatidylcholine biosynthetic process	TAS
GO:0006836	Process	Neurotransmitter transport	TAS
GO:0007274	Process	Neuromuscular synaptic transmission	IBA
GO:0008292	Process	Acetylcholine biosynthetic process	IBA
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0043005	Component	Neuron projection	IBA
GO:0045202	Component	Synapse	IEA

MIM	HGNC	e!Ensembl
118490	1912	ENSG00000070748

P28329

Protein name

Choline O-acetyltransferase (CHOACTase) (ChAT) (Choline acetylase) (EC 2.3.1.6)

Protein function

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

PDB

2FY2 , 2FY3 , 2FY4 , 2FY5 , 7AMD

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00755	Carn_acyltransf	131 → 719	Choline/Carnitine o-acyltransferase	Family

Sequence

MGLRTAKKRGLGGGGKWKREEGGGTRGRREVRPACFLQSGGRGDPGDVGGPAGNPGCSPH
PRAATRPPPLPAHTPAHTPEWCGAASAEAAEPRRAGPHLCIPAPGLTKTPILEKVPRKMA
AKTPSSEESGLPKLPVPPLQQTLATYLQCMRHLVSEEQFRKSQAIVQQFGAPGGLGETLQ
QKLLERQEKTANWVSEYWLNDMYLNNRLALPVNSSPAVIFARQHFPGTDDQLRFAASLIS
GVLSYKALLDSHSIPTDCAKGQLSGQPLCMKQYYGLFSSYRLPGHTQDTLVAQNSSIMPE
PEHVIVACCNQFFVLDVVINFRRLSEGDLFTQLRKIVKMASNEDERLPPIGLLTSDGRSE
WAEARTVLVKDSTNRDSLDMIERCICLVCLDAPGGVELSDTHRALQLLHGGGYSKNGANR
WYDKSLQFVVGRDGTCGVVCEHSPFDGIVLVQCTEHLLKHVTQSSRKLIRADSVSELPAP
RRLRWKCSPEIQGHLASSAEKLQRIVKNLDFIVYKFDNYGKTFIKKQKCSPDAFIQVALQ
LAFYRLHRRLVPTYESASIRRFQEGRVDNIRSATPEALAFVRAVTDHKAAVPASEKLLLL
KDAIRAQTAYTVMAITGMAIDNHLLALRELARAMCKELPEMFMDETYLMSNRFVLSTSQV
PTTTEMFCCYGPVVPNGYGACYNPQPETILFCISSFHSCKETSSSKFAKAVEESLIDMRD
LCSLLPPTESKPLATKEKATRPSQGHQP

Sequence length

748

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism Cholinergic synapse		Synthesis of PC Acetylcholine Neurotransmitter Release Cycle

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the musculature	Likely pathogenic; Pathogenic	rs121912823	RCV001813998	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital myasthenic syndrome	Likely pathogenic; Pathogenic	rs1409506586, rs2538864425, rs777679246, rs764497513, rs1306112783, rs904408037, rs121912819, rs121912821, rs75466054, rs121912822, rs376808313, rs1279554995, rs369251527, rs372760913, rs753652169	RCV005912594 RCV002283393 RCV002470113 RCV003155154 RCV006262823 View all (10 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Congenital myasthenic syndrome 4C	Likely pathogenic; Pathogenic	rs1590576560, rs753652169	RCV001004338 RCV001004339	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial infantile myasthenia	Likely pathogenic; Pathogenic	rs2132811750, rs1409506586, rs1838635016, rs2132735050, rs777684375, rs142889639, rs757303526, rs747108035, rs2132852540, rs1458796820, rs1207292931, rs2132820703, rs371470622, rs2132735749, rs2538864425 View all (69 more)	RCV001379275 RCV001377468 RCV001380873 RCV001385922 RCV001387068 View all (83 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (28)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ALZHEIMERS DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANGLE CLOSURE GLAUCOMA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHAT-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGEN MYASTHENIC SYNDROMES PRESYNAPTIC	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL MYASTHENIC SYNDROME 6	—	ClinGen, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL MYASTHENIC SYNDROME WITH EPISODIC APNEA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEPRESSIVE DISORDER	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETIC NEPHROPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FEBRILE CONVULSIONS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA, ANGLE-CLOSURE	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HODGKINS LYMPHOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL DEPRESSION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYASTHENIC SYNDROME, CONGENITAL, 21, PRESYNAPTIC	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYASTHENIC SYNDROME, CONGENITAL, 6, PRESYNAPTIC	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYASTHENIC SYNDROME, CONGENITAL, ASSOCIATED WITH ACETYLCHOLINE RECEPTOR DEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYASTHENIC SYNDROMES, CONGENITAL	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRESYNAPTIC CONGENITAL MYASTHENIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRESYNAPTIC CONGENITAL MYASTHENIC SYNDROMES	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEIZURES	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLEEP APNEA, CENTRAL	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

CHAT (choline O-acetyltransferase)