CHRND

protein-coding

cholinergic receptor nicotinic delta subunit, the group of Cholinergic receptors nicotinic subunits

Gene summary

The acetylcholine receptor of muscle has 5 subunits of 4 different types: 2 alpha and 1 each of beta, gamma and delta subunits. After acetylcholine binding, the receptor undergoes an extensive conformation change that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. Defects in this gene are a cause of multiple pterygium syndrome lethal type (MUPSL), congenital myasthenic syndrome slow-channel type (SCCMS), and congenital myasthenic syndrome fast-channel type (FCCMS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

Previous symbols:
  • ACHRD

MANE transcript

NM_000751.3

Inheritance

AR, AD

ClinVar variants

P:54U:286B:133

Top phenotype

Myasthenic syndrome, congenital, 3A, slow-channel; Myasthenic syndrome, congenital, 3B, fast-channel; Myasthenic syndrome, congenital, 3C, associated with acetylcholine receptor deficiency

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr2:232,525,993-232,536,667

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~10.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

lethal multiple pterygium syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009668

Submitter: Orphanet

lethal multiple pterygium syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009668

Submitter: Labcorp Genetics (formerly Invitae)

congenital myasthenic syndrome 3ASTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014583

Submitter: Labcorp Genetics (formerly Invitae)

congenital myasthenic syndrome 3ASTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014583

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 3CSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014585

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 3BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014584

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 3CSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014585

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Myasthenic syndrome, congenital, 3A, slow-channel; Myasthenic syndrome, congenital, 3B, fast-channel; Myasthenic syndrome, congenital, 3C, 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: 11435464; 11782989; 18252226; 12499478; 16916845; 18398509; 23108489; 25792100Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHRND variants in ClinVar

16 Conditions Cataloged
Lethal multiple pterygium syndromeTotal: 495
not providedTotal: 143
Inborn genetic diseasesTotal: 67
not specifiedTotal: 35
Congenital myasthenic syndromeTotal: 34
Congenital myasthenic syndrome 3BTotal: 28
CHRND-related disorderTotal: 24
Congenital myasthenic syndrome 3ATotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000751.3. 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
6
clinvar
113
clinvar
119
missense
3
clinvar
13
clinvar
273
clinvar
17
clinvar
3
clinvar
309
nonsense
2
clinvar
5
clinvar
2
clinvar
9
start loss
1
clinvar
1
frameshift
10
clinvar
10
clinvar
2
clinvar
22
splice donor/acceptor (+/-2bp)
2
clinvar
8
clinvar
3
clinvar
13
Total18362861303473

Highest pathogenic variant AF is 0.00015715574

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000751.3RefSeqNP_000742.112MANE Select
ENST00000258385.8EnsemblENSP00000258385.312MANE Select
NM_001256657.2RefSeqNP_001243586.111Standard
NM_001311195.2RefSeqNP_001298124.17Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
chrndDanio rerio

Structure: fast muscle cell

Quality: decreased object quality

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

  • skeletal muscle contraction
  • cation transport
  • muscle contraction
  • signal transduction
  • chemical synaptic transmission

Molecular Function

  • extracellular ligand-gated ion channel activity
  • acetylcholine receptor activity
  • acetylcholine-gated cation-selective channel activity
  • acetylcholine binding
  • transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential

Cellular Component

  • nucleoplasm
  • cytosol
  • plasma membrane
  • integral component of plasma membrane
  • acetylcholine-gated channel complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000258385
Coding exons
12
Length
10675
Individuals with no LoFs
125630
Homozygous LoFs
0
Heterozygous LoFs
118
Defined
125748
p
0.000469
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.05402962990.9910.00002013377
Missense (PolyPhen)128124.891.02491434
Synonymous-0.05841241231.010.000007961058
Loss of Function1.651726.10.6520.00000149272

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish00.0absent
East Asian0.000330.00033rare
Finnish0.000830.00083rare
European (Non-Finnish)0.000670.00067rare
South Asian0.0000980.000098rare
Other0.000650.00065rare

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: Multiple pterygium syndrome, lethal type (LMPS) [MIM:253290]: Multiple pterygia are found infrequently in children with arthrogryposis and in fetuses with fetal akinesia syndrome. In lethal multiple pterygium syndrome there is intrauterine growth retardation, multiple pterygia, and flexion contractures causing severe arthrogryposis and fetal akinesia. Subcutaneous edema can be severe, causing fetal hydrops with cystic hygroma and lung hypoplasia. Oligohydramnios and facial anomalies are frequent. {ECO:0000269|PubMed:18252226}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 3A, slow-channel (CMS3A) [MIM:616321]: 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. CMS3A 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:11782989, ECO:0000269|PubMed:8872460}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 3B, fast-channel (CMS3B) [MIM:616322]: 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. CMS3B 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:11435464, ECO:0000269|PubMed:12499478, ECO:0000269|PubMed:18398509}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 3C, associated with acetylcholine receptor deficiency (CMS3C) [MIM:616323]: 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. CMS3C 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:16916845, ECO:0000269|PubMed:18398509}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.172

Intolerance Scores

LoFtool
0.230
RVIS EVS
-0.4
RVIS percentile EVS
26.93

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.524

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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