IL7

interleukin 7, the group of Interleukins

Basic information

Region (hg38): 8:78675743-78805523

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
epidermodysplasia verruciformis, susceptibility to, 5 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 130 with HPV-related verrucosis	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.

not_specified (18 variants)
Epidermodysplasia_verruciformis,_susceptibility_to,_5 (5 variants)
IL7-related_disorder (4 variants)
not_provided (3 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. These statistics are base on transcript: NM_000000880.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			18 clinvar	1 clinvar	1 clinvar	20
nonsense	1 clinvar					1
start loss	1					1
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	3	0	18	2	2

Highest pathogenic variant AF is 6.8473264e-7

Loading clinvar variants...

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