CHRNA3
Basic information
Region (hg38): 15:78593052-78621295
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Bladder dysfunction, autonomic, with impaired pupillary reflex and secondary congenital anomalies of the kidney and urinary tract | AR | Renal | The 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; Renal | 31708116 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 20 | 28 | ||||
missense | 25 | 32 | ||||
nonsense | 1 | |||||
start loss | 1 | |||||
frameshift | 5 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 3 | 4 | |||
non coding | 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) | ||
15-78593235-T-G | not specified | Uncertain significance (Mar 18, 2024) | ||
15-78593805-T-C | Lung adenocarcinoma | Uncertain significance (Jun 06, 2022) | ||
15-78594000-T-C | Squamous cell carcinoma | Uncertain significance (Jun 06, 2022) | ||
15-78596626-AG-A | Uncertain significance (Apr 12, 2022) | |||
15-78596629-G-A | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
15-78596634-C-T | Likely benign (Jul 21, 2022) | |||
15-78596644-C-G | Inborn genetic diseases | Uncertain significance (Jul 27, 2021) | ||
15-78596650-G-A | Uncertain significance (Jun 12, 2024) | |||
15-78596663-A-T | Uncertain significance (May 03, 2022) | |||
15-78596692-C-T | Inborn genetic diseases | Uncertain significance (Aug 05, 2023) | ||
15-78596693-G-T | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
15-78596749-TAAAA-T | Benign (Oct 23, 2023) | |||
15-78596749-TAAAAG-T | Likely benign (Sep 26, 2022) | |||
15-78601259-G-A | Benign (Jan 25, 2024) | |||
15-78601288-CAAT-C | Uncertain significance (Nov 08, 2022) | |||
15-78601290-A-G | CHRNA3-related disorder | Likely benign (Oct 13, 2022) | ||
15-78601295-C-T | Likely benign (Nov 08, 2022) | |||
15-78601310-G-A | Likely benign (Apr 09, 2023) | |||
15-78601383-G-A | Likely benign (Sep 29, 2023) | |||
15-78601399-A-C | Benign (Dec 13, 2023) | |||
15-78601445-G-A | Urinary bladder, atony of;Smoking as a quantitative trait locus 3 | Benign/Likely benign (Jan 27, 2024) | ||
15-78601473-C-G | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
15-78601479-G-A | Likely benign (Aug 19, 2023) | |||
15-78601492-T-C | Inborn genetic diseases | Uncertain significance (Mar 30, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CHRNA3 | protein_coding | protein_coding | ENST00000326828 | 6 | 28244 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.42e-7 | 0.618 | 125642 | 0 | 106 | 125748 | 0.000422 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.735 | 247 | 282 | 0.877 | 0.0000166 | 3288 |
Missense in Polyphen | 119 | 155.9 | 0.76331 | 1816 | ||
Synonymous | -2.55 | 158 | 122 | 1.29 | 0.00000842 | 1016 |
Loss of Function | 1.09 | 13 | 18.0 | 0.722 | 7.67e-7 | 226 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000666 | 0.000666 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000436 | 0.000435 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000511 | 0.000510 |
Middle Eastern | 0.000436 | 0.000435 |
South Asian | 0.000655 | 0.000653 |
Other | 0.000815 | 0.000815 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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