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

935

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the musculature	Likely pathogenic; Pathogenic	rs121912823	RCV001813998
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 RCV004783108 RCV005417435 RCV005237394 RCV000235033 RCV004799748 RCV002469176 RCV005407652 RCV003155228 RCV003479154 RCV005408765
Congenital myasthenic syndrome 4C	Likely pathogenic; Pathogenic	rs1590576560, rs753652169	RCV001004338 RCV001004339
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 RCV001780494 RCV001780769 RCV001877174 RCV002033442 RCV002000015 RCV002024417 RCV002007489 RCV002007604 RCV002009419 RCV003471308 RCV002571448 RCV002471349 RCV002471451 RCV003062258 RCV003058248 RCV002629111 RCV003631091 RCV003118054 RCV002771633 RCV000291500 RCV003468381 RCV003468382 RCV003468383 RCV003468384 RCV003468387 RCV003468388 RCV003468389 RCV003468390 RCV003468392 RCV003468393 RCV003468394 RCV003517548 RCV003518591 RCV003518728 RCV003516739 RCV003517603 RCV003517103 RCV003517659 RCV003631412 RCV003631449 RCV003631823 RCV003631974 RCV003631943 RCV003631944 RCV003632112 RCV003632210 RCV003632450 RCV003632838 RCV003832678 RCV003858150 RCV003990330 RCV000019058 RCV000019060 RCV000019061 RCV000019062 RCV000019064 RCV000019065 RCV000019066 RCV000019067 RCV004575634 RCV004575635 RCV004575636 RCV004575637 RCV004575638 RCV004575639 RCV004575640 RCV004575641 RCV000813390 RCV000688376 RCV000499766 RCV000552083 RCV000529557 RCV000527144 RCV000636628 RCV003517254 RCV000660559 RCV000804335 RCV003467554 RCV003769403 RCV001064081 RCV001230067 RCV001232268 RCV001232267

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
CHAT-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs143662656, rs41306415, rs201381950, rs116390167, rs115510708, rs61731734, rs764193541, rs1055036701, rs1371387178, rs79414242, rs150236872, rs1554804021, rs376994468, rs141794970, rs141690626 View all (3 more)	RCV003898397 RCV003921209 RCV003971147 RCV003970945 RCV003895243 RCV003891963 RCV004753691 RCV003909157 RCV003967012 RCV003912591 RCV003942773 RCV003403523 RCV003908367 RCV003908280 RCV004753061 RCV003948279 RCV003923252 RCV004753176
Gastric cancer	Benign	rs3810948	RCV005888017
Thymoma	Benign	rs3810948	RCV005888018

Show/Hide Text Mining Associations (32)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acute cholinergic dysautonomia	Associate	35563582
Alzheimer Disease	Inhibit	1409664, 20164549, 21700583, 8618881
Alzheimer Disease	Associate	16223550, 18322398, 21691765, 21883924, 29759072
Apnea	Associate	26080897
Ataxia	Associate	21948486
Bipolar Disorder	Associate	34387669
Choline Deficiency	Associate	21786365
Colorectal Neoplasms	Associate	18653726, 37828429
Congenital myasthenic syndrome with episodic apnea	Associate	21786365, 29189923
Constipation	Associate	21948486
Deglutition Disorders	Associate	21948486
Dementia	Associate	29343737
Emergence Delirium	Associate	32988381
Epilepsy	Associate	21948486
Esophageal Achalasia	Stimulate	16105888
Kleefstra Syndrome	Associate	39343771
Leiomyoma	Associate	30841718
Lung Neoplasms	Stimulate	25591716
Multiple Sclerosis	Associate	21691765
Muscle Hypotonia	Associate	21948486
Myasthenic Syndromes Congenital	Associate	15381704, 21786365, 26080897, 36308527
Neoplasms	Associate	20233874
Neuroblastoma	Associate	21163949
Nystagmus Pathologic	Associate	21948486
Parkinson Disease	Associate	37013599
Ptosis Hereditary Congenital 2	Associate	21948486
Pulmonary Disease Chronic Obstructive	Stimulate	22440430
Renal Insufficiency	Associate	15381704
Sepsis	Associate	29885947
Sleep Apnea Syndromes	Associate	21948486
Systemic Inflammatory Response Syndrome	Associate	29885947
Vesico Ureteral Reflux	Associate	21948486

CHAT (choline O-acetyltransferase)