congenital myasthenic syndrome 4C

disease
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Also known as Cms IdCMS4Ccongenital myasthenic syndrome associated with acetylcholine receptor deficiencycongenital myasthenic syndrome type 4Cmyasthenia, familial infantile, 1myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiencymyasthenic syndrome, congenital, associated with acetylcholine receptor deficiency

Summary

congenital myasthenic syndrome 4C (MONDO:0012157) is a disease caused by CHRNE (GenCC Strong), with 8 cohort genes.

At a glance

  • Causal gene: CHRNE (GenCC Strong)
  • Cohort genes: 8
  • ClinVar variants: 178

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecongenital myasthenic syndrome 4C
Mondo IDMONDO:0012157
OMIM608931
DOIDDOID:0110679
UMLSC1837091
MedGen373251
GARD0010108
Is cancer (heuristic)no

Also known as: Cms Id · CMS4C · congenital myasthenic syndrome associated with acetylcholine receptor deficiency · congenital myasthenic syndrome type 4C · myasthenia, familial infantile, 1 · myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiency · myasthenic syndrome, congenital, associated with acetylcholine receptor deficiency

Data availability: 178 ClinVar variants · 1 GenCC gene-disease record · 3 cell lines.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disordercongenital nervous system disorderpostsynaptic congenital myasthenic syndromecongenital myasthenic syndrome 4congenital myasthenic syndrome 4C

Related subtypes (2): congenital myasthenic syndrome 4A, congenital myasthenic syndrome 4B

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

178 retrieved; paginated sample, class counts are floors:

46 uncertain significance, 33 conflicting classifications of pathogenicity, 30 pathogenic/likely pathogenic, 24 likely pathogenic, 23 pathogenic, 15 benign, 6 benign/likely benign, 1 likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1299524NM_000048.4(ASL):c.1327del (p.Thr443fs)ASLPathogeniccriteria provided, single submitter
18345NM_000080.4(CHRNE):c.500G>T (p.Arg167Leu)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
18347NM_000080.4(CHRNE):c.250C>T (p.Arg84Ter)C17orf107Pathogeniccriteria provided, multiple submitters, no conflicts
18357NM_000080.4(CHRNE):c.614_620del (p.Trp205fs)C17orf107Pathogeniccriteria provided, multiple submitters, no conflicts
243031NM_000080.4(CHRNE):c.1327delC17orf107Pathogeniccriteria provided, multiple submitters, no conflicts
372325NM_000080.4(CHRNE):c.905C>G (p.Pro302Arg)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
449451NM_000080.4(CHRNE):c.934_936del (p.Met312del)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
465864NM_000080.4(CHRNE):c.764C>T (p.Ser255Leu)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
534249NM_000080.4(CHRNE):c.293T>C (p.Leu98Pro)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
567393NM_000080.4(CHRNE):c.794del (p.Pro265fs)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
694659NM_000080.4(CHRNE):c.442T>A (p.Cys148Ser)C17orf107Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
803298NM_000080.4(CHRNE):c.854T>C (p.Val285Ala)C17orf107Pathogeniccriteria provided, single submitter
863073NM_000080.4(CHRNE):c.803-2A>GC17orf107Pathogeniccriteria provided, multiple submitters, no conflicts
813415NM_020549.5(CHAT):c.982del (p.Asp328fs)CHATPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1417628NM_000080.4(CHRNE):c.847C>T (p.Gln283Ter)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1454210NM_000080.4(CHRNE):c.105T>A (p.Tyr35Ter)CHRNEPathogeniccriteria provided, multiple submitters, no conflicts
1458892NM_000080.4(CHRNE):c.1219+2T>GCHRNEPathogeniccriteria provided, multiple submitters, no conflicts
1694812NM_000080.4(CHRNE):c.1255G>T (p.Glu419Ter)CHRNEPathogeniccriteria provided, multiple submitters, no conflicts
18346NM_000080.4(CHRNE):c.422C>T (p.Pro141Leu)CHRNEPathogeniccriteria provided, multiple submitters, no conflicts
18348NM_000080.4(CHRNE):c.971del (p.Ile324fs)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
18349NM_000080.4(CHRNE):c.344+1G>ACHRNEPathogenicno assertion criteria provided
18350NM_000080.4(CHRNE):c.1030del (p.His344fs)CHRNEPathogenicno assertion criteria provided
18355NM_000080.4(CHRNE):c.1161_1162insT (p.Lys388Ter)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
18358NM_000080.4(CHRNE):c.991C>T (p.Arg331Trp)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
18361NM_000080.4(CHRNE):c.1291G>C (p.Ala431Pro)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189225NM_000080.4(CHRNE):c.1033-2A>TCHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2170253NM_000080.4(CHRNE):c.1192C>T (p.Gln398Ter)CHRNEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
243030NM_000080.4(CHRNE):c.130dup (p.Glu44fs)CHRNEPathogeniccriteria provided, multiple submitters, no conflicts
243032NM_000080.4(CHRNE):c.1353dup (p.Asn452fs)CHRNEPathogeniccriteria provided, multiple submitters, no conflicts
2498162NM_000080.4(CHRNE):c.1032+1G>CCHRNEPathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 8 · Orphanet: 10 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
CHRNEDefinitiveAutosomal recessivecongenital myasthenic syndrome8

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CHRNEOrphanet:98913Postsynaptic congenital myasthenic syndrome
CHATOrphanet:98914Presynaptic congenital myasthenic syndromes
CHRNB1Orphanet:98913Postsynaptic congenital myasthenic syndrome
GFPT1Orphanet:353327Congenital myasthenic syndrome with glycosylation defect
ASLOrphanet:23Argininosuccinic aciduria
MUSKOrphanet:98913Postsynaptic congenital myasthenic syndrome
MUSKOrphanet:994Fetal akinesia deformation sequence
RAPSNOrphanet:33108Lethal multiple pterygium syndrome
RAPSNOrphanet:98913Postsynaptic congenital myasthenic syndrome
RAPSNOrphanet:994Fetal akinesia deformation sequence

Cohort genes → proteins

8 cohort genes, 8 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence8

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CHRNEHGNC:1966ENSG00000108556Q04844Acetylcholine receptor subunit epsilongencc,clinvar
CHATHGNC:1912ENSG00000070748P28329Choline O-acetyltransferaseclinvar
CHRNB1HGNC:1961ENSG00000170175P11230Acetylcholine receptor subunit betaclinvar
C17orf107HGNC:37238ENSG00000205710Q6ZR85Uncharacterized protein C17orf107clinvar
GFPT1HGNC:4241ENSG00000198380Q06210Glutamine–fructose-6-phosphate aminotransferase [isomerizing] 1clinvar
ASLHGNC:746ENSG00000126522P04424Argininosuccinate lyaseclinvar
MUSKHGNC:7525ENSG00000030304O15146Muscle, skeletal receptor tyrosine-protein kinaseclinvar
RAPSNHGNC:9863ENSG00000165917Q1370243 kDa receptor-associated protein of the synapseclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CHRNEAcetylcholine receptor subunit epsilonAfter 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.
CHATCholine O-acetyltransferaseCatalyzes the reversible synthesis of acetylcholine (ACh) from acetyl CoA and choline at cholinergic synapses.
CHRNB1Acetylcholine receptor subunit betaAfter 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.
GFPT1Glutamine–fructose-6-phosphate aminotransferase [isomerizing] 1Rate-limiting enzyme of the hexosamine biosynthetic pathway (HBP) that catalyzes the formation of glucosamine-6-phosphate from fructose-6-phosphate and glutamine, thereby controlling the flux of glucose into this pathway.
ASLArgininosuccinate lyaseCatalyzes the reversible cleavage of L-argininosuccinate to fumarate and L-arginine, an intermediate step reaction in the urea cycle mostly providing for hepatic nitrogen detoxification into excretable urea as well as de novo L-arginine sy…
MUSKMuscle, skeletal receptor tyrosine-protein kinaseReceptor tyrosine kinase which plays a central role in the formation and the maintenance of the neuromuscular junction (NMJ), the synapse between the motor neuron and the skeletal muscle.
RAPSN43 kDa receptor-associated protein of the synapsePostsynaptic protein required for clustering of nicotinic acetylcholine receptors (nAChRs) at the neuromuscular junction.

Protein-family classification

Druggable: 4 · Difficult: 1 · Unknown: 3 · Druggable fraction: 0.5

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Enzyme (other)34.5×0.094
Kinase13.5×0.509
Transcription factor11.0×0.859
Other/Unknown30.7×0.919

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CHRNEOther/UnknownnoNicotinic_acetylcholine_rcpt, Neurotrans-gated_channel_TM, Neur_channel
CHATEnzyme (other)yes2.3.1.6Carn_acyl_trans, CAT-like_dom_sf, Cho/carn_acyl_trans_1_2
CHRNB1Other/UnknownnoNicotinic_acetylcholine_rcpt, Neurotrans-gated_channel_TM, Neur_channel
C17orf107Other/UnknownnoC17orf107
GFPT1Enzyme (other)yes2.6.1.16SIS_dom, GFAT, GATase_2_dom
ASLEnzyme (other)yes4.3.2.1Fumarate_lyase_fam, L-Aspartase-like, Argininosuccinate_lyase
MUSKKinaseyesProt_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Ig_sub2
RAPSNTranscription factornoPostsynaptic, Znf_RING, TPR-like_helical_dom_sf

Expression context

Cohort genes with no expression data: 0.

6 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)8
unknown0

Top tissues across cohort

TissueCohort genes
male germ line stem cell (sensu Vertebrata) in testis3
adenohypophysis2
right atrium auricular region2
gastrocnemius2
hindlimb stylopod muscle2
cardiac atrium1
primordial germ cell in gonad1
putamen1
muscle of leg1
pituitary gland1
colonic mucosa1
mucosa of sigmoid colon1
secondary oocyte1
liver1
mucosa of transverse colon1
right lobe of liver1
mucosa of stomach1
sural nerve1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CHRNE162broadyesright atrium auricular region, cardiac atrium, adenohypophysis
CHAT68tissue_specificmarkerprimordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, putamen
CHRNB1137ubiquitousmarkergastrocnemius, hindlimb stylopod muscle, muscle of leg
C17orf107131broadyesadenohypophysis, pituitary gland, right atrium auricular region
GFPT1287ubiquitousmarkermucosa of sigmoid colon, colonic mucosa, secondary oocyte
ASL145ubiquitousmarkerright lobe of liver, liver, mucosa of transverse colon
MUSK151tissue_specificmarkermale germ line stem cell (sensu Vertebrata) in testis, mucosa of stomach, sural nerve
RAPSN159tissue_specificmarkerhindlimb stylopod muscle, male germ line stem cell (sensu Vertebrata) in testis, gastrocnemius

Protein interactions among cohort

Intra-cohort edges: 10.

Hub genes (top 10 by interactor count)

SymbolInteractor count
GFPT12,798
MUSK1,809
CHAT1,743
ASL1,486
CHRNE896
RAPSN715
CHRNB1711
C17orf107110

Intra-cohort edges

ABSources
C17orf107CHRNEstring_interaction
CHRNB1CHRNEstring_interaction
CHRNB1GFPT1string_interaction
CHRNB1MUSKstring_interaction
CHRNB1RAPSNstring_interaction
CHRNEGFPT1string_interaction
CHRNEMUSKstring_interaction
CHRNERAPSNstring_interaction
GFPT1RAPSNstring_interaction
MUSKRAPSNstring_interaction

Structural data

PDB: 6 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
GFPT1Q0621016
CHRNEQ0484413
CHRNB1P1123013
CHATP283298
MUSKO151464
ASLP044242

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
RAPSNQ1370293.29
C17orf107Q6ZR8558.75

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 18. Enrichment computed across 8 evidence-associated genes (5 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective GFPT1 causes CMSTA112284.0×0.004GFPT1
ASL variants cause argininosuccinate aciduria12284.0×0.004ASL
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors1326.3×0.014CHRNE
Synthesis of UDP-N-acetyl-glucosamine1285.5×0.014GFPT1
Presynaptic nicotinic acetylcholine receptors1190.3×0.014CHRNE
Urea cycle1175.7×0.014ASL
Acetylcholine binding and downstream events1163.1×0.014CHRNE
Postsynaptic nicotinic acetylcholine receptors1163.1×0.014CHRNE
Acetylcholine Neurotransmitter Release Cycle1134.3×0.015CHAT
Synthesis of PC181.6×0.022CHAT
XBP1(S) activates chaperone genes143.1×0.038GFPT1
ECM proteoglycans130.1×0.049MUSK
Neurotransmitter receptors and postsynaptic signal transmission120.0×0.068CHRNE
Transmission across Chemical Synapses115.2×0.082CHRNE
Metabolism of amino acids and derivatives113.5×0.086ASL
Extracellular matrix organization112.6×0.086MUSK
Neuronal System18.8×0.114CHRNE
Metabolism12.3×0.362ASL

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 7 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
synaptic transmission, cholinergic3343.9×3e-06CHRNE, CHRNB1, RAPSN
skeletal muscle acetylcholine-gated channel clustering2535.0×1e-04MUSK, RAPSN
acetylcholine receptor signaling pathway2178.3×6e-04CHRNE, CHRNB1
neuromuscular synaptic transmission2172.0×6e-04CHAT, CHRNB1
skeletal muscle contraction2145.9×6e-04CHRNE, CHRNB1
membrane depolarization2145.9×6e-04CHRNE, CHRNB1
ammonia assimilation cycle12407.4×0.002ASL
regulation of postsynaptic membrane organization12407.4×0.002RAPSN
establishment of protein localization to postsynaptic membrane12407.4×0.002RAPSN
positive regulation of protein geranylgeranylation12407.4×0.002MUSK
muscle contraction259.4×0.002CHRNE, CHRNB1
monoatomic ion transmembrane transport259.4×0.002CHRNE, CHRNB1
obsolete L-arginine biosynthetic process via ornithine11203.7×0.003ASL
positive regulation of motor neuron apoptotic process11203.7×0.003RAPSN
L-arginine biosynthetic process1802.5×0.003ASL
acetylcholine biosynthetic process1802.5×0.003CHAT
positive regulation of neuromuscular synaptic transmission1802.5×0.003RAPSN
postsynaptic membrane organization1601.9×0.004CHRNB1
UDP-N-acetylglucosamine metabolic process1401.2×0.006GFPT1
arginine metabolic process1343.9×0.007ASL
chemical synaptic transmission222.1×0.008CHRNE, RAPSN
behavioral response to nicotine1267.5×0.008CHRNB1
regulation of synaptic assembly at neuromuscular junction1240.7×0.008MUSK
UDP-N-acetylglucosamine biosynthetic process1218.9×0.009GFPT1
urea cycle1185.2×0.010ASL
nervous system process1172.0×0.010CHRNB1
fructose 6-phosphate metabolic process1160.5×0.010GFPT1
motor neuron apoptotic process1160.5×0.010RAPSN
energy reserve metabolic process1150.5×0.011GFPT1
muscle cell development1133.8×0.012CHRNB1

Therapeutics

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 4 · Phased (≥1): 4 · Undrugged: 4

Druggability breadth: 6 of 8 evidence-associated genes (75%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
CHRNEMECAMYLAMINE
CHRNB1VARENICLINE
MUSKFEDRATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
MUSK204
CHRNB1104
CHRNE44
CHAT13
C17orf10700
GFPT100
ASL00
RAPSN00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MECAMYLAMINE4CHRNB1, CHRNE
NICOTINE4CHRNB1, CHRNE
DONEPEZIL4CHRNE
TACRINE4CHRNE
VARENICLINE4CHRNB1
TROPISETRON4CHRNB1
BUPROPION4CHRNB1
FEDRATINIB4MUSK
SORAFENIB4MUSK
NINTEDANIB4MUSK
SUNITINIB4MUSK
QUIZARTINIB4MUSK
CRIZOTINIB4MUSK
COENZYME_A3CHAT
DEXMECAMYLAMINE3CHRNB1
CYTISINICLINE3CHRNB1
LINIFANIB3MUSK
DOVITINIB3MUSK
LESTAURTINIB3MUSK
RADAFAXINE2CHRNB1
GTS-212CHRNB1
DORAMAPIMOD2MUSK
FORETINIB2MUSK
SU-0148132MUSK
DEFOSBARASERTIB2MUSK
R-4062MUSK
MILREBRUTINIB2MUSK
TOZASERTIB2MUSK
BMS-7548072MUSK
TC-22161CHRNB1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
MUSK247Binding:247
CHRNB187Binding:51, Functional:36
CHRNE28Binding:26, Functional:2
GFPT18Binding:8
CHAT7Binding:7
RAPSN1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
CHAT2.3.1.6choline O-acetyltransferase
GFPT12.6.1.16glutamine-fructose-6-phosphate transaminase (isomerizing)
ASL4.3.2.1argininosuccinate lyase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
MUSK247

Pharmacogenomics

Cohort genes with a PharmGKB record: 8; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

30 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
MECAMYLAMINE4CHRNB1, CHRNE
NICOTINE4CHRNB1, CHRNE
DONEPEZIL4CHRNE
TACRINE4CHRNE
VARENICLINE4CHRNB1
TROPISETRON4CHRNB1
BUPROPION4CHRNB1
FEDRATINIB4MUSK
SORAFENIB4MUSK
NINTEDANIB4MUSK
SUNITINIB4MUSK
QUIZARTINIB4MUSK
CRIZOTINIB4MUSK
COENZYME_A3CHAT
DEXMECAMYLAMINE3CHRNB1
CYTISINICLINE3CHRNB1
LINIFANIB3MUSK
DOVITINIB3MUSK
LESTAURTINIB3MUSK
RADAFAXINE2CHRNB1
GTS-212CHRNB1
DORAMAPIMOD2MUSK
FORETINIB2MUSK
SU-0148132MUSK
DEFOSBARASERTIB2MUSK
R-4062MUSK
MILREBRUTINIB2MUSK
TOZASERTIB2MUSK
BMS-7548072MUSK
TC-22161CHRNB1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3CHRNE, CHRNB1, MUSK
BPhased (≥1) drug, not yet approved1CHAT
CDruggable family + PDB, no drug2GFPT1, ASL
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2C17orf107, RAPSN

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
C17orf1070CHRNE
RAPSN1MUSK, CHRNB1
GFPT18
ASL0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.