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): 21:44215381-44241446

Previous symbols: [ "ICOSL" ]

Links

ENSG00000160223 ∙ NCBI:23308 ∙ OMIM:605717 ∙ HGNC:17087 ∙ Uniprot:O75144 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

ClinVar

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

• not provided (185 variants)
• Inborn genetic diseases (12 variants)
• Combined immunodeficiency (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.

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			1	51	5	57
missense		1	74	9	3	87
nonsense			3	1		4
start loss						0
frameshift				1		1
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1	1			2
splice region			1	8		9
non coding				25	2	27
Total	0	2	80	87	10

Variants in ICOSLG

This is a list of pathogenic ClinVar variants found in the ICOSLG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-44229035-C-G			Uncertain significance (Nov 28, 2023)
21-44229040-G-A			Likely benign (Dec 10, 2023)
21-44229058-T-A			Likely benign (Dec 09, 2023)
21-44229058-T-G			Likely benign (Jun 26, 2022)
21-44229064-A-G			Benign (Nov 28, 2023)
21-44229635-G-A			Likely benign (Jan 01, 2024)
21-44229656-C-T			Likely benign (Nov 01, 2022)
21-44229659-G-A			Likely benign (Mar 01, 2023)
21-44229669-C-T			Likely benign (Aug 01, 2022)
21-44229713-G-A			Likely benign (Apr 01, 2024)
21-44229740-G-A			Likely benign (Nov 01, 2022)
21-44229831-C-T			Likely benign (Apr 01, 2024)
21-44229832-G-A			Likely benign (Oct 01, 2023)
21-44229899-G-A			Likely benign (Nov 01, 2022)
21-44229931-A-T			Likely benign (Nov 01, 2022)
21-44230041-AC-A			Benign/Likely benign (Feb 01, 2024)
21-44230042-C-T			Likely benign (Jan 03, 2024)
21-44230058-G-A			Likely benign (Dec 25, 2023)
21-44230063-C-T		not specified	Uncertain significance (May 23, 2023)
21-44230070-C-G			Likely benign (Jan 17, 2023)
21-44230071-G-A		not specified	Conflicting classifications of pathogenicity (Dec 23, 2023)
21-44230082-C-T			Uncertain significance (May 28, 2023)
21-44230085-G-A			Likely benign (Jul 29, 2022)
21-44230086-G-A		not specified	Conflicting classifications of pathogenicity (Dec 30, 2023)
21-44230087-C-T			Uncertain significance (Oct 29, 2023)

GnomAD

Source: gnomAD

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: 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

	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