CHRNE

protein-coding

cholinergic 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

NM_000080.4

Inheritance

AR, AD

ClinVar variants

P:308U:394B:417

Top phenotype

Myasthenic syndrome, congenital, 4A, slow-channel; Myasthenic syndrome, congenital, 4B, fast-channel; Myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiency

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr17:4,897,771-4,934,438

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital myasthenic syndrome 4ASTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011600

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 4BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014586

Submitter: Natera

congenital myasthenic syndrome 4CDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012157

Submitter: Natera

congenital myasthenic syndrome 4CSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012157

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 4BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014586

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 4ASTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011600

Submitter: Genomics England PanelApp

congenital myasthenic syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018940

Submitter: Illumina

congenital myasthenic syndrome 4ADEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011600

Submitter: Natera

congenital myasthenic syndrome 4ASTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011600

Submitter: Labcorp Genetics (formerly Invitae)

congenital myasthenic syndrome 4BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014586

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Myasthenic syndrome, congenital, 4A, slow-channel; Myasthenic syndrome, congenital, 4B, fast-channel; Myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiencyAD/AR

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

Refs: 8232384; 7538206; 7531341; 8957026; 8872460; 8755487; 9158150; 0514102; 10211467; 10962020; 10534268; 11030414; 12141316; 12034803; 15322984; 16087917; 19064877; 20301347; 20562457; 23108489; 25792100Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHRNE variants in ClinVar

21 Conditions Cataloged
Congenital myasthenic syndrome 4ATotal: 1223
Congenital myasthenic syndromeTotal: 320
not providedTotal: 237
Inborn genetic diseasesTotal: 116
Congenital myasthenic syndrome 4CTotal: 101
Congenital myasthenic syndrome 4BTotal: 97
not specifiedTotal: 66
CHRNE-related disorderTotal: 57

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.

EffectPLPVUSLBBSum
synonymous
13
clinvar
393
clinvar
4
clinvar
410
missense
9
clinvar
54
clinvar
374
clinvar
19
clinvar
1
clinvar
457
nonsense
25
clinvar
26
clinvar
4
clinvar
55
start loss
2
clinvar
2
frameshift
71
clinvar
74
clinvar
1
clinvar
146
splice donor/acceptor (+/-2bp)
15
clinvar
32
clinvar
2
clinvar
49
Total12018839441251119

Highest pathogenic variant AF is 0.0011394095

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000080.4RefSeqNP_000071.112MANE Select
ENST00000649488.2EnsemblENSP00000497829.112MANE Select
ENST00000649830.1EnsemblENSP00000496907.13Standard
ENST00001017166.1EnsemblENSP00000686983.112Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
chrneDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.8503593161.130.00002253127
Missense (PolyPhen)154140.531.09591444
Synonymous-2.921881441.310.00001181013
Loss of Function1.601725.80.6600.00000142259

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000580.00055rare
Latino/Admixed American0.00100.0010notable
Ashkenazi Jewish0.00330.0030notable
East Asian0.000350.00033rare
Finnish0.0000550.000046rare
European (Non-Finnish)0.000350.00033rare
South Asian0.000430.00042rare
Other0.000830.00081rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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