IL16

interleukin 16, the group of PDZ domain containing|Interleukins

Basic information

Region (hg38): 15:81159574-81314058

Links

ENSG00000172349 ∙ NCBI:3603 ∙ OMIM:603035 ∙ HGNC:5980 ∙ Uniprot:Q14005 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL16 gene.

• Inborn genetic diseases (54 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL16 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				3	3	6
missense			48	4	3	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	50	7	7

Variants in IL16

This is a list of pathogenic ClinVar variants found in the IL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-81225407-C-T		not specified	Uncertain significance (Oct 02, 2023)
15-81225418-G-A		not specified	Likely benign (Oct 03, 2022)
15-81225422-G-C		not specified	Uncertain significance (Jan 23, 2024)
15-81225428-G-T		not specified	Uncertain significance (Jul 12, 2022)
15-81225572-A-C		not specified	Uncertain significance (Jun 11, 2021)
15-81225691-A-G		not specified	Uncertain significance (Feb 27, 2024)
15-81259872-A-T		not specified	Uncertain significance (May 31, 2023)
15-81265725-A-G		not specified	Uncertain significance (Dec 06, 2023)
15-81265778-G-A		not specified	Uncertain significance (Nov 06, 2023)
15-81269557-G-A		not specified	Uncertain significance (Sep 15, 2021)
15-81269580-G-A		not specified	Uncertain significance (Oct 25, 2023)
15-81269590-C-A		not specified	Uncertain significance (Feb 28, 2023)
15-81273108-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-81273175-C-A		not specified	Uncertain significance (Jan 04, 2022)
15-81273186-G-T		not specified	Uncertain significance (Aug 12, 2021)
15-81278849-A-G		not specified	Uncertain significance (Feb 13, 2024)
15-81279573-C-T		not specified	Uncertain significance (Aug 02, 2023)
15-81279598-G-A		not specified	Uncertain significance (Aug 28, 2023)
15-81279604-C-T		not specified	Likely benign (Jul 20, 2021)
15-81279629-C-A		not specified	Uncertain significance (Aug 13, 2021)
15-81279636-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-81279640-C-T		not specified	Uncertain significance (Nov 30, 2021)
15-81279670-G-A		not specified	Uncertain significance (Mar 08, 2024)
15-81279712-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-81279729-G-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL16	protein_coding	protein_coding	ENST00000302987	18	153189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-10	1.00	125636	1	111	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.700	697	751	0.928	0.0000422	8592
Missense in Polyphen		204	242.58	0.84097		2760
Synonymous	-0.843	330	311	1.06	0.0000186	2826
Loss of Function	3.35	25	50.8	0.492	0.00000271	604

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000964	0.000935
Ashkenazi Jewish	0.000412	0.000397
East Asian	0.000334	0.000326
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.000334	0.000326
South Asian	0.00108	0.00105
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interleukin-16 stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. Primes CD4+ T-cells for IL-2 and IL-15 responsiveness. Also induces T-lymphocyte expression of interleukin 2 receptor. Ligand for CD4.; FUNCTION: Isoform 3 is involved in cell cycle progression in T- cells. Appears to be involved in transcriptional regulation of SKP2 and is probably part of a transcriptional repression complex on the core promoter of the SKP2 gene. May act as a scaffold for GABPB1 (the DNA-binding subunit the GABP transcription factor complex) and HDAC3 thus maintaining transcriptional repression and blocking cell cycle progression in resting T-cells.
• Pathway: Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.717
• rvis_EVS: -0.07
• rvis_percentile_EVS: 47.8

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.420
• ghis: 0.566

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Il16
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: immune response;regulation of signaling receptor activity;viral process;cytokine-mediated signaling pathway;leukocyte chemotaxis;induction of positive chemotaxis;regulation of calcium ion transport
• Cellular component: extracellular region;extracellular space;cytosol;plasma membrane;nuclear speck
• Molecular function: cytokine activity;CD4 receptor binding