CHRNE
protein-codingcholinergic receptor nicotinic epsilon subunit, the group of Cholinergic receptors nicotinic subunits
Gene summary
Acetylcholine receptors at mature mammalian neuromuscular junctions are pentameric protein complexes composed of four subunits in the ratio of two alpha subunits to one beta, one epsilon, and one delta subunit. The acetylcholine receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the epsilon subunit are associated with congenital myasthenic syndrome. [provided by RefSeq, Sep 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011600
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014586
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0012157
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0012157
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014586
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0011600
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0018940
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0011600
Submitter: Natera
Inheritance Pattern: AD
Disease ID:MONDO:0011600
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014586
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Musculoskeletal; Neurologic
Intervention: Musculoskeletal; Neurologic; Pharmacogenomic
Rationale: Most individuals with Myasthenic syndrome, congenital, benefit from AChE inhibitors and/or potassium channel blocker 3,4-diaminopyridine (3,4-DAP), though caution must be used in giving 3,4-DAP to young children and individuals with fast-channel syndromes; For Slow-channel congenital myasthenic syndrome, effective treatment has been reported with therapies such as quinidine, fluoxetine, and ephedrine, while cholinesterase inhibitors and amifampridine should be avoided; Additional neurologic monitoring in pregnancy may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CHRNE variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000080.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 13 | 393 | 4 | 410 | ||
| missense | 9 | 54 | 374 | 19 | 1 | 457 |
| nonsense | 25 | 26 | 4 | 55 | ||
| start loss | 2 | 2 | ||||
| frameshift | 71 | 74 | 1 | 146 | ||
| splice donor/acceptor (+/-2bp) | 15 | 32 | 2 | 49 | ||
| Total | 120 | 188 | 394 | 412 | 5 | 1119 |
Highest pathogenic variant AF is 0.0011394095
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000071.1 | 12 | MANE Select | |
| Ensembl | ENSP00000497829.1 | 12 | MANE Select | |
| Ensembl | ENSP00000496907.1 | 3 | Standard | |
| Ensembl | ENSP00000686983.1 | 12 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| chrne | Danio rerio | Structure: synaptic transmission, cholinergic Quality: amplitude abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
- Highly sodium permeable acetylcholine nicotinic receptors
- Neuronal System
- Neurotransmitter receptors and postsynaptic signal transmission
- Transmission across Chemical Synapses
Biological Process
- muscle contraction
- signal transduction
- chemical synaptic transmission
- synaptic transmission, cholinergic
- neuromuscular synaptic transmission
Molecular Function
- extracellular ligand-gated ion channel activity
- cation transmembrane transporter activity
- acetylcholine receptor activity
- acetylcholine-gated cation-selective channel activity
- acetylcholine binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- acetylcholine-gated channel complex
- cell junction
- neuromuscular junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000293780
- Coding exons
- 12
- Length
- 5301
- Individuals with no LoFs
- 125611
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 137
- Defined
- 125748
- p
- 0.000545
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.850 | 359 | 316 | 1.13 | 0.0000225 | 3127 |
| Missense (PolyPhen) | 154 | 140.53 | 1.0959 | 1444 | ||
| Synonymous | -2.92 | 188 | 144 | 1.31 | 0.0000118 | 1013 |
| Loss of Function | 1.60 | 17 | 25.8 | 0.660 | 0.00000142 | 259 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00058 | 0.00055 | rare |
| Latino/Admixed American | 0.0010 | 0.0010 | notable |
| Ashkenazi Jewish | 0.0033 | 0.0030 | notable |
| East Asian | 0.00035 | 0.00033 | rare |
| Finnish | 0.000055 | 0.000046 | rare |
| European (Non-Finnish) | 0.00035 | 0.00033 | rare |
| South Asian | 0.00043 | 0.00042 | rare |
| Other | 0.00083 | 0.00081 | rare |
dbNSFP Gene Annotations
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. {ECO:0000269|PubMed:27375219}.;
- Disease
- DISEASE: Note=The muscle AChR is the major target antigen in the autoimmune disease myasthenia gravis. Myasthenia gravis is characterized by sporadic muscular fatigability and weakness, occurring chiefly in muscles innervated by cranial nerves, and characteristically improved by cholinesterase-inhibiting drugs.; DISEASE: Myasthenic syndrome, congenital, 4A, slow-channel (CMS4A) [MIM:605809]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. CMS4A is a slow-channel myasthenic syndrome. It is caused by kinetic abnormalities of the AChR, resulting in prolonged AChR channel opening episodes, prolonged endplate currents, and depolarization block. This is associated with calcium overload, which may contribute to subsequent degeneration of the endplate and postsynaptic membrane. {ECO:0000269|PubMed:12141316, ECO:0000269|PubMed:27375219, ECO:0000269|PubMed:7531341, ECO:0000269|PubMed:7538206, ECO:0000269|PubMed:8872460}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 4B, fast-channel (CMS4B) [MIM:616324]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. CMS4B is a fast-channel myasthenic syndrome. It is caused by kinetic abnormalities of the AChR, resulting in brief opening and activity of the channel, with a rapid decay in endplate current, failure to achieve threshold depolarization of the endplate and consequent failure to fire an action potential. {ECO:0000269|PubMed:10962020, ECO:0000269|PubMed:22592360, ECO:0000269|PubMed:8755487}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiency (CMS4C) [MIM:608931]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. CMS4C is an autosomal recessive disorder of postsynaptic neuromuscular transmission, due to deficiency of AChR at the endplate that results in low amplitude of the miniature endplate potential and current. {ECO:0000269|PubMed:9158150}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.160
- RVIS EVS
- -0.91
- RVIS percentile EVS
- 10.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.710
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |