JAG2
protein-codingjagged canonical Notch ligand 2, the group of MicroRNA protein coding host genes
Gene summary
The Notch signaling pathway is an intercellular signaling mechanism that is essential for proper embryonic development. Members of the Notch gene family encode transmembrane receptors that are critical for various cell fate decisions. The protein encoded by this gene is one of several ligands that activate Notch and related receptors. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0030456
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0030456
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0015152
Submitter: ClinGen
JAG2 encodes jagged canonical Notch ligand 2, one of several ligands that activate Notch and related receptors. JAG2 was first reported in relation to autosomal recessive limb girdle muscular dystrophy in 2021 (Coppens et al., PMID: 33861953). Among the 27 patients from 16 families described to date, symptom onset ranges from infancy to adolescence/young adulthood. Muscle weakness is typically progressive with lower extremity and proximal dominance; loss of ambulation occurs in a subset of individuals. Reduced or absent deep tendon reflexes are common, and serum CK is normal or mildly elevated. Muscle biopsy findings are primarily dystrophic but may also include myopathic features. Additional features observed in some patients include scoliosis, joint contractures, ptosis and mild facial weakness, muscle atrophy or hypertrophy, cardiac features, asymptomatic moderate respiratory muscle weakness, intellectual disability or global developmental delay, speech delay, and autism spectrum disorder. Eighteen variants (13 missense, 1 in-frame indel, 1 nonsense, 2 frameshift, and 1 large deletion) reported in 16 probands in three publications (PMID: 33861953, 34878394, 39121631) are included in this curation. Co-segregation of JAG2 variants in affected family members was observed in multiple families, including three with at least three affected individuals. The mechanism of pathogenicity appears to be loss of function. However, additional investigation is needed as the effects of missense variants on gene function have not yet been determined, and many missense variants were identified in a homozygous state, often in consanguineous families. This gene-disease relationship is also supported by experimental evidence, including altered Notch pathway gene expression in patient muscle tissue and murine myoblasts following shRNA-mediated JAG2 knockdown as well as age-related locomotor decline in Drosophila following RNAi-mediated downregulation of Serrate (JAG2 ortholog)-dependent Notch signaling in adult muscle progenitors (PMID: 33861953, 39121631). In summary, there is moderate evidence supporting the relationship between JAG2 and autosomal recessive limb girdle muscular dystrophy. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Muscular Dystrophies and Myopathies GCEP on August 13, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0030456
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: The condition can include cardiomyopathy and arrhythmia, and awareness may allow early diagnosis and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JAG2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002226.5. 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 | 2 | 47 | 13 | 62 | ||
| missense | 5 | 257 | 16 | 3 | 281 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 3 | 4 | |||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 1 | 7 | 264 | 63 | 16 | 351 |
Highest pathogenic variant AF is 0.00017246042
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002217.3 | 26 | MANE Select | |
| Ensembl | ENSP00000328169.3 | 26 | MANE Select | |
| RefSeq | NP_660142.1 | 25 | Standard | |
| Ensembl | ENSP00000328566.2 | 25 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| jag2b | Danio rerio | Structure: pronephric tubule Quality: has extra parts of type abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Breast cancer - Homo sapiens (human)
- Th1 and Th2 cell differentiation - Homo sapiens (human)
- Pathways in cancer - Homo sapiens (human)
- Notch signaling pathway - Homo sapiens (human)
- NOTCH-Core
Biological Process
- skeletal system development
- in utero embryonic development
- respiratory system process
- Notch signaling pathway
- spermatogenesis
Molecular Function
- Notch binding
- calcium ion binding
- protein binding
- growth factor activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000331782
- Coding exons
- 26
- Length
- 27844
- Individuals with no LoFs
- 125282
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125291
- p
- 0.0000359
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.20 | 626 | 801 | 0.782 | 0.0000589 | 8019 |
| Missense (PolyPhen) | 207 | 354.69 | 0.5836 | 3584 | ||
| Synonymous | -2.34 | 413 | 357 | 1.16 | 0.0000312 | 2372 |
| Loss of Function | 6.95 | 4 | 63.9 | 0.0626 | 0.00000328 | 685 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00021 | 0.00019 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000048 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative Notch ligand involved in the mediation of Notch signaling. Involved in limb development (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.354
Intolerance Scores
- LoFtool
- 0.00958
- RVIS EVS
- -1.3
- RVIS percentile EVS
- 4.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |