ICOSLG

inducible T cell costimulator ligand, the group of Receptor ligands|B7 family|V-set domain containing|CD molecules|C2-set domain containing

Basic information

Region (hg38): 21:44215382-44241446

Previous symbols: [ "ICOSL" ]

Links

ENSG00000160223NCBI:23308OMIM:605717HGNC:17087Uniprot:O75144AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • combined immunodeficiency (Moderate), mode of inheritance: AR
  • immunodeficiency 119 (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ICOSLG gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
65
clinvar
5
clinvar
72
missense
1
clinvar
114
clinvar
12
clinvar
3
clinvar
130
nonsense
6
clinvar
6
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
3
Total 0 2 125 77 8
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ICOSLGprotein_codingprotein_codingENST00000407780 717976
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003550.9561247990181248170.0000721
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.131531980.7740.00001321971
Missense in Polyphen4962.7050.78143695
Synonymous-0.81610191.11.110.00000730593
Loss of Function1.80815.70.5099.08e-7155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001450.000145
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004640.0000464
European (Non-Finnish)0.0001070.000106
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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