ICOSLG
Basic information
Region (hg38): 21:44215382-44241446
Previous symbols: [ "ICOSL" ]
Links
Phenotypes
GenCC
Source:
- combined immunodeficiency (Moderate), mode of inheritance: AR
- immunodeficiency 119 (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (271 variants)
- not_specified (39 variants)
- Combined_immunodeficiency (1 variants)
- Immunodeficiency_119 (1 variants)
- Inborn_genetic_diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICOSLG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015259.6. 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 | 65 | 72 | ||||
missense | 114 | 12 | 130 | |||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
Total | 0 | 2 | 125 | 77 | 8 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ICOSLG | protein_coding | protein_coding | ENST00000407780 | 7 | 17976 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000355 | 0.956 | 124799 | 0 | 18 | 124817 | 0.0000721 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.13 | 153 | 198 | 0.774 | 0.0000132 | 1971 |
Missense in Polyphen | 49 | 62.705 | 0.78143 | 695 | ||
Synonymous | -0.816 | 101 | 91.1 | 1.11 | 0.00000730 | 593 |
Loss of Function | 1.80 | 8 | 15.7 | 0.509 | 9.08e-7 | 155 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000145 | 0.000145 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000464 | 0.0000464 |
European (Non-Finnish) | 0.000107 | 0.000106 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand for the T-cell-specific cell surface receptor ICOS. Acts as a costimulatory signal for T-cell proliferation and cytokine secretion; induces also B-cell proliferation and differentiation into plasma cells. Could play an important role in mediating local tissue responses to inflammatory conditions, as well as in modulating the secondary immune response by co- stimulating memory T-cell function (By similarity). {ECO:0000250}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);the co-stimulatory signal during t-cell activation;Costimulation by the CD28 family;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.206
Intolerance Scores
- loftool
- 0.680
- rvis_EVS
- 0.84
- rvis_percentile_EVS
- 88.3
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.247
- ghis
- 0.462
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.527
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Icosl
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- adaptive immune response;defense response;hyperosmotic response;signal transduction;T cell costimulation;positive regulation of activated T cell proliferation;T cell activation;B cell activation;regulation of immune response;T cell receptor signaling pathway
- Cellular component
- plasma membrane;external side of plasma membrane;integral component of membrane;cytoplasmic ribonucleoprotein granule;extracellular exosome
- Molecular function
- signaling receptor binding;protein binding;identical protein binding