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

Gene ID: 1138, updated on 14-Nov-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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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

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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
not available

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

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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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)

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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

  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

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