U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    CHRNA5 cholinergic receptor nicotinic alpha 5 subunit [ Homo sapiens (human) ]

    Gene ID: 1138, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    CHRNA5provided by HGNC
    Official Full Name
    cholinergic receptor nicotinic alpha 5 subunitprovided by HGNC
    Primary source
    HGNC:HGNC:1959
    See related
    Ensembl:ENSG00000169684 MIM:118505; AllianceGenome:HGNC:1959
    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
    Summary
    The protein encoded by this gene is a nicotinic acetylcholine receptor subunit and a member of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. These receptors are thought to be heteropentamers composed of separate but similar subunits. Defects in this gene have been linked to susceptibility to lung cancer type 2 (LNCR2).[provided by RefSeq, Jun 2010]
    Expression
    Broad expression in gall bladder (RPKM 1.4), colon (RPKM 1.2) and 19 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See CHRNA5 in Genome Data Viewer
    Location:
    15q25.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (78565520..78595269)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (76428193..76457938)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78857862..78887611)

    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 3 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. CHRNA5 rs16969968 Polymorphism Association with Risk of Lung Cancer--Evidence from 17,962 Lung Cancer Cases and 77,216 Control Subjects. Xu ZW, et al. Asian Pac J Cancer Prev, 2015. PMID 26434895
    2. Association of CHRNA5-A3-B4 SNP rs2036527 with smoking cessation therapy response in African-American smokers. Zhu AZ, et al. Clin Pharmacol Ther, 2014 Aug. PMID 24733007, Free PMC Article
    3. CHRNA5 variants moderate the effect of nicotine deprivation on a neural index of cognitive control. Evans DE, et al. Genes Brain Behav, 2014 Sep. PMID 24934182, Free PMC Article
    4. Interplay of genetic risk (CHRNA5) and environmental risk (partner smoking) on cigarette smoking reduction. Chen LS, et al. Drug Alcohol Depend, 2014 Oct 1. PMID 25073833, Free PMC Article
    5. Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5. Wang JC, et al. Hum Mol Genet, 2009 Aug 15. PMID 19443489, Free PMC Article

    See all (265) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Nicotinic Receptor Alpha-5 Subunit Gene Polymorphism is Associated With Heavy Smoking Under a Range of Nicotine Dosing Conditions.
      Title: Nicotinic Receptor Alpha-5 Subunit Gene Polymorphism is Associated With Heavy Smoking Under a Range of Nicotine Dosing Conditions.
    2. CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease.
      Title: CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease.
    3. PLEK2 mediates metastasis and invasion via alpha5-nAChR activation in nicotine-induced lung adenocarcinoma.
      Title: PLEK2 mediates metastasis and invasion via α5-nAChR activation in nicotine-induced lung adenocarcinoma.
    4. The rs16969968 Tobacco Smoking-Related Single-Nucleotide Variant Is Associated with Clinical Markers in Patients with Severe COVID-19.
      Title: The rs16969968 Tobacco Smoking-Related Single-Nucleotide Variant Is Associated with Clinical Markers in Patients with Severe COVID-19.
    5. CHRNA5 gene variation affects the response of VTA dopaminergic neurons during chronic nicotine exposure and withdrawal.
      Title: CHRNA5 gene variation affects the response of VTA dopaminergic neurons during chronic nicotine exposure and withdrawal.
    6. CHRNA5 Is Overexpressed in Patients with Psoriasis and Promotes Psoriasis-Like Inflammation in Mouse Models.
      Title: CHRNA5 Is Overexpressed in Patients with Psoriasis and Promotes Psoriasis-Like Inflammation in Mouse Models.
    7. The Nicotinic Receptor Polymorphism rs16969968 Is Associated with Airway Remodeling and Inflammatory Dysregulation in COPD Patients.
      Title: The Nicotinic Receptor Polymorphism rs16969968 Is Associated with Airway Remodeling and Inflammatory Dysregulation in COPD Patients.
    8. 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.
    9. alpha5-nAChR associated with Ly6E modulates cell migration via TGF-beta1/Smad signaling in non-small cell lung cancer.
      Title: α5-nAChR associated with Ly6E modulates cell migration via TGF-β1/Smad signaling in non-small cell lung cancer.
    10. Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases.
      Title: Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases.
    Submit: New GeneRIF Correction See all GeneRIFs (199)

    Phenotypes

    Go to the top of the page Help

    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

    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
    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
    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 association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
    EBI GWAS Catalog
    Genome-wide meta-analyses of smoking behaviors in African Americans.
    EBI GWAS Catalog
    IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease.
    EBI GWAS Catalog
    Meta-analysis and imputation refines the association of 15q25 with smoking quantity.
    EBI GWAS Catalog
    Variants in FAM13A are associated with chronic obstructive pulmonary disease.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Potential readthrough

    Included gene: PSMA4

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetylcholine receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetylcholine-gated monoatomic cation-selective channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine-gated monoatomic cation-selective channel activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables acetylcholine-gated monoatomic cation-selective channel activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables ligand-gated monoatomic ion channel activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acetylcholine receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in behavioral response to nicotine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chemical synaptic transmission TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in excitatory postsynaptic potential IEA
    Inferred from Electronic Annotation
    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 neuromuscular synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in presynaptic modulation of chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to nicotine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic transmission, cholinergic IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of acetylcholine-gated channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of acetylcholine-gated channel complex IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in cholinergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dopaminergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    neuronal acetylcholine receptor subunit alpha-5
    Names
    Cholinergic receptor, neuronal nicotinic, alpha polypeptide-5
    acetylcholine receptor, nicotinic, alpha 5 (neuronal)
    cholinergic receptor, nicotinic alpha 5
    cholinergic receptor, nicotinic, alpha 5 (neuronal)
    neuronal nicotinic acetylcholine receptor, alpha5 subunit

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_023328.1 RefSeqGene

      Range
      5001..34750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000745.4 → NP_000736.2  neuronal acetylcholine receptor subunit alpha-5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_000736.2

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Consensus CDS
      CCDS10304.1
      UniProtKB/Swiss-Prot
      P30532, Q15824, Q99554
      Related
      ENSP00000299565.5, ENST00000299565.9
      Conserved Domains (3) summary
      TIGR00860
      Location:39 → 449
      LIC; Cation transporter family protein
      pfam02931
      Location:47 → 250
      Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
      pfam02932
      Location:257 → 447
      Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

    2. NM_001307945.2 → NP_001294874.1  neuronal acetylcholine receptor subunit alpha-5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001294874.1

      Status: REVIEWED

      Source sequence(s)
      AC027228, AJ584706, BM839817, BX332469
      Consensus CDS
      CCDS76786.1
      UniProtKB/TrEMBL
      H0YM98
      Related
      ENSP00000453519.1, ENST00000559554.5
      Conserved Domains (1) summary
      pfam02931
      Location:47 → 154
      Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

    3. NM_001395171.1 → NP_001382100.1  neuronal acetylcholine receptor subunit alpha-5 isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Conserved Domains (2) summary
      cd19018
      Location:45 → 251
      LGIC_ECD_nAChR_A5; extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (CHRNA5)
      cd19064
      Location:251 → 340
      LGIC_TM_nAChR; transmembrane domain of nicotinic acetylcholine receptor (nAChR)

    4. NM_001395172.1 → NP_001382101.1  neuronal acetylcholine receptor subunit alpha-5 isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Conserved Domains (3) summary
      cd03559
      Location:208 → 229
      LGIC_TM; TM4 helix [structural motif]
      cl28912
      Location:45 → 198
      LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))
      cl38911
      Location:207 → 230
      LGIC_TM; transmembrane domain of Cys-loop neurotransmitter-gated ion channels

    5. NM_001395173.1 → NP_001382102.1  neuronal acetylcholine receptor subunit alpha-5 isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Conserved Domains (1) summary
      cl28912
      Location:45 → 240
      LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))

    6. NM_001395174.1 → NP_001382103.1  neuronal acetylcholine receptor subunit alpha-5 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Conserved Domains (2) summary
      cd03558
      Location:170 → 184
      LGIC_ECD; Cys-loop [structural motif]
      cl28912
      Location:45 → 236
      LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))

    7. NM_001395175.1 → NP_001382104.1  neuronal acetylcholine receptor subunit alpha-5 isoform 7 precursor

      Status: REVIEWED

      Source sequence(s)
      AC027228
      Conserved Domains (1) summary
      cl28912
      Location:45 → 152
      LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))

    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
      78565520..78595269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      76428193..76457938
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P30532.2 GenPept UniProtKB/Swiss-Prot:P30532

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous