CHRNA3 (cholinergic receptor nicotinic alpha 3 subunit)

Gene

• Entrez ID: 1136
• Gene name: Cholinergic receptor nicotinic alpha 3 subunit
• Gene symbol: CHRNA3
• Synonyms: BAIPRCK, LNCR2, NACHRA3, PAOD2
• Chromosome: 15
• Chromosome location: 15q25.1
• Summary: This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains charac

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs578776	G>A,C	Drug-response	3 prime UTR variant, intron variant
rs1051730	G>A	Drug-response, risk-factor	Non coding transcript variant, coding sequence variant, synonymous variant
rs199547652	A>C,G	Pathogenic	Splice donor variant
rs200551904	G>C	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1596073421	GT>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT891725	hsa-miR-1197	CLIP-seq
MIRT891726	hsa-miR-1206	CLIP-seq
MIRT891727	hsa-miR-1224-5p	CLIP-seq
MIRT891728	hsa-miR-1294	CLIP-seq
MIRT891729	hsa-miR-129-5p	CLIP-seq
MIRT891730	hsa-miR-3148	CLIP-seq
MIRT891731	hsa-miR-3607-5p	CLIP-seq
MIRT891732	hsa-miR-4316	CLIP-seq
MIRT891733	hsa-miR-450b-5p	CLIP-seq
MIRT891734	hsa-miR-4640-3p	CLIP-seq
MIRT891735	hsa-miR-4704-3p	CLIP-seq
MIRT891736	hsa-miR-4751	CLIP-seq
MIRT891737	hsa-miR-507	CLIP-seq
MIRT891738	hsa-miR-548ae	CLIP-seq
MIRT891739	hsa-miR-548aj	CLIP-seq
MIRT891740	hsa-miR-548am	CLIP-seq
MIRT891741	hsa-miR-548x	CLIP-seq
MIRT891742	hsa-miR-557	CLIP-seq
MIRT891743	hsa-miR-3685	CLIP-seq
MIRT891744	hsa-miR-384	CLIP-seq
MIRT891745	hsa-miR-586	CLIP-seq
MIRT891729	hsa-miR-129-5p	CLIP-seq
MIRT1964287	hsa-miR-150	CLIP-seq
MIRT1964288	hsa-miR-192	CLIP-seq
MIRT1964289	hsa-miR-215	CLIP-seq
MIRT1964290	hsa-miR-4312	CLIP-seq
MIRT891733	hsa-miR-450b-5p	CLIP-seq
MIRT1964291	hsa-miR-4535	CLIP-seq
MIRT1964292	hsa-miR-4776-5p	CLIP-seq
MIRT1964293	hsa-miR-492	CLIP-seq
MIRT891737	hsa-miR-507	CLIP-seq
MIRT891742	hsa-miR-557	CLIP-seq
MIRT1964287	hsa-miR-150	CLIP-seq
MIRT1964288	hsa-miR-192	CLIP-seq
MIRT1964289	hsa-miR-215	CLIP-seq
MIRT1964290	hsa-miR-4312	CLIP-seq
MIRT1964291	hsa-miR-4535	CLIP-seq
MIRT1964292	hsa-miR-4776-5p	CLIP-seq
MIRT1964293	hsa-miR-492	CLIP-seq
MIRT2427324	hsa-miR-4261	CLIP-seq
MIRT2427325	hsa-miR-4666-5p	CLIP-seq
MIRT2427326	hsa-miR-494	CLIP-seq
MIRT2427327	hsa-miR-587	CLIP-seq
MIRT1964287	hsa-miR-150	CLIP-seq
MIRT2503228	hsa-miR-1915	CLIP-seq
MIRT2503229	hsa-miR-3617	CLIP-seq
MIRT2503230	hsa-miR-3913-3p	CLIP-seq
MIRT2503231	hsa-miR-4269	CLIP-seq
MIRT2503232	hsa-miR-4457	CLIP-seq
MIRT2503233	hsa-miR-4514	CLIP-seq
MIRT2503234	hsa-miR-4645-5p	CLIP-seq
MIRT2503235	hsa-miR-4673	CLIP-seq
MIRT2503236	hsa-miR-4692	CLIP-seq
MIRT2503237	hsa-miR-4713-5p	CLIP-seq
MIRT2503238	hsa-miR-4726-3p	CLIP-seq
MIRT2503239	hsa-miR-4731-3p	CLIP-seq
MIRT2503240	hsa-miR-4753-3p	CLIP-seq
MIRT2503241	hsa-miR-4801	CLIP-seq
MIRT2503242	hsa-miR-489	CLIP-seq
MIRT2503243	hsa-miR-532-3p	CLIP-seq
MIRT2503244	hsa-miR-641	CLIP-seq
MIRT2503245	hsa-miR-642b	CLIP-seq
MIRT2503246	hsa-miR-656	CLIP-seq
MIRT2503247	hsa-miR-940	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
ASCL1	Unknown	20124469

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	27344019
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	IBA	21873635
GO:0005892	Component	Acetylcholine-gated channel complex	IDA	8906617
GO:0006811	Process	Ion transport	NAS	8906617
GO:0006940	Process	Regulation of smooth muscle contraction	ISS
GO:0007165	Process	Signal transduction	IBA	21873635
GO:0007165	Process	Signal transduction	IDA	8906617
GO:0007171	Process	Activation of transmembrane receptor protein tyrosine kinase activity	ISS
GO:0007268	Process	Chemical synaptic transmission	IBA	21873635
GO:0007271	Process	Synaptic transmission, cholinergic	ISS
GO:0007399	Process	Nervous system development	IMP	11450844
GO:0007626	Process	Locomotory behavior	ISS
GO:0014056	Process	Regulation of acetylcholine secretion, neurotransmission	ISS
GO:0014069	Component	Postsynaptic density	ISS
GO:0015276	Function	Ligand-gated ion channel activity	TAS	20438829
GO:0015464	Function	Acetylcholine receptor activity	IDA	8906617
GO:0016021	Component	Integral component of membrane	NAS	8906617
GO:0022848	Function	Acetylcholine-gated cation-selective channel activity	IDA	8906617
GO:0022848	Function	Acetylcholine-gated cation-selective channel activity	ISS
GO:0022848	Function	Acetylcholine-gated cation-selective channel activity	TAS	20438829
GO:0030425	Component	Dendrite	ISS
GO:0030594	Function	Neurotransmitter receptor activity	IBA	21873635
GO:0034220	Process	Ion transmembrane transport	IBA	21873635
GO:0035095	Process	Behavioral response to nicotine	IMP	18227835
GO:0042166	Function	Acetylcholine binding	IC	8906617
GO:0042391	Process	Regulation of membrane potential	IBA	21873635
GO:0042391	Process	Regulation of membrane potential	ISS
GO:0043005	Component	Neuron projection	IBA	21873635
GO:0043025	Component	Neuronal cell body	ISS
GO:0044853	Component	Plasma membrane raft	ISS
GO:0045202	Component	Synapse	IBA	21873635
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0048814	Process	Regulation of dendrite morphogenesis	ISS
GO:0050877	Process	Nervous system process	IBA	21873635
GO:0060079	Process	Excitatory postsynaptic potential	ISS
GO:0060084	Process	Synaptic transmission involved in micturition	IMP	11450844
GO:0095500	Process	Acetylcholine receptor signaling pathway	ISS
GO:1905144	Process	Response to acetylcholine	ISS

Other IDs

• MIM: 118503
• HGNC: 1957
• e!Ensembl: ENSG00000080644

Protein

• UniProt ID: P32297
• Protein name: Neuronal acetylcholine receptor subunit alpha-3
• Protein function: Component of neuronal acetylcholine receptors (nAChRs) that function as pentameric, ligand-gated cation channels with high calcium permeability among other activities. nAChRs are excitatory neurotrasnmitter receptors formed by a collection of nA
• PDB: 4ZK4, 5SYO, 5TVC, 6PV7, 6PV8
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02931	Neur_chan_LBD	35 → 241	Neurotransmitter-gated ion-channel ligand binding domain	Family
  PF02932	Neur_chan_memb	248 → 495	Neurotransmitter-gated ion-channel transmembrane region	Family

• Sequence:

  MGSGPLSLPLALSPPRLLLLLLLSLLPVARASEAEHRLFERLFEDYNEIIRPVANVSDPV
  IIHFEVSMSQLVKVDEVNQIMETNLWLKQIWNDYKLKWNPSDYGGAEFMRVPAQKIWKPD
  IVLYNNAVGDFQVDDKTKALLKYTGEVTWIPPAIFKSSCKIDVTYFPFDYQNCTMKFGSW
  SYDKAKIDLVLIGSSMNLKDYWESGEWAIIKAPGYKHDIKYNCCEEIYPDITYSLYIRRL
  PLFYTINLIIPCLLISFLTVLVFYLPSDCGEKVTLCISVLLSLTVFLLVITETIPSTSLV
  IPLIGEYLLFTMIFVTLSIVITVFVLNVHYRTPTTHTMPSWVKTVFLNLLPRVMFMTRPT
  SNEGNAQKPRPLYGAELSNLNCFSRAESKGCKEGYPCQDGMCGYCHHRRIKISNFSANLT
  RSSSSESVDAVLSLSALSPEIKEAIQSVKYIAENMKAQNEAKEIQDDWKYVAMVIDRIFL
  WVFTLVCILGTAGLFLQPLMAREDA

• Sequence length: 505

Pathways

KEGG:

Neuroactive ligand-receptor interaction
Cholinergic synapse
Chemical carcinogenesis - receptor activation

Reactome:

Highly sodium permeable postsynaptic acetylcholine nicotinic receptors
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors
Highly calcium permeable nicotinic acetylcholine receptors

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Chronic obstructive pulmonary disease	Chronic Obstructive Airway Disease	rs2227956, rs1008438, rs1043618, rs562047, rs1061581, rs2763979, rs6457452, rs13147758, rs1828591, rs13118928	25101718, 25241909, 29767774, 26634245, 29631575, 30804561, 21921092, 24621683
Congenital anomalies of kidney and urinary tract	Cakut	rs267606865, rs121908436, rs281875326, rs879255515, rs75462234, rs869320679, rs760905589, rs797045022, rs869320624, rs745597204, rs1114167358, rs1555879360, rs1577330805, rs1008555507	31708116
Dysautonomia	Dysautonomia	rs111033171, rs137853022, rs28939712, rs754348901, rs749052963, rs1057517169, rs1057516865, rs763445509, rs767527819, rs781333644, rs1239081703, rs1554696574, rs539544212, rs1201626345, rs774890086, rs1554703061, rs1554703613, rs1319053366, rs1554703851, rs868073099, rs926177767, rs376078668, rs1554695299, rs1554696648, rs1554696934, rs1554699327, rs1554691572, rs1554695846, rs1554697001, rs770668926, rs1554698037, rs759412460, rs1554702142, rs765572951, rs1554702880, rs1554703831, rs760774999, rs1554696650, rs757972943, rs1554703874, rs1554703907, rs571348995	31708116
Lung carcinoma	Squamous cell carcinoma of lung, Carcinoma of lung	rs1805076, rs121909071, rs121913530, rs112445441, rs121913529, rs121913535, rs121913297, rs121913279, rs104886003, rs397516975, rs11554290, rs121913364, rs121913351, rs121913369, rs121913355, rs121912470, rs121913273, rs121913281, rs121913348, rs727503093, rs121913353, rs397516890, rs397516896, rs121913378, rs397516897, rs397516977, rs397516978, rs397516979, rs397516980, rs397516981, rs397516982, rs121913240, rs17851045, rs397517086, rs121913428, rs397517094, rs397517098, rs397517106, rs121913465, rs397517108, rs397517111, rs397517112, rs397517114, rs397517116, rs1554350366, rs397517127, rs397517200, rs397517202, rs121913283, rs121913370, rs121913357, rs727503106, rs121913238, rs727503108, rs397517040, rs397516976, rs1555618025, rs1057519729, rs1584238193	28604730, 29924316, 30104567, 18978787, 18978790
Lung adenocarcinoma	Adenocarcinoma of lung (disorder)	rs28934576, rs121913530, rs397516975, rs587776805, rs121913469, rs121913364, rs121913351, rs121913366, rs397516896, rs397516977, rs397516981, rs397517127, rs121913344, rs727504233, rs121913370, rs760043106, rs1057519788, rs1131692238, rs1131692237, rs1554350382	19836008
Lung cancer	Malignant neoplasm of lung	rs121913530, rs121913529, rs878855122, rs1057519784, rs770315135	18385676, 18385738, 19654303, 18978787, 22899653, 18978790
Nasopharyngeal carcinoma	Nasopharyngeal carcinoma	rs200046052	20512145
Schizophrenia	Schizophrenia	rs74315508, rs74315509, rs13447324, rs1558507406, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346, rs863223347, rs863223351, rs863223352, rs61734270, rs797045205, rs869312829, rs869312830, rs770913157, rs869312832, rs869312831, rs781720548, rs1262969313	29483656, 26198764, 31268507, 25056061, 30285260, 28991256, 31374203, 28540026, 20393456
Seizure	Complex partial seizures, Generalized seizures, Visual seizure, Tonic - clonic seizures, Single Seizure	rs587784365, rs28939683, rs74315390, rs28939684, rs74315391, rs267607198, rs74315392, rs118192244, rs118192250, rs121917749, rs121917750, rs121917751, rs121917752, rs267606670, rs267607061, rs121912707, rs118192249, rs118192251, rs118192217, rs118192218, rs118192219, rs118192222, rs118192226, rs118192228, rs118192234, rs118192236, rs118192235, rs118192241, rs118192242, rs118192185, rs118192188, rs118192245, rs118192246, rs118192186, rs118192194, rs118192197, rs118192199, rs118192201, rs118192202, rs118192203, rs118192204, rs118192205, rs118192206, rs118192208, rs118192211, rs118192216, rs118192239, rs387906684, rs387906686, rs387906687, rs1596893185, rs387907126, rs387907281, rs397515405, rs587778771, rs730882067, rs730882073, rs397514579, rs397514582, rs587776976, rs398122394, rs121918784, rs121918751, rs121918735, rs398123588, rs587780450, rs61749751, rs587777620, rs727503974, rs730882124, rs794726710, rs794726697, rs794726799, rs794727444, rs794727740, rs796053166, rs794726825, rs796052676, rs796053219, rs796053220, rs796053228, rs796052653, rs759584387, rs796052650, rs796052641, rs796052626, rs796052623, rs796052663, rs796052615, rs796052802, rs797044999, rs797045047, rs797045942, rs797045941, rs118192212, rs797044938, rs777257591, rs864321712, rs879255652, rs886039268, rs886039517, rs886039529, rs199497486, rs886039496, rs886039903, rs886041300, rs769827124, rs886041339, rs886041591, rs587783092, rs1555850151, rs1057516123, rs1057516121, rs1057516115, rs1057516111, rs1057516106, rs1057516105, rs756921902, rs1057516089, rs1057516087, rs1057516080, rs1057516076, rs1060499544, rs1555850512, rs1057517919, rs118192231, rs1057520413, rs1060503101, rs1064796294, rs1064794981, rs1064794632, rs1064797245, rs1131691830, rs1131692231, rs1131691936, rs1554626549, rs1553579225, rs1553531385, rs121918736, rs1554898088, rs1553579282, rs763353895, rs1553463119, rs1554093891, rs77838305, rs1555408401, rs1554627439, rs1554097873, rs1555850403, rs1064794719, rs1315483224, rs1567134495, rs770187706, rs1057518555, rs1576983339, rs1574192005, rs1459374430, rs1586800133, rs1574641522, rs1572096837, rs1572630269, rs1574554892, rs1574556643, rs1574571769, rs1574641605, rs1574697769, rs1574716524, rs1574746733, rs1574746935, rs1574752700, rs1574754680, rs863225030, rs1601545088, rs1600714727, rs1371059392, rs1600767259, rs1339542565, rs1600785769, rs2065899210, rs1600732174, rs1162306056, rs879255709, rs1900111672, rs2066910297, rs1554122080, rs796052941, rs1600789325, rs2082695884, rs1737677036, rs1737495759, rs868389022, rs1737685202, rs1737672350, rs762737130	15275829

Unknown
Disease name	Disease term	dbSNP ID	References
Clonic seizures	Clonic Seizures		15275829
Coronary heart disease	Coronary heart disease	rs9289231, rs281864746	21347282
Development disorder	Child Development Disorders, Pervasive		28540026
Bronchitis	Bronchitis, Chronic		25241909
Hypotonic seizures	Epileptic drop attack		15275829
Jacksonian seizure	Jacksonian Seizure		15275829
Lung neoplasms	Lung Neoplasms		18385738