CHRNA7
cholinergic receptor nicotinic alpha 7 subunit, the group of Cholinergic receptors nicotinic subunits
Basic information
Region (hg38): 15:31923438-32173018
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AD
- epilepsy (Refuted Evidence), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurocognitive dysfunction with distinctive craniofacial features | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Neurologic | 22775350 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (53 variants)
- not_provided (27 variants)
- CHRNA7-related_disorder (4 variants)
- Chromosome_15q13.3_microdeletion_syndrome (1 variants)
- Epilepsy,_idiopathic_generalized,_susceptibility_to,_7 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000746.6. 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 | 10 | 11 | ||||
| missense | 54 | 59 | ||||
| nonsense | 1 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 57 | 13 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHRNA7 | protein_coding | protein_coding | ENST00000454250 | 10 | 142032 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000415 | 0.992 | 125714 | 0 | 34 | 125748 | 0.000135 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 190 | 245 | 0.776 | 0.0000139 | 3347 |
| Missense in Polyphen | 51 | 88.223 | 0.57808 | 1264 | ||
| Synonymous | 0.706 | 98 | 107 | 0.913 | 0.00000701 | 1010 |
| Loss of Function | 2.34 | 9 | 20.4 | 0.440 | 9.48e-7 | 266 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000560 | 0.000547 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000172 | 0.000167 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000338 | 0.0000327 |
| Other | 0.00 | 0.00 |
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. The channel is blocked by alpha-bungarotoxin.;
- Pathway
- Nicotine addiction - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Sympathetic Nerve Pathway (Pre- and Post- Ganglionic Junction);Phosphodiesterases in neuronal function;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;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
- 0.345
Haploinsufficiency Scores
- pHI
- 0.452
- hipred
- hipred_score
- ghis
- 0.444
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.792
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chrna7
- Phenotype
- endocrine/exocrine gland phenotype; taste/olfaction phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; limbs/digits/tail 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); digestive/alimentary phenotype; pigmentation phenotype; normal 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); reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- activation of MAPK activity;response to hypoxia;positive regulation of protein phosphorylation;ion transport;calcium ion transport;cellular calcium ion homeostasis;signal transduction;chemical synaptic transmission;synaptic transmission, cholinergic;learning or memory;memory;short-term memory;positive regulation of cell population proliferation;negative regulation of tumor necrosis factor production;ion transmembrane transport;response to nicotine;regulation of membrane potential;positive regulation of angiogenesis;synapse organization;nervous system process;cognition;sensory processing;positive regulation of protein metabolic process;excitatory postsynaptic potential;positive regulation of ERK1 and ERK2 cascade;calcium ion transmembrane transport;acetylcholine receptor signaling pathway;dendritic spine organization;modulation of excitatory postsynaptic potential;dendrite arborization;positive regulation of long-term synaptic potentiation;regulation of neuron death;positive regulation of amyloid-beta formation;negative regulation of amyloid-beta formation;regulation of amyloid precursor protein catabolic process;response to amyloid-beta;response to acetylcholine;regulation of amyloid fibril formation;positive regulation of CoA-transferase activity;positive regulation of excitatory postsynaptic potential
- Cellular component
- plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;integral component of membrane;cell junction;neuron projection;plasma membrane raft;synapse;postsynaptic membrane;postsynapse
- Molecular function
- amyloid-beta binding;transmembrane signaling receptor activity;ion channel activity;extracellular ligand-gated ion channel activity;calcium channel activity;protein binding;acetylcholine receptor activity;toxic substance binding;chloride channel regulator activity;acetylcholine-gated cation-selective channel activity;acetylcholine binding;protein homodimerization activity