AGRN
protein-codingagrin, 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]
- AGRIN
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
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).
Inheritance Pattern: AR
Disease ID:MONDO:0014052
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014052
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014052
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to AGRN variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 17 | 725 | 10 | 752 | ||
| missense | 2 | 8 | 1085 | 99 | 6 | 1200 |
| nonsense | 10 | 4 | 2 | 16 | ||
| start loss | 1 | 1 | ||||
| frameshift | 20 | 9 | 3 | 32 | ||
| splice donor/acceptor (+/-2bp) | 14 | 10 | 2 | 26 | ||
| Total | 32 | 36 | 1117 | 826 | 16 | 2027 |
Highest pathogenic variant AF is 0.000079103644
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940978.2 | 36 | MANE Select | |
| Ensembl | ENSP00000368678.2 | 36 | MANE Select | |
| RefSeq | NP_001292204.1 | 39 | Standard | |
| RefSeq | NP_001351656.1 | 36 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| agrn | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.226 | 1303 | 1.33e+3 | 0.983 | 0.0000995 | 12779 |
| Missense (PolyPhen) | 342 | 394.87 | 0.86611 | 3727 | ||
| Synonymous | -3.96 | 727 | 603 | 1.20 | 0.0000496 | 4373 |
| Loss of Function | 6.01 | 29 | 90.9 | 0.319 | 0.00000500 | 963 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00025 | rare |
| Latino/Admixed American | 0.00046 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00030 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |