AGRN

protein-coding

agrin, the group of Proteoglycans

Gene summary

This gene encodes one of several proteins that are critical in the development of the neuromuscular junction (NMJ), as identified in mouse knock-out studies. The encoded protein contains several laminin G, Kazal type serine protease inhibitor, and epidermal growth factor domains. Additional post-translational modifications occur to add glycosaminoglycans and disulfide bonds. In one family with congenital myasthenic syndrome affecting limb-girdle muscles, a mutation in this gene was found. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]

Previous symbols:
  • AGRIN

MANE transcript

NM_198576.4

Inheritance

AR

ClinVar variants

P:68U:1117B:842

Top phenotype

Myasthenic syndrome, congenital 8

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr1:1,020,120-1,056,119

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital myasthenic syndrome 8DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014052

Submitter: ClinGen

*AGRN* was first reported in relation to autosomal recessive congenital myasthenic syndrome (CMS) in 2009 (Huze et al. PMID: 19631309). Two siblings from a Swiss family presented with childhood onset of mild limb muscle weakness and unilateral ptosis were found to be homozygous for a missense variant in exon 29 of the AGRN gene. Skeletal muscle biopsy showed type I fiber predominance and type II fiber atrophy along with pre- and postsynaptic defects at the neuromuscular junction. Twenty-six variants (twenty-three missense, two nonsense, and one splice-site) that have been reported in eighteen probands in twelve publications (PMIDs: 19631309, 22205389, 24951643, 28937031, 29258548, 31167812, 32221959, 32271162, 32328026, 35670010, 33756069, 36099689) are included in this curation. Patients with *AGRN*-related CMS are reported to develop muscle weakness with varying severity and progression, mostly of involving proximal or distal limbs, myopathy, ptosis, neuromuscular transmission defects, and rarely respiratory insufficiency requiring support (PMID: 24951643, 32271162). Interestingly, Geremek et al. reported a fetus with fetal akinesis deformation sequence, considered as a severe form of CMS, who harbored a frameshift variant *AGRN*:c.4657delT (p.C1553fs) in trans with a large deletion involving AGRN as well as other genes (PMID: 31730230). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity is reported to be dominant negative. This gene-disease relationship is also supported by animal models and in vitro acetylocholine receptor binding studies (PMIDs: 21890498, 24951643, 32271162). In vitro AChR binding assays in which C2C12 myotubes showed reduced AChR clustering when incubated with conditioned media containing the *AGRN* variants p.G76S, p.S1180L, p.R1509W, p.G1675S, and p.Y1877D (PMID: 24951643, 32271162). In 1999, Burgess et al. used nerve–muscle cocultures, surgical chimeras, neonatal mutant mice to assess the roles of agrin isoforms in the formation of the NMJ (PMID: 10402191) and concluded agrin promotes presynaptic differentiation by causing the postsynaptic apparatus to produce or localize appropriate retrograde signals (PMID: 10402191). Later, Bogdanik and Burgess reported a mouse model with a homozygous missense mutation (p.Phe1061Ser) in the SEA domain of agrin that replicated neuromuscular symptoms observed in human congenital myasthenic syndrome (PMID 21890498). Agrin has been shown to play an important role in mediation of cell contact-induced acetylcholine receptor clustering with other postsynaptic proteins on muscle fibers and congenital myasthenic syndromes associated with pathogenic variants in* AGRN* alter this crucial function in the formation and maintenance of the neuromuscular junction (PMID: 1659950, 19631309, 22205389). In summary, there is definitive evidence supporting the relationship between *AGRN* and autosomal recessive congenital myasthenic syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Congenital Myopathies GCEP on the meeting date August 25th, 2025 (SOP Version 11).

congenital myasthenic syndrome 8STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014052

Submitter: Labcorp Genetics (formerly Invitae)

congenital myasthenic syndrome 8STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014052

Submitter: Genomics England PanelApp

congenital myasthenic syndrome 8STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014052

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Myasthenic syndrome, congenital 8AR

Manifestation: Musculoskeletal; Neurologic

Intervention: Musculoskeletal; Neurologic; Pharmacogenomic

Rationale: Ephedrine treatment has been reported as effective in affected inviduals; Medical treatment with acetylcholine esterase inhibitors and/or potassium channel blocker 3,4-diaminopyridine may be beneficial in many individuals; In infancy, the use of apnea monitors may be indicated; Agents that affect neuromuscular transmission and exacerbate myasthenic manifestations should be avoided

Refs: 19631309; 20301347; 22205389; 22678886Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGRN variants in ClinVar

12 Conditions Cataloged
Congenital myasthenic syndrome 8Total: 2196
Inborn genetic diseasesTotal: 441
not providedTotal: 378
not specifiedTotal: 183
AGRN-related disorderTotal: 92
Congenital myasthenic syndromeTotal: 9
See casesTotal: 4
Neurodevelopmental disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198576.4. 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
17
clinvar
725
clinvar
10
clinvar
752
missense
2
clinvar
8
clinvar
1085
clinvar
99
clinvar
6
clinvar
1200
nonsense
10
clinvar
4
clinvar
2
clinvar
16
start loss
1
clinvar
1
frameshift
20
clinvar
9
clinvar
3
clinvar
32
splice donor/acceptor (+/-2bp)
14
clinvar
10
clinvar
2
clinvar
26
Total32361117826162027

Highest pathogenic variant AF is 0.000079103644

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_198576.4RefSeqNP_940978.236MANE Select
ENST00000379370.7EnsemblENSP00000368678.236MANE Select
NM_001305275.2RefSeqNP_001292204.139Standard
NM_001364727.2RefSeqNP_001351656.136Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
agrnDanio rerio

Structure: CaP motoneuron

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • ECM-receptor interaction - Homo sapiens (human)
  • Primary Focal Segmental Glomerulosclerosis FSGS
  • Splicing factor NOVA regulated synaptic proteins
  • Developmental Biology
  • Signaling by GPCR

Biological Process

  • retinoid metabolic process
  • glycosaminoglycan biosynthetic process
  • glycosaminoglycan catabolic process
  • cytoskeleton organization
  • signal transduction

Molecular Function

  • dystroglycan binding
  • structural constituent of cytoskeleton
  • extracellular matrix structural constituent
  • calcium ion binding
  • protein binding

Cellular Component

  • extracellular region
  • basement membrane
  • Golgi lumen
  • cytosol
  • plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000379370
Coding exons
36
Length
35994
Individuals with no LoFs
125566
Homozygous LoFs
0
Heterozygous LoFs
64
Defined
125630
p
0.000255
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.22613031.33e+30.9830.000099512779
Missense (PolyPhen)342394.870.866113727
Synonymous-3.967276031.200.00004964373
Loss of Function6.012990.90.3190.00000500963

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000260.00025rare
Latino/Admixed American0.000460.00043rare
Ashkenazi Jewish0.000410.00040rare
East Asian0.000170.00016rare
Finnish00.0absent
European (Non-Finnish)0.000320.00030rare
South Asian0.000140.00013rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Isoform 1: heparan sulfate basal lamina glycoprotein that plays a central role in the formation and the maintenance of the neuromuscular junction (NMJ) and directs key events in postsynaptic differentiation. Component of the AGRN-LRP4 receptor complex that induces the phosphorylation and activation of MUSK. The activation of MUSK in myotubes induces the formation of NMJ by regulating different processes including the transcription of specific genes and the clustering of AChR in the postsynaptic membrane. Calcium ions are required for maximal AChR clustering. AGRN function in neurons is highly regulated by alternative splicing, glycan binding and proteolytic processing. Modulates calcium ion homeostasis in neurons, specifically by inducing an increase in cytoplasmic calcium ions. Functions differentially in the central nervous system (CNS) by inhibiting the alpha(3)- subtype of Na+/K+-ATPase and evoking depolarization at CNS synapses. This secreted isoform forms a bridge, after release from motor neurons, to basal lamina through binding laminin via the NtA domain.; FUNCTION: Isoform 1, isoform 4 and isoform 5: neuron-specific (z+) isoforms that contain C-terminal insertions of 8-19 AA are potent activators of AChR clustering. Isoform 5, agrin (z+8), containing the 8-AA insert, forms a receptor complex in myotubules containing the neuronal AGRN, the muscle-specific kinase MUSK and LRP4, a member of the LDL receptor family. The splicing factors, NOVA1 and NOVA2, regulate AGRN splicing and production of the 'z' isoforms.; FUNCTION: Agrin N-terminal 110 kDa subunit: is involved in regulation of neurite outgrowth probably due to the presence of the glycosaminoglcan (GAG) side chains of heparan and chondroitin sulfate attached to the Ser/Thr- and Gly/Ser-rich regions. Also involved in modulation of growth factor signaling (By similarity). {ECO:0000250, ECO:0000269|PubMed:19631309, ECO:0000269|PubMed:21969364}.;
Disease
DISEASE: Myasthenic syndrome, congenital, 8 (CMS8) [MIM:615120]: 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. CMS8 is an autosomal recessive disease characterized by prominent defects of both the pre- and postsynaptic regions. Affected individuals have onset of muscle weakness in early childhood; the severity of the weakness and muscles affected is variable. {ECO:0000269|PubMed:19631309, ECO:0000269|PubMed:22205389, ECO:0000269|PubMed:24951643}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.645

Intolerance Scores

LoFtool
0.421
RVIS EVS
-0.22
RVIS percentile EVS
37.33

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.883

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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