JAG2
jagged canonical Notch ligand 2, the group of MicroRNA protein coding host genes
Basic information
Region (hg38): 14:105140982-105168824
Links
Phenotypes
GenCC
Source:
- muscular dystrophy, limb-girdle, autosomal recessive 27 (Strong), mode of inheritance: AR
- muscular dystrophy, limb-girdle, autosomal recessive 27 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Muscular dystrophy, limb-girdle, autosomal recessive 27 | AR | Cardiovascular | The condition can include cardiomyopathy and arrhythmia, and awareness may allow early diagnosis and management | Cardiovascular; Musculoskeletal | 33861953 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (205 variants)
- JAG2-related_disorder (59 variants)
- not_provided (56 variants)
- Muscular_dystrophy,_limb-girdle,_autosomal_recessive_27 (27 variants)
- Mendelian_syndromes_with_cleft_lip/palate (1 variants)
- Orofacial_cleft_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the JAG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002226.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 36 | 12 | 48 | |||
| missense | 227 | 15 | 249 | |||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 5 | 230 | 51 | 15 |
Highest pathogenic variant AF is 0.005725809
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| JAG2 | protein_coding | protein_coding | ENST00000331782 | 26 | 27844 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 5.39e-8 | 125282 | 0 | 9 | 125291 | 0.0000359 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.20 | 626 | 801 | 0.782 | 0.0000589 | 8019 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000242 | 0.000214 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000477 | 0.0000442 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Putative Notch ligand involved in the mediation of Notch signaling. Involved in limb development (By similarity). {ECO:0000250}.;
- Pathway
- 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;Notch Signaling Pathway;NOTCH1 regulation of human endothelial cell calcification;Canonical and Non-canonical Notch signaling;EMT transition in Colorectal Cancer;Notch Signaling Pathway;Notch Signaling Pathway;Notch;Disease;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor;Notch;p73 transcription factor network;Signaling by NOTCH1;Signaling by NOTCH2;NOTCH3 Activation and Transmission of Signal to the Nucleus;Signaling by NOTCH3;Signaling by NOTCH4;Signaling by NOTCH;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;NOTCH2 Activation and Transmission of Signal to the Nucleus;Notch signaling pathway;Constitutive Signaling by NOTCH1 HD Domain Mutants;Signaling by NOTCH1 HD Domain Mutants in Cancer;GPCR signaling-G alpha i;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Diseases of signal transduction;Activated NOTCH1 Transmits Signal to the Nucleus
(Consensus)
Recessive Scores
- pRec
- 0.354
Intolerance Scores
- loftool
- 0.00958
- rvis_EVS
- -1.3
- rvis_percentile_EVS
- 4.99
Haploinsufficiency Scores
- pHI
- 0.802
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Jag2
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- jag2b
- Affected structure
- pronephric tubule
- Phenotype tag
- abnormal
- Phenotype quality
- has extra parts of type
Gene ontology
- Biological process
- skeletal system development;in utero embryonic development;respiratory system process;Notch signaling pathway;spermatogenesis;auditory receptor cell fate commitment;regulation of signaling receptor activity;morphogenesis of embryonic epithelium;cell differentiation;regulation of cell adhesion;T cell differentiation;regulation of cell population proliferation;odontogenesis of dentin-containing tooth;gamma-delta T cell differentiation;thymic T cell selection;positive regulation of Notch signaling pathway;epithelial cell apoptotic process involved in palatal shelf morphogenesis
- Cellular component
- plasma membrane;integral component of plasma membrane
- Molecular function
- Notch binding;calcium ion binding;protein binding;growth factor activity