EBI3
Epstein-Barr virus induced 3, the group of Fibronectin type III domain containing|Minor histocompatibility antigens
Basic information
Region (hg38): 19:4229523-4237528
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBI3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005755.3. 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 | 1 | |||||
| missense | 35 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 5 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EBI3 | protein_coding | protein_coding | ENST00000221847 | 5 | 8034 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.108 | 0.865 | 125718 | 0 | 20 | 125738 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.276 | 152 | 143 | 1.06 | 0.00000931 | 1454 |
| Missense in Polyphen | 43 | 38.906 | 1.1052 | 401 | ||
| Synonymous | -0.348 | 61 | 57.6 | 1.06 | 0.00000383 | 479 |
| Loss of Function | 1.90 | 3 | 9.22 | 0.326 | 4.72e-7 | 90 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000426 | 0.000419 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000555 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000565 | 0.0000527 |
| Middle Eastern | 0.0000555 | 0.0000544 |
| South Asian | 0.0000330 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Associates with IL27 to form the IL-27 interleukin, a heterodimeric cytokine which functions in innate immunity. IL-27 has pro- and anti-inflammatory properties, that can regulate T- helper cell development, suppress T-cell proliferation, stimulate cytotoxic T-cell activity, induce isotype switching in B-cells, and that has diverse effects on innate immune cells. Among its target cells are CD4 T-helper cells which can differentiate in type 1 effector cells (TH1), type 2 effector cells (TH2) and IL17 producing helper T-cells (TH17). It drives rapid clonal expansion of naive but not memory CD4 T-cells. It also strongly synergizes with IL-12 to trigger interferon-gamma/IFN-gamma production of naive CD4 T-cells, binds to the cytokine receptor WSX-1/TCCR. Another important role of IL-27 is its antitumor activity as well as its antiangiogenic activity with activation of production of antiangiogenic chemokines. {ECO:0000269|PubMed:12121660}.;
- Pathway
- Interleukin-12 family signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Interleukin-27 signaling;IL27-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.584
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.36
Haploinsufficiency Scores
- pHI
- 0.0842
- hipred
- N
- hipred_score
- 0.182
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.741
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ebi3
- 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- humoral immune response;regulation of signaling receptor activity;T-helper 1 type immune response;T cell proliferation;positive regulation of interferon-gamma biosynthetic process;positive regulation of alpha-beta T cell proliferation;interleukin-27-mediated signaling pathway;ciliary neurotrophic factor-mediated signaling pathway;interleukin-35-mediated signaling pathway
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum lumen;plasma membrane;external side of plasma membrane;receptor complex;ciliary neurotrophic factor receptor complex;CNTFR-CLCF1 complex
- Molecular function
- cytokine receptor activity;ciliary neurotrophic factor receptor activity;cytokine activity;protein binding;cytokine binding;interleukin-27 receptor binding