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	1134
Gene name	Cholinergic receptor nicotinic alpha 1 subunit
Gene symbol	CHRNA1
Synonyms (NCBI Gene)	ACHRAACHRDCHRNACMS1ACMS1BCMS2AFCCMSSCCMS
Chromosome	2
Chromosome location	2q31.1
Summary	The muscle acetylcholine receptor consiststs of 5 subunits of 4 different types: 2 alpha subunits and 1 each of the beta, gamma, and delta subunits. This gene encodes an alpha subunit that plays a role in acetlycholine binding/channel gating. Alternativel

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SNP ID	Visualize variation	Clinical significance	Consequence
rs137852798	G>A,C,T	Uncertain-significance, pathogenic	Synonymous variant, coding sequence variant, missense variant
rs137852799	C>A,G,T	Pathogenic	Coding sequence variant, missense variant
rs137852800	G>A	Pathogenic	Coding sequence variant, missense variant
rs137852801	C>T	Pathogenic	Coding sequence variant, missense variant
rs137852802	C>A	Pathogenic	Coding sequence variant, missense variant
rs137852803	C>A,G,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs137852804	C>T	Pathogenic	Coding sequence variant, missense variant
rs137852805	A>C	Pathogenic	Coding sequence variant, missense variant
rs137852806	A>G	Pathogenic	Coding sequence variant, missense variant
rs137852807	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs137852808	G>A,C	Pathogenic	Synonymous variant, coding sequence variant, missense variant
rs137852809	C>A,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs141733086	G>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs149292107	A>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs150638770	G>A,T	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, missense variant, coding sequence variant
rs199470445	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs374391312	G>A,C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs483353046	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs545520806	G>A	Likely-pathogenic	Synonymous variant, coding sequence variant
rs750329103	G>A	Pathogenic	Coding sequence variant, stop gained
rs768407867	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs886043372	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs1064793397	->C	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1064795046	C>T	Likely-pathogenic	Splice acceptor variant
rs1131691893	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1291364532	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1553469070	C>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1574007436	TT>-	Likely-pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (22)

miRTarBase ID	miRNA	Experiments
MIRT891681	hsa-miR-3646	CLIP-seq
MIRT891682	hsa-miR-875-3p	CLIP-seq
MIRT2200384	hsa-miR-3922-5p	CLIP-seq
MIRT2200385	hsa-miR-4753-5p	CLIP-seq
MIRT2447005	hsa-miR-3194-3p	CLIP-seq
MIRT2447006	hsa-miR-4490	CLIP-seq
MIRT2447007	hsa-miR-4774-5p	CLIP-seq
MIRT2447008	hsa-miR-767-3p	CLIP-seq
MIRT2447009	hsa-miR-938	CLIP-seq
MIRT2447010	hsa-miR-942	CLIP-seq
MIRT2447005	hsa-miR-3194-3p	CLIP-seq
MIRT2447006	hsa-miR-4490	CLIP-seq
MIRT2447007	hsa-miR-4774-5p	CLIP-seq
MIRT2447008	hsa-miR-767-3p	CLIP-seq
MIRT2447009	hsa-miR-938	CLIP-seq
MIRT2447010	hsa-miR-942	CLIP-seq
MIRT2447005	hsa-miR-3194-3p	CLIP-seq
MIRT2447006	hsa-miR-4490	CLIP-seq
MIRT2447007	hsa-miR-4774-5p	CLIP-seq
MIRT2447008	hsa-miR-767-3p	CLIP-seq
MIRT2447009	hsa-miR-938	CLIP-seq
MIRT2447010	hsa-miR-942	CLIP-seq

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Transcription factor	Regulation	Reference
AIRE	Unknown	17687331

Show/Hide all (68)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003009	Process	Skeletal muscle contraction	IBA
GO:0003009	Process	Skeletal muscle contraction	IEA
GO:0003009	Process	Skeletal muscle contraction	IMP	8872460
GO:0004888	Function	Transmembrane signaling receptor activity	IEA
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005230	Function	Extracellular ligand-gated monoatomic ion channel activity	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS	8872460
GO:0005886	Component	Plasma membrane	TAS
GO:0005892	Component	Acetylcholine-gated channel complex	IBA
GO:0005892	Component	Acetylcholine-gated channel complex	IEA
GO:0005892	Component	Acetylcholine-gated channel complex	ISS	8872460
GO:0005892	Component	Acetylcholine-gated channel complex	TAS	7619526
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006812	Process	Monoatomic cation transport	IEA
GO:0007271	Process	Synaptic transmission, cholinergic	IBA
GO:0007274	Process	Neuromuscular synaptic transmission	IBA
GO:0007274	Process	Neuromuscular synaptic transmission	IMP	9221765
GO:0007528	Process	Neuromuscular junction development	IMP	9221765
GO:0009986	Component	Cell surface	IDA	12928480
GO:0009986	Component	Cell surface	IEA
GO:0015464	Function	Acetylcholine receptor activity	IBA
GO:0015464	Function	Acetylcholine receptor activity	IEA
GO:0015464	Function	Acetylcholine receptor activity	ISS	8872460
GO:0015464	Function	Acetylcholine receptor activity	TAS	7619526
GO:0016020	Component	Membrane	IEA
GO:0019228	Process	Neuronal action potential	IMP	8872460
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	IBA
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	IEA
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	IEA
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	IMP	9221765
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	ISS	8872460
GO:0022848	Function	Acetylcholine-gated monoatomic cation-selective channel activity	TAS	7619526
GO:0031594	Component	Neuromuscular junction	IDA	9221765
GO:0031594	Component	Neuromuscular junction	IDA	9221765
GO:0031594	Component	Neuromuscular junction	IEA
GO:0031594	Component	Neuromuscular junction	IMP	9221765
GO:0031594	Component	Neuromuscular junction	ISS	8872460
GO:0034220	Process	Monoatomic ion transmembrane transport	IBA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0035094	Process	Response to nicotine	IBA
GO:0042166	Function	Acetylcholine binding	IEA
GO:0042166	Function	Acetylcholine binding	ISS	8872460
GO:0042391	Process	Regulation of membrane potential	IEA
GO:0042391	Process	Regulation of membrane potential	IEA
GO:0042391	Process	Regulation of membrane potential	IMP	9221765
GO:0042391	Process	Regulation of membrane potential	IMP	8872460
GO:0043005	Component	Neuron projection	IBA
GO:0045202	Component	Synapse	IBA
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0045211	Component	Postsynaptic membrane	NAS	18252226
GO:0046716	Process	Muscle cell cellular homeostasis	IMP	8872460
GO:0048630	Process	Skeletal muscle tissue growth	IMP	18252226
GO:0050881	Process	Musculoskeletal movement	IMP	18252226
GO:0050905	Process	Neuromuscular process	IMP	9546329
GO:0051899	Process	Membrane depolarization	IBA
GO:0060078	Process	Regulation of postsynaptic membrane potential	IEA
GO:0060079	Process	Excitatory postsynaptic potential	IEA
GO:0070050	Process	Neuron cellular homeostasis	IMP	8872460
GO:0095500	Process	Acetylcholine receptor signaling pathway	IBA
GO:0098793	Component	Presynapse	IEA
GO:0099171	Process	Presynaptic modulation of chemical synaptic transmission	IBA
GO:0099634	Component	Postsynaptic specialization membrane	IEA
GO:1904315	Function	Transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IDA	9221765
GO:1904315	Function	Transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IMP	9221765

MIM	HGNC	e!Ensembl
100690	1955	ENSG00000138435

P02708

Protein name

Acetylcholine receptor subunit alpha

Protein function

[Isoform 1]: Upon acetylcholine binding, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. ; [

PDB

4ZJS , 5HBT

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02931	Neur_chan_LBD	24 → 79	Neurotransmitter-gated ion-channel ligand binding domain	Family
PF02931	Neur_chan_LBD	97 → 256	Neurotransmitter-gated ion-channel ligand binding domain	Family
PF02932	Neur_chan_memb	263 → 403	Neurotransmitter-gated ion-channel transmembrane region	Family
PF02932	Neur_chan_memb	394 → 471	Neurotransmitter-gated ion-channel transmembrane region	Family

Tissue specificity

TISSUE SPECIFICITY: Isoform 1 is only expressed in skeletal muscle. Isoform 2 is constitutively expressed in skeletal muscle, brain, heart, kidney, liver, lung and thymus.

Sequence

MEPWPLLLLFSLCSAGLVLGSEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQL
INVDEVNQIVTTNVRLKQGDMVDLPRPSCVTLGVPLFSHLQNEQWVDYNLKWNPDDYGGV
KKIHIPSEKIWRPDLVLYNNADGDFAIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHF
PFDEQNCSMKLGTWTYDGSVVAINPESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPD
TPYLDITYHFVMQRLPLYFIVNVIIPCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTV
FLLVIVELIPSTSSAVPLIGKYMLFTMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKV
FIDTIPNIMFFSTMKRPSREKQDKKIFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSA
IEGIKYIAETMKSDQESNNAAAEWKYVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQ
QG

Sequence length

482

Interactions

View interactions

	KEGG		Reactome
	Virion - Ebolavirus, Lyssavirus and Morbillivirus Neuroactive ligand-receptor interaction		Highly calcium permeable postsynaptic nicotinic acetylcholine receptors Highly calcium permeable nicotinic acetylcholine receptors

548

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism	Likely pathogenic; Pathogenic	rs768407867	RCV000679850
Centronuclear myopathy	Likely pathogenic; Pathogenic	rs768407867	RCV004586756
Congenital myasthenic syndrome	Likely pathogenic; Pathogenic	rs1574007436	RCV000825633
Congenital myasthenic syndrome 1A	Likely pathogenic; Pathogenic	rs2105350715, rs137852798, rs137852800, rs137852801, rs137852802, rs137852808, rs1064793397	RCV004813177 RCV000020044 RCV000020046 RCV000020047 RCV000020048 RCV000020055 RCV002496853
Congenital myopathy	Likely pathogenic; Pathogenic	rs137852801	RCV004586016
Lethal multiple pterygium syndrome	Pathogenic; Likely pathogenic	rs753250273, rs2105350715, rs1684009556, rs199470442, rs2468895247, rs1574011727, rs768863116, rs1457407106, rs137852801, rs137852805, rs1684052200, rs374391312, rs1064793397, rs750329103, rs768407867 View all (5 more)	RCV001384441 RCV001533178 RCV001934247 RCV003110599 RCV003043768 RCV003317980 RCV003518162 RCV003517021 RCV000556947 RCV003517130 RCV000020057 RCV000803477 RCV001383195 RCV003114619 RCV000542688 RCV000534544 RCV005253650 RCV001070130 RCV001036947 RCV001229186 RCV003516662
Myasthenic syndrome, congenital, 1B, fast-channel	Likely pathogenic; Pathogenic	rs137852801, rs137852804, rs137852805, rs137852806, rs137852807, rs1477401624, rs2105350984, rs374391312, rs1064793397	RCV005409604 RCV000020050 RCV000020051 RCV000020052 RCV000020053 RCV000020054 RCV000022417 RCV000022418 RCV002496853
Non-immune hydrops fetalis	Likely pathogenic	rs545520806	RCV000170571
Seizure	Likely pathogenic; Pathogenic	rs768407867	RCV000679850
Slow-Channel Congenital Myasthenia Syndrome	Pathogenic	rs483353046	RCV000122732

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autosomal recessive multiple pterygium syndrome	Benign; Conflicting classifications of pathogenicity	rs34695580, rs1491478953, rs67309103	RCV000311146 RCV000283001 RCV000407750 RCV000407715
CHRNA1-Related Congenital Myasthenic Syndrome	Uncertain significance	rs1558909889	RCV000714729
CHRNA1-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs199555685, rs2105345213, rs141733086, rs1684050172, rs1683771023, rs146899588, rs368959759, rs143252724, rs367751078, rs182459320, rs2468899638, rs758613275, rs751153789, rs759020321, rs2468902304 View all (6 more)	RCV003930976 RCV003401890 RCV003955088 RCV003402809 RCV003414170 RCV003957712 RCV003972404 RCV004751482 RCV004751481 RCV003940335 RCV004750936 RCV003982790 RCV003896359 RCV003901596 RCV003911472 RCV004751560 RCV003935645 RCV003953147 RCV004751774 RCV004751771 RCV003940749
Congenital Myasthenic Syndrome, Dominant/Recessive	Benign; Conflicting classifications of pathogenicity	rs34695580, rs1491478953, rs67309103	RCV000401626 RCV000342138 RCV000338507 RCV000297624
Epilepsy	Uncertain significance	rs780391418, rs1558911753	RCV000781968 RCV000678787
Fetal ascites	Uncertain significance	rs1180739514	RCV001257364
Gastric cancer	Benign	rs2600684	RCV005905572
Hydrops fetalis	Uncertain significance	rs1180739514	RCV001257364
Juvenile myoclonic epilepsy	Conflicting classifications of pathogenicity	rs140268343	RCV000678786
Lung cancer	Benign	rs2600684	RCV005905574
Pleural effusion	Uncertain significance	rs1180739514	RCV001257364
See cases	Uncertain significance	rs560121316	RCV002252725
Uterine carcinosarcoma	Benign	rs2600684	RCV005905573
Uterine corpus endometrial carcinoma	Likely benign	rs753193	RCV005920663

Show/Hide Text Mining Associations (14)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Colitis Ulcerative	Associate	37055577
Fatigue	Associate	8827715
Fetal akinesia syndrome X linked	Associate	18179903, 23037934
Fetal Diseases	Associate	23037934
Lung Neoplasms	Associate	20234319, 23094028, 23232035
Multiple pterygium syndrome	Associate	18179903
Multiple Pterygium Syndrome Autosomal Dominant	Associate	23037934
Muscle Weakness	Associate	21316238, 33216040
Myasthenia Gravis	Associate	10227809, 15627975, 16891216, 1979338, 2564730, 35074870, 7910962, 8827715
Myasthenic Syndromes Congenital	Associate	12588888, 15731194, 19147685, 20562457, 21316238, 22728938, 31570625, 33216040, 33652901, 35466948
Ophthalmoplegia	Associate	21316238
Pena Shokeir syndrome type 1	Associate	25537362
Ptosis Hereditary Congenital 2	Associate	21316238
Schizophrenia	Associate	31342675

CHRNA1 (cholinergic receptor nicotinic alpha 1 subunit)