ICOSLG

protein-coding

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

Gene summary

Enables identical protein binding activity and receptor ligand activity. Involved in T follicular helper cell differentiation. Located in extracellular exosome. Is active in plasma membrane. Implicated in immunodeficiency 119. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:
  • ICOSL

MANE transcript

NM_015259.6

Inheritance

AR

ClinVar variants

P:3U:144B:93

Top phenotype

Immunodeficiency 119

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr21:44,215,382-44,241,446

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency 119MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0970993

Submitter: PanelApp Australia

combined immunodeficiencyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0015131

Submitter: ClinGen

The relationship between ICOSLG and Combined Immunodeficiency, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of April, 2023. Features of combined immunodeficiency due to ICOSLG variants include recurrent infections, panhypogammaglobulinemia and pneumonia. ICOSLG is an important protein that plays a role in regulating T- Cells. ICOSLG is expressed on antigen presenting cells while ICOS is expressed on T- Cells. The two interact to secrete cytokines that promote proliferation and differentiation of T- Cells, enhancing the immune response (Roussel, et al; PMID: 30498080). Patients with autosomal recessive NIK deficiency (MAP3K14 gene) have low ICOSL as this is regulated by NIK (PMID: 21768353 and PMID: 25406581). ICOSLG was first reported in relation to autosomal recessive combined immunodeficiency in 2018 (Roussel L 2018, PMID: 30498080). Summary Case Level Data (2 points): Variants in this gene have been reported in at least two individuals from two publications, both of French Canadian origin (PMID: 30498080, 34694545). Both individuals were homozygous for the missense variant in ICOSLG, Asn219Lys. Although only two apparently unrelated individuals have been reported with the same missense variant, each proband was scored the full 1 point due to the potential for a common founder variant in the French Canadian population, similar to ICOS deficiency. EXPERIMENTAL EVIDENCE (5 points): This gene-disease association is supported by a mouse model and functional assays. Icosl-/- mice show reduced antibody production and impaired helper T cell differentiation. Icosl-/- mice developed attenuated allergic airway disease and showed an interference with the B- Cell isotype class switching (Mak, et al; PMID: 12833154). ICOSL binds to the receptor ICOS and this interaction is critical for the maturation of germinal center B cells to affinity-matured memory B cells and long-lived plasma cells. This gene-disease association is supported by functional alteration; the authors cocultured Jurkat cells activated by TNFα to induce ICOS expression and measure gene responses of cytokines. This showed that there was a significant reduction in of the expression of ICOSL protein on the cell surface. The variant transfected into HMEC1 cells resulted in defective transendothelial migration of T cells and neutrophils (Roussel, et al; PMID: 3049808). In summary, the level of evidence to support the gene-disease relationship of ICOSLG and autosomal recessive Combined Immunodeficiency is moderate. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. The interaction of ICOSL with ICOS to promote proliferation and differentiation of T- Cells, enhancing the immune response, is well understood. ICOS deficiency is well described and the ICOS- Common Variable Immunodeficiency gene disease relationship is definitive. Based on ICOS and ICOSL belonging to the same pathway, the Antibody Deficiencies GCEP determined that the ICOSL- Combined Immunodeficiency relationship should reach a moderate classification. This classification was approved by the Antibody Deficiencies GCEP on April 25th, 2023 (SOP v9).

immunodeficiency 119LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0970993

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ICOSLG variants in ClinVar

5 Conditions Cataloged
not providedTotal: 290
not specifiedTotal: 82
Immunodeficiency 119Total: 3
Combined immunodeficiencyTotal: 1
Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015259.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
73
clinvar
3
clinvar
78
missense
1
clinvar
129
clinvar
16
clinvar
1
clinvar
147
nonsense
6
clinvar
6
start loss
0
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
7
Total03144894240
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015259.6RefSeqNP_056074.17MANE Select
ENST00000407780.8EnsemblENSP00000384432.37MANE Select
NM_001283050.2RefSeqNP_001269979.17Standard
NM_001283051.2RefSeqNP_001269980.16Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

Biological Process

  • adaptive immune response
  • defense response
  • hyperosmotic response
  • signal transduction
  • T cell costimulation

Molecular Function

  • signaling receptor binding
  • protein binding
  • identical protein binding

Cellular Component

  • plasma membrane
  • external side of plasma membrane
  • integral component of membrane
  • cytoplasmic ribonucleoprotein granule
  • extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000407780
Coding exons
7
Length
17976
Individuals with no LoFs
124799
Homozygous LoFs
0
Heterozygous LoFs
18
Defined
124817
p
0.0000721
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.131531980.7740.00001321971
Missense (PolyPhen)4962.7050.78143695
Synonymous-0.81610191.11.110.00000730593
Loss of Function1.80815.70.5099.08e-7155

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000150.00014rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.000110.00011rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.206

Intolerance Scores

LoFtool
0.680
RVIS EVS
0.84
RVIS percentile EVS
88.3

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.527

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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