JAG1

protein-coding

jagged 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]

Previous symbols:
  • AGS
  • JAGL1

MANE transcript

NM_000214.3

Inheritance

AD

ClinVar variants

P:496U:1163B:616

Top phenotype

Alagille syndrome; Deafness, congenital heart defects, and posterior embryotoxon

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr20:10,637,684-10,673,999

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Charcot-Marie-Tooth disease, axonal, Type 2HHSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030458

Submitter: Labcorp Genetics (formerly Invitae)

Charcot-Marie-Tooth disease, axonal, Type 2HHLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0030458

Submitter: Ambry Genetics

Alagille syndrome due to a JAG1 point mutationSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0016862

Submitter: PanelApp Australia

tetralogy of fallotSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008542

Submitter: Orphanet

Alagille syndrome due to a JAG1 point mutationSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0016862

Submitter: Labcorp Genetics (formerly Invitae)

Alagille syndrome due to a JAG1 point mutationDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016862

Submitter: Ambry Genetics

Alagille syndrome due to a JAG1 point mutationDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016862

Submitter: G2P

Charcot-Marie-Tooth disease, axonal, Type 2HHSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030458

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Alagille syndrome; Deafness, congenital heart defects, and posterior embryotoxonAD

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

Refs: 803282; 9039994; 9207788; 9207787; 9585603; 9700188; 9890073; 10590916; 10213047; 11152664; 11313761; 11511567; 11139239; 12022040; 12244552; 12239725; 12509572; 14993126; 16013021; 16573599; 17286312; 19597493; 19948535; 20301450; 20437614; 22040217; 22105858; 22488849; 22521120; 22759690; 22937766; 23752887; 23801938; 23956173; 32065591Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JAG1 variants in ClinVar

27 Conditions Cataloged
Alagille syndrome due to a JAG1 point mutationTotal: 1572
Cardiovascular phenotypeTotal: 633
not providedTotal: 531
Tetralogy of FallotTotal: 223
Charcot-Marie-Tooth disease, axonal, Type 2HHTotal: 213
Deafness, congenital heart defects, and posterior embryotoxonTotal: 212
JAG1-related disorderTotal: 173
not specifiedTotal: 80

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
54
clinvar
405
clinvar
7
clinvar
467
missense
17
clinvar
39
clinvar
1093
clinvar
197
clinvar
7
clinvar
1353
nonsense
105
clinvar
12
clinvar
5
clinvar
122
start loss
1
clinvar
4
clinvar
5
frameshift
200
clinvar
60
clinvar
3
clinvar
263
splice donor/acceptor (+/-2bp)
26
clinvar
31
clinvar
8
clinvar
65
Total3501461163602142275

Highest pathogenic variant AF is 0.000006572807

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000214.3RefSeqNP_000205.126MANE Select
ENST00000254958.10EnsemblENSP00000254958.426MANE Select
ENST00000613518.1EnsemblENSP00000481034.13Standard
ENST00000622545.1EnsemblENSP00000484139.14Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
jag1bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.254556960.6540.00004268128
Missense (PolyPhen)1102860.384623349
Synonymous0.1262742770.9900.00001972158
Loss of Function6.88462.80.06370.00000330772

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000440.000035rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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