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

Gene ID: 1136, updated on 8-May-2016
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 HPRD:07511; MIM:118503; Vega:OTTHUMG00000143863
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; 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]
Orthologs
Location:
15q24
Exon count:
10
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 15 NC_000015.10 (78593052..78621295, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78885394..78913637, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene hydroxylysine kinase Neighboring gene proteasome 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Smoking as a quantitative trait locus 3
MedGen: C3150168 OMIM: 612052 GeneReviews: Not available
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NHGRI GWAS Catalog

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

Markers

Homology

Clone Names

  • MGC104879

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to acetylcholine binding IBA
Inferred from Biological aspect of Ancestor
more info
 
acetylcholine binding IC
Inferred by Curator
more info
PubMed 
acetylcholine receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
acetylcholine-activated cation-selective channel activity IDA
Inferred from Direct Assay
more info
PubMed 
acetylcholine-activated cation-selective channel activity TAS
Traceable Author Statement
more info
PubMed 
drug binding IEA
Inferred from Electronic Annotation
more info
 
ligand-gated ion channel activity TAS
Traceable Author Statement
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
activation of transmembrane receptor protein tyrosine kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
behavioral response to nicotine IMP
Inferred from Mutant Phenotype
more info
PubMed 
cation transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
ion transport NAS
Non-traceable Author Statement
more info
PubMed 
locomotory behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein heterooligomerization IEA
Inferred from Electronic Annotation
more info
 
regulation of acetylcholine secretion, neurotransmission ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of membrane potential ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of smooth muscle contraction ISS
Inferred from Sequence or Structural Similarity
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to inorganic substance IEA
Inferred from Electronic Annotation
more info
 
signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
synaptic transmission involved in micturition IMP
Inferred from Mutant Phenotype
more info
PubMed 
synaptic transmission, cholinergic IBA
Inferred from Biological aspect of Ancestor
more info
 
synaptic transmission, cholinergic ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
acetylcholine-gated channel complex IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
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

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
    5001..33244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000743.4NP_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, OTTHUMP00000185024, ENST00000326828, OTTHUMT00000290111
    Conserved Domains (3) summary
    pfam02931
    Location:35241
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:248495
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
    TIGR00860
    Location:30496
    LIC; Cation transporter family protein
  2. NM_001166694.1NP_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, OTTHUMP00000185025, ENST00000348639, OTTHUMT00000290112
    Conserved Domains (2) summary
    pfam02931
    Location:35241
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:248466
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

RNA

  1. NR_046313.1 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 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p2 Primary Assembly

    Range
    78593052..78621295 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720382.1XP_006720445.1  

    Conserved Domains (2) summary
    pfam02931
    Location:2174
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:181428
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
  2. XM_011521173.1XP_011519475.1  

    Conserved Domains (3) summary
    pfam02931
    Location:8214
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:221468
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
    TIGR00860
    Location:3469
    LIC; Cation transporter family protein

Alternate CHM1_1.1

Genomic

  1. NC_018926.2 Alternate CHM1_1.1

    Range
    79003962..79032196 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)