JAG1
protein-codingjagged canonical Notch ligand 1, the group of MicroRNA protein coding host genes|CD molecules
Gene summary
The jagged 1 protein encoded by JAG1 is the human homolog of the Drosophilia jagged protein. Human jagged 1 is the ligand for the receptor notch 1, the latter is involved in signaling processes. Mutations that alter the jagged 1 protein cause Alagille syndrome. Jagged 1 signalling through notch 1 has also been shown to play a role in hematopoiesis. [provided by RefSeq, Nov 2019]
- AGS
- JAGL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0030458
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030458
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0016862
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0008542
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016862
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0016862
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0016862
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0030458
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal
Intervention: Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Renal
Rationale: For Alagille syndrome, individuals may have hepatic complications, and medications (eg, ursodeoxycholic acid, cholestyramine), and, when necessary, partial external biliary diversion may be beneficial; Other treatments, such as fat-soluble vitamin supplementation may be beneficial; Surveillance for other manifestations, including cardiac and renal manifestations, may be beneficial in order to allow early diagnosis and treatment and/or preventive measures; Contact sports should be avoided; For Deafness, congenital heart defects, and posterior embryotoxon, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development
Comments: Liver transplantation has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JAG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000214.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 54 | 405 | 7 | 467 | |
| missense | 17 | 39 | 1093 | 197 | 7 | 1353 |
| nonsense | 105 | 12 | 5 | 122 | ||
| start loss | 1 | 4 | 5 | |||
| frameshift | 200 | 60 | 3 | 263 | ||
| splice donor/acceptor (+/-2bp) | 26 | 31 | 8 | 65 | ||
| Total | 350 | 146 | 1163 | 602 | 14 | 2275 |
Highest pathogenic variant AF is 0.000006572807
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000205.1 | 26 | MANE Select | |
| Ensembl | ENSP00000254958.4 | 26 | MANE Select | |
| Ensembl | ENSP00000481034.1 | 3 | Standard | |
| Ensembl | ENSP00000484139.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| jag1b | Danio rerio | Structure: pillar of the lateral semicircular canal Quality: increased thickness abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Breast cancer - Homo sapiens (human)
- TNF signaling pathway - Homo sapiens (human)
- Apelin signaling pathway - Homo sapiens (human)
- Th1 and Th2 cell differentiation - Homo sapiens (human)
- Pathways in cancer - Homo sapiens (human)
Biological Process
- angiogenesis
- cell fate determination
- negative regulation of cell-matrix adhesion
- blood vessel remodeling
- morphogenesis of an epithelial sheet
Molecular Function
- Notch binding
- structural molecule activity
- calcium ion binding
- protein binding
- phospholipid binding
Cellular Component
- extracellular region
- plasma membrane
- integral component of plasma membrane
- adherens junction
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254958
- Coding exons
- 26
- Length
- 36363
- Individuals with no LoFs
- 125740
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125747
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.25 | 455 | 696 | 0.654 | 0.0000426 | 8128 |
| Missense (PolyPhen) | 110 | 286 | 0.38462 | 3349 | ||
| Synonymous | 0.126 | 274 | 277 | 0.990 | 0.0000197 | 2158 |
| Loss of Function | 6.88 | 4 | 62.8 | 0.0637 | 0.00000330 | 772 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ligand for multiple Notch receptors and involved in the mediation of Notch signaling (PubMed:18660822, PubMed:20437614). May be involved in cell-fate decisions during hematopoiesis (PubMed:9462510). Seems to be involved in early and late stages of mammalian cardiovascular development. Inhibits myoblast differentiation (By similarity). Enhances fibroblast growth factor-induced angiogenesis (in vitro). {ECO:0000250, ECO:0000269|PubMed:18660822, ECO:0000269|PubMed:20437614, ECO:0000269|PubMed:9462510}.;
- Disease
- DISEASE: Alagille syndrome 1 (ALGS1) [MIM:118450]: A form of Alagille syndrome, an autosomal dominant multisystem disorder. It is clinically defined by hepatic bile duct paucity and cholestasis in association with cardiac, skeletal, and ophthalmologic manifestations. There are characteristic facial features and less frequent clinical involvement of the renal and vascular systems. {ECO:0000269|PubMed:10220506, ECO:0000269|PubMed:10533065, ECO:0000269|PubMed:11058898, ECO:0000269|PubMed:11139247, ECO:0000269|PubMed:11157803, ECO:0000269|PubMed:11180599, ECO:0000269|PubMed:12442286, ECO:0000269|PubMed:12497640, ECO:0000269|PubMed:15712272, ECO:0000269|PubMed:16575836, ECO:0000269|PubMed:20437614, ECO:0000269|PubMed:23801938, ECO:0000269|PubMed:9207788, ECO:0000269|PubMed:9585603}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tetralogy of Fallot (TOF) [MIM:187500]: A congenital heart anomaly which consists of pulmonary stenosis, ventricular septal defect, dextroposition of the aorta (aorta is on the right side instead of the left) and hypertrophy of the right ventricle. In this condition, blood from both ventricles (oxygen-rich and oxygen-poor) is pumped into the body often causing cyanosis. {ECO:0000269|PubMed:11152664, ECO:0000269|PubMed:20437614}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Deafness, congenital heart defects, and posterior embryotoxon (DCHE) [MIM:617992]: An autosomal dominant disease characterized by mild to severe combined hearing loss, congenital heart defects, and posterior embryotoxon, a corneal abnormality consisting of a central collagen core surrounded by a thin layer of Descemets membrane and separated from the anterior chamber by a layer of endothelium. Congenital heart defects include tetralogy of Fallot, ventricular septal defect, or isolated peripheral pulmonic stenosis. {ECO:0000269|PubMed:12022040, ECO:0000269|PubMed:20437614}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.705
Intolerance Scores
- LoFtool
- 0.00627
- RVIS EVS
- -2.14
- RVIS percentile EVS
- 1.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Indispensability pred.
- E
- Indispensability score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |