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

Gene ID: 1136, updated on 22-May-2022

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
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Genomic context

See CHRNA3 in Genome Data Viewer
Location:
15q25.1
Exon count:
9
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (78593052..78620996, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (76455721..76484482, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78885394..78913338, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene hydroxylysine kinase Neighboring gene proteasome 20S subunit alpha 4 Neighboring gene cholinergic receptor nicotinic alpha 5 subunit Neighboring gene cholinergic receptor nicotinic beta 4 subunit Neighboring gene ribosomal protein L18 pseudogene 11 Neighboring gene uncharacterized LOC105370913

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC104879

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in acetylcholine receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in activation of transmembrane receptor protein tyrosine kinase activity 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 chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in ion transport NAS
Non-traceable Author Statement
more info
PubMed 
involved_in locomotory behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nervous system process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of acetylcholine secretion, neurotransmission ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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, cholinergic ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
part_of acetylcholine-gated channel complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
 
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
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 density ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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

  1. NG_016143.1 RefSeqGene

    Range
    5300..33244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000743.5NP_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
    Related
    ENSP00000315602.5, ENST00000326828.6
    Conserved Domains (1) summary
    cl27321
    Location:30496
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
  2. NM_001166694.2NP_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
    UniProtKB/Swiss-Prot
    P32297
    Related
    ENSP00000267951.4, ENST00000348639.7
    Conserved Domains (2) summary
    cl00788
    Location:432489
    MttA_Hcf106; mttA/Hcf106 family
    cl27321
    Location:30360
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

RNA

  1. 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    78593052..78620996 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam02931
    Location:1174
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:181428
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    76455721..76484482 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)