CHRNA6
Basic information
Region (hg38): 8:42752620-42796392
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004198.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 38 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 2 | 4 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHRNA6 | protein_coding | protein_coding | ENST00000276410 | 6 | 43773 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.57e-8 | 0.559 | 125553 | 1 | 192 | 125746 | 0.000768 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.125 | 262 | 268 | 0.979 | 0.0000136 | 3275 |
| Missense in Polyphen | 125 | 136.52 | 0.91559 | 1754 | ||
| Synonymous | 0.565 | 97 | 104 | 0.930 | 0.00000586 | 954 |
| Loss of Function | 1.06 | 14 | 19.0 | 0.737 | 9.06e-7 | 229 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000750 | 0.000750 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000653 | 0.000653 |
| Finnish | 0.000926 | 0.000924 |
| European (Non-Finnish) | 0.00117 | 0.00116 |
| Middle Eastern | 0.000653 | 0.000653 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.000979 | 0.000978 |
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
- Nicotine addiction - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Nicotine Activity on Dopaminergic Neurons;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
- 0.148
Intolerance Scores
- loftool
- 0.353
- rvis_EVS
- -0.78
- rvis_percentile_EVS
- 12.97
Haploinsufficiency Scores
- pHI
- 0.0566
- hipred
- N
- hipred_score
- 0.197
- ghis
- 0.436
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.178
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chrna6
- 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);
Gene ontology
- Biological process
- signal transduction;chemical synaptic transmission;synaptic transmission, cholinergic;neuromuscular synaptic transmission;regulation of dopamine secretion;ion transmembrane transport;response to nicotine;regulation of membrane potential;nervous system process;membrane depolarization;excitatory postsynaptic potential;regulation of synaptic vesicle exocytosis
- Cellular component
- plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;cell junction;neuron projection;synapse;dopaminergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
- Molecular function
- extracellular ligand-gated ion channel activity;protein binding;acetylcholine receptor activity;acetylcholine-gated cation-selective channel activity;acetylcholine binding