IL2RB
Basic information
Region (hg38): 22:37118666-37175118
Previous symbols: [ "IL15RB" ]
Links
Phenotypes
GenCC
Source:
- immunodeficiency 63 with lymphoproliferation and autoimmunity (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Immunodeficiency 63 with lymphoproliferation and autoimmunity | AR | Allergy/Immunology/Infectious | Individuals have been described with immunodeficiency and immune dysregulation; immune suppression has been described as being beneficial prior to HSCT | Allergy/Immunology/Infectious; Gastrointestinal | 31040184; 31040185 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL2RB gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 106 | 112 | ||||
missense | 143 | 156 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 7 | |||||
splice region | 5 | 15 | 3 | 23 | ||
non coding | 39 | 11 | 52 | |||
Total | 4 | 6 | 154 | 152 | 20 |
Highest pathogenic variant AF is 0.00000658
Variants in IL2RB
This is a list of pathogenic ClinVar variants found in the IL2RB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-37128100-A-G | not specified | Uncertain significance (Jul 07, 2023) | ||
22-37128113-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
22-37128117-C-T | Likely benign (Sep 09, 2023) | |||
22-37128121-C-T | Uncertain significance (Nov 27, 2021) | |||
22-37128154-G-A | Uncertain significance (Jun 09, 2022) | |||
22-37128164-G-A | Uncertain significance (Feb 08, 2022) | |||
22-37128169-C-T | not specified | Uncertain significance (Aug 11, 2022) | ||
22-37128170-G-A | Uncertain significance (Oct 17, 2022) | |||
22-37128172-G-A | not specified | Uncertain significance (Jun 18, 2024) | ||
22-37128182-C-T | Uncertain significance (Aug 06, 2022) | |||
22-37128198-C-G | Likely benign (Jul 11, 2022) | |||
22-37128201-A-C | Likely benign (Dec 21, 2022) | |||
22-37128202-G-A | not specified | Uncertain significance (Jun 07, 2024) | ||
22-37128205-G-A | not specified | Uncertain significance (Oct 30, 2023) | ||
22-37128211-GACCAGGGGAA-G | Uncertain significance (May 28, 2021) | |||
22-37128216-G-T | Likely benign (Jul 12, 2023) | |||
22-37128217-G-A | Uncertain significance (Jun 22, 2022) | |||
22-37128226-A-C | Uncertain significance (May 14, 2022) | |||
22-37128228-T-G | Likely benign (Nov 14, 2020) | |||
22-37128233-C-T | Uncertain significance (Sep 06, 2022) | |||
22-37128240-G-A | Likely benign (Dec 25, 2023) | |||
22-37128246-G-A | Likely benign (Jun 04, 2023) | |||
22-37128251-G-A | Uncertain significance (May 25, 2022) | |||
22-37128254-C-A | Uncertain significance (Aug 16, 2021) | |||
22-37128257-C-G | Uncertain significance (May 09, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IL2RB | protein_coding | protein_coding | ENST00000216223 | 9 | 49217 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.291 | 0.709 | 125666 | 2 | 80 | 125748 | 0.000326 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.441 | 284 | 306 | 0.929 | 0.0000172 | 3527 |
Missense in Polyphen | 54 | 77.591 | 0.69596 | 966 | ||
Synonymous | 0.180 | 139 | 142 | 0.981 | 0.00000899 | 1151 |
Loss of Function | 3.26 | 5 | 21.2 | 0.236 | 0.00000101 | 213 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00168 | 0.00168 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000441 | 0.0000439 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00359 | 0.00326 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for interleukin-2. This beta subunit is involved in receptor mediated endocytosis and transduces the mitogenic signals of IL2.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;IL-2 Signaling Pathway;Signaling by GPCR;Signal Transduction;Signaling by Interleukins;il 2 signaling pathway;il-2 receptor beta chain in t cell activation;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;Interleukin-15 signaling;Interleukin receptor SHC signaling;Interleukin-2 family signaling;IL-2 signaling;SHP2 signaling;JAK STAT MolecularVariation 2;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;IL2;IL2-mediated signaling events;Interleukin-2 signaling;IL5;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;IL2 signaling events mediated by STAT5;Downstream signaling in naïve CD8+ T cells;IL2 signaling events mediated by PI3K;IL12-mediated signaling events;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.509
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.91
Haploinsufficiency Scores
- pHI
- 0.535
- hipred
- Y
- hipred_score
- 0.671
- ghis
- 0.447
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.339
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il2rb
- Phenotype
- immune system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; hematopoietic system phenotype; growth/size/body region phenotype; reproductive 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); 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); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- MAPK cascade;signal transduction;viral process;cytokine-mediated signaling pathway;interleukin-15-mediated signaling pathway;interleukin-2-mediated signaling pathway;negative regulation of apoptotic process;protein-containing complex assembly
- Cellular component
- endosome;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;membrane
- Molecular function
- interleukin-2 receptor activity;Ras guanyl-nucleotide exchange factor activity;protein binding;interleukin-2 binding