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

Summary

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

Location:: 15q25.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (78565520..78595269)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (76428193..76457938)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (78857862..78887611)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
Nicotinic acetylcholine gene cluster CHRNA5-A3-B4 variants influence smoking status in a Bangladeshi population.
Title: Nicotinic acetylcholine gene cluster CHRNA5-A3-B4 variants influence smoking status in a Bangladeshi population.

Submit: New GeneRIF Correction See all GeneRIFs (198)

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	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 EBI GWAS CatalogPubMed
A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. EBI GWAS Catalog EBI GWAS CatalogPubMed
A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Beyond cigarettes-per-day: A genome-wide association study of the biomarker carbon monoxide. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and fine mapping of serum protein loci through transethnic meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses of smoking behaviors in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis and imputation refines the association of 15q25 with smoking quantity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in FAM13A are associated with chronic obstructive pulmonary disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

NoName (e-PCR)
- UniSTS:481088

SHGC-36097 (e-PCR)
- UniSTS:83285

D15S1477 (e-PCR)
- UniSTS:474482

Chrna5 (e-PCR), detects polymorphism
- UniSTS:545913

RH80030 (e-PCR)
- UniSTS:87680

D11S3114 (e-PCR)
- UniSTS:152207

STS-M83712 (e-PCR)
- UniSTS:55724

CHRNA5_1914 (e-PCR)
- UniSTS:280499

Chrna5 (e-PCR), detects polymorphism
- UniSTS:532478

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 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 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

NG_023328.1 RefSeqGene

Range

5001..34750

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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)
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
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))
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))
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))