CHRNA3 cholinergic receptor nicotinic alpha 3 subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHRNA3provided by HGNC
Official Full Name: cholinergic receptor nicotinic alpha 3 subunitprovided by HGNC
Primary source: HGNC:HGNC:1957
See related: Ensembl:ENSG00000080644 MIM:118503; AllianceGenome:HGNC:1957
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: LNCR2; PAOD2; BAIPRCK; NACHRA3
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 characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
Expression: Biased expression in adrenal (RPKM 16.5), appendix (RPKM 2.4) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q25.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (78593052..78620996, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (76455721..76484482, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (78885394..78913338, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association of Polymorphism CHRNA5 and CHRNA3 Gene in People Addicted to Nicotine.
Title: Association of Polymorphism CHRNA5 and CHRNA3 Gene in People Addicted to Nicotine.
Progressive Encephalomyelitis with Rigidity and Myoclonus (PERM)-like Symptoms Associated with Anti-ganglionic Acetylcholine Receptor Antibodies.
Title: Progressive Encephalomyelitis with Rigidity and Myoclonus (PERM)-like Symptoms Associated with Anti-ganglionic Acetylcholine Receptor Antibodies.
Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants.
Title: Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants.
Association Between Nicotine-dependent Gene Polymorphism and Smoking Cessation in Patients With Lung Cancer.
Title: Association Between Nicotine-dependent Gene Polymorphism and Smoking Cessation in Patients With Lung Cancer.
The relationship between CHRNA5/A3/B4 gene cluster polymorphisms and lung cancer risk: An updated meta-analysis and systematic review.
Title: The relationship between CHRNA5/A3/B4 gene cluster polymorphisms and lung cancer risk: An updated meta-analysis and systematic review.
Antibodies to the alpha3 subunit of the ganglionic-type nicotinic acetylcholine receptors in patients with autoimmune encephalitis.
Title: Antibodies to the α3 subunit of the ganglionic-type nicotinic acetylcholine receptors in patients with autoimmune encephalitis.
[Analysis of polymorphism rs1051730 of CHRNA3 in patients with dual pathology in a Mexican population].", trans "Analisis del polimorfismo rs1051730 de CHRNA3 en pacientes con patologia dual en poblacion mexicana.
Title: [Analysis of polymorphism rs1051730 of CHRNA3 in patients with dual pathology in a Mexican population].
Results find rs578776 polymorphism in CHRNA3 not associated with head and neck cancer (HNC) risk.
Title: Polymorphisms of CHRNA3 and CHRNA5: Head and neck cancer and cigarette consumption intensity in a Brazilian population.
Truncating mutations in CHRNA3 gene causes Congenital anomalies of the kidney and urinary tract and Autonomic Dysfunction.
Title: CAKUT and Autonomic Dysfunction Caused by Acetylcholine Receptor Mutations.
Gene variance in the CHRNA5/CHRNA3 is associated with risk of lumbar disc herniation.
Title: CHRNA5/CHRNA3 gene cluster is a risk factor for lumbar disc herniation: a case-control study.

Submit: New GeneRIF Correction See all GeneRIFs (151)

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
SMOKING AS A QUANTITATIVE TRAIT LOCUS 3 MedGen: C3150168 OMIM: 612052 GeneReviews: Not available	Compare labs
Urinary bladder, atony of MedGen: C5231389 OMIM: 191800 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. EBI GWAS Catalog EBI GWAS CatalogPubMed
A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Beyond cigarettes-per-day: A genome-wide association study of the biomarker carbon monoxide. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common 5p15.33 and 6p21.33 variants influence lung cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and fine mapping of serum protein loci through transethnic meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic susceptibility for chronic bronchitis in chronic obstructive pulmonary disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses identify multiple loci associated with smoking behavior. EBI GWAS Catalog EBI GWAS CatalogPubMed
IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Lung cancer susceptibility locus at 5p15.33. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis and imputation refines the association of 15q25 with smoking quantity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in FAM13A are associated with chronic obstructive pulmonary disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-36097 (e-PCR)
- UniSTS:83285

RH98633 (e-PCR)
- UniSTS:88412

RH121399 (e-PCR)
- UniSTS:134245

CHRNA3_541 (e-PCR)
- UniSTS:277097

CHRNA3 (e-PCR)
- UniSTS:480423

STS-M83712 (e-PCR)
- UniSTS:55724

CHRNA5_1914 (e-PCR)
- UniSTS:280499

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acetylcholine binding	IC Inferred by Curator more info	PubMed
enables acetylcholine receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables acetylcholine receptor activity	IEA Inferred from Electronic Annotation more info
enables acetylcholine-gated monoatomic cation-selective channel activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to acetylcholine-gated monoatomic cation-selective channel activity	IDA Inferred from Direct Assay more info	PubMed
enables acetylcholine-gated monoatomic cation-selective channel activity	IDA Inferred from Direct Assay more info	PubMed
enables acetylcholine-gated monoatomic cation-selective channel activity	IEA Inferred from Electronic Annotation more info
enables acetylcholine-gated monoatomic cation-selective channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables acetylcholine-gated monoatomic cation-selective channel activity	TAS Traceable Author Statement more info	PubMed
enables extracellular ligand-gated monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables ligand-gated monoatomic ion channel activity	TAS Traceable Author Statement more info	PubMed
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in acetylcholine receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in acetylcholine receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in acetylcholine receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in behavioral response to nicotine	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in locomotory behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane depolarization	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization	IDA Inferred from Direct Assay more info	PubMed
involved_in membrane depolarization	ISS Inferred from Sequence or Structural Similarity more info
involved_in monoatomic ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	NAS Non-traceable Author Statement more info	PubMed
involved_in nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuromuscular synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in presynaptic modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of acetylcholine secretion, neurotransmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of appetite	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of dendrite morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of membrane potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of smooth muscle contraction	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to acetylcholine	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to nicotine	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic transmission involved in micturition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic transmission involved in micturition	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic transmission, cholinergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, cholinergic	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
part_of acetylcholine-gated channel complex	IBA Inferred from Biological aspect of Ancestor more info
part_of acetylcholine-gated channel complex	IDA Inferred from Direct Assay more info	PubMed
part_of acetylcholine-gated channel complex	IEA Inferred from Electronic Annotation more info
part_of acetylcholine-gated channel complex	IPI Inferred from Physical Interaction more info	PubMed
part_of acetylcholine-gated channel complex	ISO Inferred from Sequence Orthology more info
part_of acetylcholine-gated channel complex	ISS Inferred from Sequence or Structural Similarity more info
part_of cation channel complex	IEA Inferred from Electronic Annotation more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
part_of neurotransmitter receptor complex	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in plasma membrane raft	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic membrane	TAS Traceable Author Statement more info	PubMed
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	TAS Traceable Author Statement more info	PubMed
located_in synaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: neuronal acetylcholine receptor subunit alpha-3

Names: cholinergic receptor, nicotinic alpha 3; cholinergic receptor, nicotinic, alpha 3 (neuronal); cholinergic receptor, nicotinic, alpha polypeptide 3; neuronal nicotinic acetylcholine receptor, alpha3 subunit

NP_000734.2

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_016143.1 RefSeqGene

Range

5300..30987

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000743.5 → NP_000734.2 neuronal acetylcholine receptor subunit alpha-3 isoform 1 precursor

See identical proteins and their annotated locations for NP_000734.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC027228, AI833126, BC002996, BC006114, BM666615

Consensus CDS

CCDS10305.1

UniProtKB/Swiss-Prot

P32297, Q15823, Q4KMN8, Q86U77, Q96RH3, Q99553, Q9BQ93, Q9BRR4

Related

ENSP00000315602.5, ENST00000326828.6

Conserved Domains (1) summary

cl27321
Location:30 → 496

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
NM_001166694.2 → NP_001160166.1 neuronal acetylcholine receptor subunit alpha-3 isoform 2 precursor

See identical proteins and their annotated locations for NP_001160166.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

BC006114

Consensus CDS

CCDS53964.1

Related

ENSP00000267951.4, ENST00000348639.7

Conserved Domains (2) summary

cl00788
Location:432 → 489

MttA_Hcf106; mttA/Hcf106 family

cl27321
Location:30 → 360

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

RNA

NR_046313.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains two alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC006114, M37981

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

78593052..78620996 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006720382.4 → XP_006720445.1 neuronal acetylcholine receptor subunit alpha-3 isoform X1

Conserved Domains (2) summary

pfam02931
Location:1 → 174

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:181 → 428

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region