IL7

interleukin 7, the group of Interleukins

Basic information

Region (hg38): 8:78675742-78805523

Links

ENSG00000104432 ∙ NCBI:3574 ∙ OMIM:146660 ∙ HGNC:6023 ∙ Uniprot:P13232 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epidermodysplasia verruciformis (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epidermodysplasia verruciformis, susceptibility to, 5	AR	Allergy/Immunology/Infectious; Oncologic	Individuals have been described with susceptibility to certain infections as well as potential increased risk of skin cancer, and awareness may allow prompt diagnosis and management of sequeleae	Allergy/Immunology/Infectious; Dermatologic; Oncologic	25981006

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL7 gene.

• Inborn genetic diseases (4 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL7 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	1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	4	0	2

Variants in IL7

This is a list of pathogenic ClinVar variants found in the IL7 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-78678605-C-T		not specified	Uncertain significance (Nov 08, 2022)
8-78678675-C-T		not specified	Uncertain significance (Sep 26, 2022)
8-78686500-A-G		not specified	Uncertain significance (Aug 02, 2023)
8-78686519-T-C		not specified	Uncertain significance (May 04, 2023)
8-78686584-C-T		not specified	Uncertain significance (Feb 27, 2023)
8-78689251-A-T			Uncertain significance (Aug 05, 2023)
8-78689309-G-A		not specified	Uncertain significance (Jun 22, 2021)
8-78689315-G-C		not specified	Uncertain significance (Dec 09, 2023)
8-78689342-C-T		not specified	Uncertain significance (May 09, 2022)
8-78689363-G-A		not specified	Uncertain significance (Oct 05, 2021)
8-78689371-G-C		not specified	Uncertain significance (Jun 22, 2023)
8-78697419-G-A		not specified	Uncertain significance (May 24, 2023)
8-78697468-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-78697483-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-78697488-G-A		not specified	Likely benign (Feb 16, 2023)
8-78697489-C-A		not specified	Uncertain significance (Jul 14, 2023)
8-78698409-A-G			Likely benign (Mar 01, 2023)
8-78733733-T-C		not specified	Uncertain significance (May 18, 2023)
8-78736505-G-A		not specified	Uncertain significance (Dec 17, 2023)
8-78736524-T-C		not specified	Uncertain significance (Jan 25, 2023)
8-78738498-G-A		IL7-related disorder	Benign (Oct 28, 2019)
8-78738508-C-T		not specified	Uncertain significance (Aug 21, 2023)
8-78740025-T-A		Epidermodysplasia verruciformis, susceptibility to, 5	risk factor (Feb 01, 2019)
8-78740075-A-G		not specified	Uncertain significance (Oct 26, 2022)
8-78746947-T-A		not specified	Benign (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL7	protein_coding	protein_coding	ENST00000263851	6	129781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0739	125294	0	1	125295	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	67	85.3	0.785	0.00000400	1178
Missense in Polyphen		9	20.084	0.44812		310
Synonymous	0.372	27	29.6	0.913	0.00000134	299
Loss of Function	2.67	0	8.31	0.00	3.48e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hematopoietic growth factor capable of stimulating the proliferation of lymphoid progenitors. It is important for proliferation during certain stages of B-cell maturation.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;IL-7 Signaling Pathway;Development and heterogeneity of the ILC family;PI3K-Akt Signaling Pathway;Cytokines and Inflammatory Response;Interleukin-7 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;IL-7 signaling;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i;IL-7 (Consensus)

Recessive Scores

• pRec: 0.496

Intolerance Scores

• loftool: 0.140
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.419
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il7
• Phenotype: immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: positive regulation of cytokine-mediated signaling pathway;T cell lineage commitment;humoral immune response;cell-cell signaling;positive regulation of cell population proliferation;animal organ morphogenesis;regulation of gene expression;regulation of signaling receptor activity;cytokine-mediated signaling pathway;positive regulation of B cell proliferation;positive regulation of chemokine production;interleukin-7-mediated signaling pathway;negative regulation of apoptotic process;negative regulation of catalytic activity;bone resorption;positive regulation of T cell differentiation;positive regulation of organ growth;homeostasis of number of cells within a tissue;regulation of peptidyl-tyrosine phosphorylation;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: extracellular region;extracellular space;collagen-containing extracellular matrix
• Molecular function: cytokine activity;interleukin-7 receptor binding;protein binding;growth factor activity