CHRNA3

cholinergic receptor nicotinic alpha 3 subunit, the group of Cholinergic receptors nicotinic subunits

Basic information

Region (hg38): 15:78593052-78621295

Links

ENSG00000080644NCBI:1136OMIM:118503HGNC:1957Uniprot:P32297AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bladder dysfunction, autonomic, with impaired pupillary reflex and secondary congenital anomalies of the kidney and urinary tractARRenalThe condition can involve chronic kidney disease andrecurrent urinary tract infections, and awareness may allow prompt diagnosis and management (of note, surgical management of VUR has not been reported as effective)Neurologic; Renal31708116

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHRNA3 gene.

  • Urinary bladder, atony of (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
20
clinvar
7
clinvar
28
missense
25
clinvar
4
clinvar
3
clinvar
32
nonsense
1
clinvar
1
start loss
1
clinvar
1
frameshift
1
clinvar
3
clinvar
1
clinvar
5
inframe indel
2
clinvar
2
clinvar
4
splice donor/acceptor (+/-2bp)
0
splice region
1
3
4
non coding
4
clinvar
3
clinvar
4
clinvar
11
Total 1 5 33 27 16

Variants in CHRNA3

This is a list of pathogenic ClinVar variants found in the CHRNA3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
15-78593158-G-C not specified Uncertain significance (Aug 14, 2023)2598899
15-78593235-T-G not specified Uncertain significance (Mar 18, 2024)3267172
15-78593805-T-C Lung adenocarcinoma Uncertain significance (Jun 06, 2022)2431162
15-78594000-T-C Squamous cell carcinoma Uncertain significance (Jun 06, 2022)2431164
15-78596626-AG-A Uncertain significance (Apr 12, 2022)1971011
15-78596629-G-A Inborn genetic diseases Uncertain significance (Oct 12, 2022)2318093
15-78596634-C-T Likely benign (Jul 21, 2022)2192524
15-78596644-C-G Inborn genetic diseases Uncertain significance (Jul 27, 2021)2239591
15-78596650-G-A Uncertain significance (Jun 12, 2024)422608
15-78596663-A-T Uncertain significance (May 03, 2022)2133189
15-78596692-C-T Inborn genetic diseases Uncertain significance (Aug 05, 2023)2616568
15-78596693-G-T Inborn genetic diseases Uncertain significance (Aug 02, 2022)2304521
15-78596749-TAAAA-T Benign (Oct 23, 2023)1971188
15-78596749-TAAAAG-T Likely benign (Sep 26, 2022)2023242
15-78601259-G-A Benign (Jan 25, 2024)2724249
15-78601288-CAAT-C Uncertain significance (Nov 08, 2022)2183741
15-78601290-A-G CHRNA3-related disorder Likely benign (Oct 13, 2022)2182780
15-78601295-C-T Likely benign (Nov 08, 2022)2183742
15-78601310-G-A Likely benign (Apr 09, 2023)3017262
15-78601383-G-A Likely benign (Sep 29, 2023)2083191
15-78601399-A-C Benign (Dec 13, 2023)736331
15-78601445-G-A Urinary bladder, atony of;Smoking as a quantitative trait locus 3 Benign/Likely benign (Jan 27, 2024)722730
15-78601473-C-G Inborn genetic diseases Uncertain significance (Oct 26, 2022)2209699
15-78601479-G-A Likely benign (Aug 19, 2023)2066696
15-78601492-T-C Inborn genetic diseases Uncertain significance (Mar 30, 2024)3267166

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHRNA3protein_codingprotein_codingENST00000326828 628244
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.42e-70.61812564201061257480.000422
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7352472820.8770.00001663288
Missense in Polyphen119155.90.763311816
Synonymous-2.551581221.290.000008421016
Loss of Function1.091318.00.7227.67e-7226

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006660.000666
Ashkenazi Jewish0.000.00
East Asian0.0004360.000435
Finnish0.00004620.0000462
European (Non-Finnish)0.0005110.000510
Middle Eastern0.0004360.000435
South Asian0.0006550.000653
Other0.0008150.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: After binding acetylcholine, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane.;
Pathway
Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Nicotine Pathway (Chromaffin Cell), Pharmacodynamics;Nicotine Metabolism Pathway;Nicotine Action Pathway;Nicotine Activity on Dopaminergic Neurons;Nicotine Activity on Chromaffin Cells;Highly sodium permeable acetylcholine nicotinic receptors;Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Highly calcium permeable nicotinic acetylcholine receptors;Presynaptic nicotinic acetylcholine receptors;Highly calcium permeable postsynaptic nicotinic acetylcholine receptors;Postsynaptic nicotinic acetylcholine receptors;Activation of Nicotinic Acetylcholine Receptors;Acetylcholine binding and downstream events (Consensus)

Recessive Scores

pRec
0.252

Intolerance Scores

loftool
0.0990
rvis_EVS
-1.11
rvis_percentile_EVS
6.78

Haploinsufficiency Scores

pHI
0.287
hipred
N
hipred_score
0.390
ghis
0.459

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.159

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Chrna3
Phenotype
vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;

Gene ontology

Biological process
ion transport;regulation of smooth muscle contraction;signal transduction;activation of transmembrane receptor protein tyrosine kinase activity;chemical synaptic transmission;synaptic transmission, cholinergic;neuromuscular synaptic transmission;nervous system development;locomotory behavior;regulation of acetylcholine secretion, neurotransmission;ion transmembrane transport;response to nicotine;behavioral response to nicotine;regulation of membrane potential;regulation of dendrite morphogenesis;nervous system process;excitatory postsynaptic potential;synaptic transmission involved in micturition;acetylcholine receptor signaling pathway;response to acetylcholine
Cellular component
plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;postsynaptic density;integral component of membrane;cell junction;dendrite;neuron projection;neuronal cell body;plasma membrane raft;synapse;postsynaptic membrane
Molecular function
extracellular ligand-gated ion channel activity;protein binding;ligand-gated ion channel activity;acetylcholine receptor activity;acetylcholine-gated cation-selective channel activity;acetylcholine binding