This gene is a member of the ligand-gated ionic channel family and nicotinic acetylcholine receptor gene superfamily. It encodes a plasma membrane protein that forms homo- or hetero-oligomeric divalent cation channels. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea. [provided by RefSeq, Feb 201... See more...

Aliases for CHRNA9 Gene

Aliases for CHRNA9 Gene

  • Cholinergic Receptor Nicotinic Alpha 9 Subunit 2 3 5
  • Cholinergic Receptor, Nicotinic, Alpha Polypeptide 9 2 3
  • Cholinergic Receptor, Nicotinic, Alpha 9 (Neuronal) 2 3
  • Neuronal Acetylcholine Receptor Subunit Alpha-9 3 4
  • Cholinergic Receptor, Nicotinic Alpha 9 2 3
  • NACHRA9 3 4
  • Acetylcholine Receptor, Neuronal Nicotinic, Alpha-9 Subunit 3
  • Neuronal Acetylcholine Receptor Protein, Alpha-9 Subunit 3
  • Acetylcholine Receptor, Nicotinic, Alpha 9 (Neuronal) 2
  • Nicotinic Acetylcholine Receptor Subunit Alpha 9 3
  • Nicotinic Acetylcholine Receptor Subunit Alpha-9 4
  • NACHR Alpha 9 3
  • NACHR Alpha-9 4
  • HSA243342 3

External Ids for CHRNA9 Gene

Previous GeneCards Identifiers for CHRNA9 Gene

  • GC04P040401
  • GC04P040620
  • GC04P040187
  • GC04P040253
  • GC04P040178
  • GC04P040032
  • GC04P039659

Summaries for CHRNA9 Gene

Entrez Gene Summary for CHRNA9 Gene

  • This gene is a member of the ligand-gated ionic channel family and nicotinic acetylcholine receptor gene superfamily. It encodes a plasma membrane protein that forms homo- or hetero-oligomeric divalent cation channels. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea. [provided by RefSeq, Feb 2012]

GeneCards Summary for CHRNA9 Gene

CHRNA9 (Cholinergic Receptor Nicotinic Alpha 9 Subunit) is a Protein Coding gene. Diseases associated with CHRNA9 include Deafness, Autosomal Recessive 25 and Tobacco Addiction. Among its related pathways are Transmission across Chemical Synapses and Postsynaptic nicotinic acetylcholine receptors. Gene Ontology (GO) annotations related to this gene include calcium channel activity. An important paralog of this gene is CHRNA10.

UniProtKB/Swiss-Prot Summary for CHRNA9 Gene

  • Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding induces a conformation change that leads to the opening of an ion-conducting channel across the plasma membrane (PubMed:11752216, PubMed:25282151). The channel is permeable to a range of divalent cations including calcium, the influx of which may activate a potassium current which hyperpolarizes the cell membrane (PubMed:11752216, PubMed:25282151). In the ear, this may lead to a reduction in basilar membrane motion, altering the activity of auditory nerve fibers and reducing the range of dynamic hearing. This may protect against acoustic trauma. May also regulate keratinocyte adhesion (PubMed:11021840).

Gene Wiki entry for CHRNA9 Gene

Additional gene information for CHRNA9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CHRNA9 Gene

Genomics for CHRNA9 Gene

GeneHancer (GH) Regulatory Elements for CHRNA9 Gene

Promoters and enhancers for CHRNA9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J040333 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 500.7 -0.5 -512 2.8 ZSCAN5C TCF12 JUND FOS ZNF639 ZNF10 REST TRIM28 KLF7 EP300 CHRNA9 RNU7-74P LOC344967 N4BP2 LINC02265
GH04J040189 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.7 -135.4 -135351 22.4 EP300 ZBTB40 TCF12 SIN3A NRF1 SP1 NCOR1 GTF2E2 ZBTB5 CLOCK RHOH N4BP2 RBM47 LOC344967 CHRNA9 UGDH-AS1 ARL4AP2 lnc-N4BP2-3 ENSG00000286089 piR-57133-453
GH04J040417 Enhancer 1.2 Ensembl ENCODE dbSUPER 16.3 +85.2 85234 6.1 TCF12 KDM6A TCF7 TOE1 TEAD1 ZKSCAN8 FOXA2 ZSCAN9 NR2F2 ESRRA RBM47 CHRNA9 RNU7-74P ENSG00000250893 piR-48369-128
GH04J040298 Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 11.9 -30.9 -30924 12.7 CTCF NRF1 SP1 PHB2 EP300 JUND REST RELA MEF2C MYC N4BP2 RHOH CHRNA9 LOC344967 PDS5A LINC02265 HSALNG0034001
GH04J040182 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.9 -150.0 -150028 5 EP300 POLR2A RELA RCOR1 TRIM22 RBM25 BCL11A ZNF316 CBFB ZNF384 HSALNG0033997 ENSG00000286089 CHRNA9 RNU7-74P UGDH-AS1 RBM47 ENSG00000260296 N4BP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHRNA9 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CHRNA9

Top Transcription factor binding sites by QIAGEN in the CHRNA9 gene promoter:
  • AP-4
  • ATF6
  • FOXD1
  • HSF2
  • IRF-2
  • MEF-2
  • MEF-2A
  • Pbx1a
  • RORalpha1
  • RORalpha2

Genomic Locations for CHRNA9 Gene

Genomic Locations for CHRNA9 Gene
chr4:40,335,329-40,355,217
(GRCh38/hg38)
Size:
19,889 bases
Orientation:
Plus strand
chr4:40,337,346-40,357,234
(GRCh37/hg19)
Size:
19,889 bases
Orientation:
Plus strand

Genomic View for CHRNA9 Gene

Genes around CHRNA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHRNA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHRNA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHRNA9 Gene

Proteins for CHRNA9 Gene

  • Protein details for CHRNA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UGM1-ACHA9_HUMAN
    Recommended name:
    Neuronal acetylcholine receptor subunit alpha-9
    Protein Accession:
    Q9UGM1
    Secondary Accessions:
    • Q14CY7
    • Q4W5A2
    • Q9NYV2

    Protein attributes for CHRNA9 Gene

    Size:
    479 amino acids
    Molecular mass:
    54807 Da
    Quaternary structure:
    • Can form homo- or heterooligomeric channels in conjunction with CHRNA10 (PubMed:11752216). The native outer hair cell receptor may be composed of CHRNA9-CHRNA10 heterooligomers. Interacts with the alpha-conotoxon RgIA (PubMed:22774872).
    Miscellaneous:
    • The heterooligomeric receptor composed of CHRNA9 and CHRNA10 has an atypical pharmacological profile, binding several non-nicotinic ligands including strychnine (a glycine receptor antagonist) and atropine (a muscarinic acetylcholine receptor antagonist).

    Three dimensional structures from OCA and Proteopedia for CHRNA9 Gene

neXtProt entry for CHRNA9 Gene

Post-translational modifications for CHRNA9 Gene

Other Protein References for CHRNA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CHRNA9 Gene

Domains & Families for CHRNA9 Gene

Gene Families for CHRNA9 Gene

Protein Domains for CHRNA9 Gene

Blocks:
  • Nicotinic acetylcholine receptor signature
  • Neurotransmitter-gated ion-channel
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CHRNA9 Gene

GenScript: Design optimal peptide antigens:
  • Nicotinic acetylcholine receptor subunit alpha-9 (ACHA9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UGM1

UniProtKB/Swiss-Prot:

ACHA9_HUMAN :
  • Belongs to the ligand-gated ion channel (TC 1.A.9) family. Acetylcholine receptor (TC 1.A.9.1) subfamily. Alpha-9/CHRNA9 sub-subfamily.
Family:
  • Belongs to the ligand-gated ion channel (TC 1.A.9) family. Acetylcholine receptor (TC 1.A.9.1) subfamily. Alpha-9/CHRNA9 sub-subfamily.
genes like me logo Genes that share domains with CHRNA9: view

Function for CHRNA9 Gene

Molecular function for CHRNA9 Gene

UniProtKB/Swiss-Prot Function:
Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding induces a conformation change that leads to the opening of an ion-conducting channel across the plasma membrane (PubMed:11752216, PubMed:25282151). The channel is permeable to a range of divalent cations including calcium, the influx of which may activate a potassium current which hyperpolarizes the cell membrane (PubMed:11752216, PubMed:25282151). In the ear, this may lead to a reduction in basilar membrane motion, altering the activity of auditory nerve fibers and reducing the range of dynamic hearing. This may protect against acoustic trauma. May also regulate keratinocyte adhesion (PubMed:11021840).

Phenotypes From GWAS Catalog for CHRNA9 Gene

Gene Ontology (GO) - Molecular Function for CHRNA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity IEA --
GO:0005216 ion channel activity IEA --
GO:0005230 contributes_to extracellular ligand-gated ion channel activity IBA 21873635
GO:0005262 calcium channel activity IEA --
GO:0005515 protein binding IPI 25282151
genes like me logo Genes that share ontologies with CHRNA9: view
genes like me logo Genes that share phenotypes with CHRNA9: view

Animal Models for CHRNA9 Gene

MGI Knock Outs for CHRNA9:

Animal Model Products

CRISPR Products

miRNA for CHRNA9 Gene

miRTarBase miRNAs that target CHRNA9

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CHRNA9 Gene

Localization for CHRNA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHRNA9 Gene

Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHRNA9 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CHRNA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA,IDA 25282151
GO:0005892 acetylcholine-gated channel complex IEA,IDA 25282151
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CHRNA9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CHRNA9 Gene

Pathways & Interactions for CHRNA9 Gene

genes like me logo Genes that share pathways with CHRNA9: view

Gene Ontology (GO) - Biological Process for CHRNA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006812 cation transport IEA --
GO:0006816 calcium ion transport IEA --
GO:0007165 signal transduction IBA 21873635
GO:0007204 positive regulation of cytosolic calcium ion concentration IGI 18420419
genes like me logo Genes that share ontologies with CHRNA9: view

No data available for SIGNOR curated interactions for CHRNA9 Gene

Drugs & Compounds for CHRNA9 Gene

(17) Drugs for CHRNA9 Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Nicotine Approved Pharma Antagonist, Activation, Activator, antagonist, Target, agonist 1469
Ethanol Approved Pharma Target 3220
Galantamine Approved Pharma Target, allosteric modulator Acetylcholinesterase inhibitor 108
Calcium Approved Nutra 7884
tetraethylammonium Experimental, Investigational Pharma Inhibitor, Pore Blocker, Antagonist, Inhibition, Target, agonist, inhibitor 1

(4) Additional Compounds for CHRNA9 Gene - From: IUPHAR

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
[<sup>125</sup>I]alpha-bungarotoxin
[<sup>3</sup>H]alpha-bungarotoxin
alpha-bungarotoxin
Antagonist
alpha-conotoxin RgIA
Antagonist

(2) ApexBio Compounds for CHRNA9 Gene

Compound Action Cas Number
ACV 1 740980-24-9
α-Conotoxin ImI 156467-85-5
genes like me logo Genes that share compounds with CHRNA9: view

Drug Products

Transcripts for CHRNA9 Gene

mRNA/cDNA for CHRNA9 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHRNA9 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP1: - - -
SP2:
SP3:

Relevant External Links for CHRNA9 Gene

GeneLoc Exon Structure for
CHRNA9

Expression for CHRNA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHRNA9 Gene

mRNA differential expression in normal tissues according to GTEx for CHRNA9 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x10.3) and Skin - Not Sun Exposed (Suprapubic) (x7.0).

Protein differential expression in normal tissues from HIPED for CHRNA9 Gene

This gene is overexpressed in Pancreas (64.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CHRNA9 Gene



Protein tissue co-expression partners for CHRNA9 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CHRNA9

SOURCE GeneReport for Unigene cluster for CHRNA9 Gene:

Hs.272278

mRNA Expression by UniProt/SwissProt for CHRNA9 Gene:

Q9UGM1-ACHA9_HUMAN
Tissue specificity: Expressed in cochlea, keratinocytes, pituitary gland, B-cells and T-cells.
genes like me logo Genes that share expression patterns with CHRNA9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CHRNA9 Gene

Orthologs for CHRNA9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CHRNA9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHRNA9 31 30
  • 99.3 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CHRNA9 31 30
  • 90.26 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CHRNA9 31 30
  • 89.63 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chrna9 30
  • 86.57 (n)
mouse
(Mus musculus)
Mammalia Chrna9 17 31 30
  • 85.46 (n)
oppossum
(Monodelphis domestica)
Mammalia CHRNA9 31
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHRNA9 31
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHRNA9 31 30
  • 71.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHRNA9 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chrna9 30
  • 70.11 (n)
zebrafish
(Danio rerio)
Actinopterygii chrna9 31 30
  • 71.58 (n)
OneToMany
CHRNA9 (1 of 3) 31
  • 62 (a)
OneToMany
chrna10a 31
  • 53 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.90 30
fruit fly
(Drosophila melanogaster)
Insecta nAcR&bgr;-21C 32
  • 31 (a)
nAcRbeta-21C 31
  • 23 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea acr-22 32
  • 34 (a)
acr-17 32
  • 34 (a)
deg-3 32
  • 33 (a)
F18G5.4 32
  • 33 (a)
Y73F8A.30 32
  • 31 (a)
acr-18 32
  • 30 (a)
Y44A6E.1 32
  • 28 (a)
C04C3.2 32
  • 28 (a)
Y57G11C.2 32
  • 25 (a)
lgc-1 31
  • 19 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 23 (a)
ManyToMany
Species where no ortholog for CHRNA9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CHRNA9 Gene

ENSEMBL:
Gene Tree for CHRNA9 (if available)
TreeFam:
Gene Tree for CHRNA9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CHRNA9: view image

Paralogs for CHRNA9 Gene

Variants for CHRNA9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CHRNA9 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs10009228 - p.Asn442Ser
rs10024518 - p.Arg96Gln
rs55633891 - p.Ala315Val

Additional dbSNP identifiers (rs#s) for CHRNA9 Gene

Structural Variations from Database of Genomic Variants (DGV) for CHRNA9 Gene

Variant ID Type Subtype PubMed ID
esv3330900 CNV duplication 20981092
esv3569393 CNV loss 25503493
nsv1074706 CNV deletion 25765185
nsv1136043 CNV deletion 24896259
nsv1139233 CNV deletion 24896259

Variation tolerance for CHRNA9 Gene

Residual Variation Intolerance Score: 94.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.18; 84.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHRNA9 Gene

Human Gene Mutation Database (HGMD)
CHRNA9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHRNA9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHRNA9 Gene

Disorders for CHRNA9 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CHRNA9 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 25
  • dfnb25
tobacco addiction
  • tobacco addiction, susceptibility to
limited scleroderma
  • crest syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CHRNA9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CHRNA9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHRNA9 Gene

Publications for CHRNA9 Gene

  1. Why do young women smoke? V. Role of direct and interactive effects of nicotinic cholinergic receptor gene variation on neurocognitive function. (PMID: 17559419) Rigbi A … Lerer B (Genes, brain, and behavior 2008) 3 23 41 54
  2. Chromosome location and characterization of the human nicotinic acetylcholine receptor subunit alpha (alpha) 9 (CHRNA9) gene. (PMID: 12697997) Lustig LR … Peng H (Cytogenetic and genome research 2002) 3 4 23 54
  3. A novel human nicotinic receptor subunit, alpha10, that confers functionality to the alpha9-subunit. (PMID: 11752216) Sgard F … Besnard F (Molecular pharmacology 2002) 3 4 23 54
  4. Crystal structures of free and antagonist-bound states of human α9 nicotinic receptor extracellular domain. (PMID: 25282151) Zouridakis M … Tzartos SJ (Nature structural & molecular biology 2014) 3 4 54
  5. Molecular basis for the differential sensitivity of rat and human α9α10 nAChRs to α-conotoxin RgIA. (PMID: 22774872) Azam L … McIntosh JM (Journal of neurochemistry 2012) 3 4 54

Products for CHRNA9 Gene

Sources for CHRNA9 Gene