CHRNA10
Basic information
Region (hg38): 11:3665587-3671384
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (87 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020402.4. 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 | 1 | |||||
| missense | 81 | 87 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 81 | 7 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHRNA10 | protein_coding | protein_coding | ENST00000250699 | 5 | 5798 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.79e-10 | 0.113 | 125633 | 1 | 114 | 125748 | 0.000457 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.140 | 317 | 310 | 1.02 | 0.0000225 | 2825 |
| Missense in Polyphen | 109 | 100.48 | 1.0848 | 1021 | ||
| Synonymous | -0.122 | 141 | 139 | 1.01 | 0.0000105 | 1013 |
| Loss of Function | 0.263 | 15 | 16.1 | 0.929 | 9.75e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000592 | 0.000591 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00218 | 0.00218 |
| Finnish | 0.000216 | 0.000139 |
| European (Non-Finnish) | 0.000337 | 0.000308 |
| Middle Eastern | 0.00218 | 0.00218 |
| South Asian | 0.000557 | 0.000555 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding may induce an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. 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. 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. {ECO:0000269|PubMed:11752216}.;
- Pathway
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.278
- rvis_EVS
- 0.84
- rvis_percentile_EVS
- 88.38
Haploinsufficiency Scores
- pHI
- 0.0349
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.462
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.204
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chrna10
- Phenotype
- hearing/vestibular/ear 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;positive regulation of cytosolic calcium ion concentration;chemical synaptic transmission;synaptic transmission, cholinergic;ion transmembrane transport;regulation of cell population proliferation;regulation of membrane potential;inner ear morphogenesis;nervous system process;detection of mechanical stimulus involved in sensory perception of sound;excitatory postsynaptic potential;negative regulation of ERK1 and ERK2 cascade;calcium ion transmembrane transport
- Cellular component
- integral component of plasma membrane;membrane;cell junction;axon;neuron projection;perikaryon;synapse;cholinergic synapse;integral component of postsynaptic specialization membrane
- Molecular function
- transmembrane signaling receptor activity;signaling receptor binding;extracellular ligand-gated ion channel activity;calcium channel activity;acetylcholine-gated cation-selective channel activity