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

    Gene ID: 1136, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CHRNA3 in Genome Data Viewer
    Location:
    15q25.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (78593052..78620996, complement)
    RS_2024_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_000015.10Genomic Context describing neighboring genes Neighboring gene hydroxylysine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:78833042-78833934 Neighboring gene proteasome 20S subunit alpha 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6713 Neighboring gene cholinergic receptor nicotinic alpha 5 subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78921681-78922180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78930031-78930532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6714 Neighboring gene cholinergic receptor nicotinic beta 4 subunit Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:78952684-78953883 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:78963837-78964728 Neighboring gene ribosomal protein L18 pseudogene 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78965621-78966511 Neighboring gene uncharacterized LOC105370913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:79019283-79019837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:79019838-79020391

    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

    Clone Names

    • MGC104879

    Gene Ontology Provided by GOA

    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 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 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 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 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 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 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, 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 
    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 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
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    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
     

    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..30987
      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, Q15823, Q4KMN8, Q86U77, Q96RH3, Q99553, Q9BQ93, Q9BRR4
      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
      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: GCF_000001405.40-RS_2024_08

    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)

    mRNA and Protein(s)

    1. XM_054377228.1XP_054233203.1  neuronal acetylcholine receptor subunit alpha-3 isoform X1