IL19

interleukin 19, the group of Interleukins

Basic information

Region (hg38): 1:206770763-206842981

Links

ENSG00000142224 ∙ NCBI:29949 ∙ OMIM:605687 ∙ HGNC:5990 ∙ Uniprot:Q9UHD0 ∙ 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 IL19 gene.

• Inflammatory bowel disease (72 variants)
• Inborn genetic diseases (10 variants)
• not specified (3 variants)
• not provided (3 variants)
• Leprosy, susceptibility to, 1 (1 variants)
• Graft-versus-host disease, resistance to (1 variants)
• Susceptibility to HIV infection (1 variants)
• Graft-versus-host disease, susceptibility to;Susceptibility to HIV infection;Rheumatoid arthritis (1 variants)
• Cholangiocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL19 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						0
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			32	35	7	74
Total	0	0	38	36	7

Variants in IL19

This is a list of pathogenic ClinVar variants found in the IL19 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-206770887-AA-GG		Inflammatory bowel disease	Likely benign (Jun 25, 2021)
1-206770888-A-G		Inflammatory bowel disease • not specified	Benign (Feb 01, 2024)
1-206770891-C-G		Inflammatory bowel disease	Likely benign (Dec 03, 2023)
1-206770892-T-G		Inflammatory bowel disease	Likely benign (Mar 09, 2023)
1-206770901-A-G		Inflammatory bowel disease	Uncertain significance (Aug 27, 2022)
1-206770910-G-T		Inflammatory bowel disease	Likely benign (Jun 05, 2019)
1-206770911-C-A		Inflammatory bowel disease	Uncertain significance (Oct 05, 2022)
1-206770911-C-T		Inflammatory bowel disease	Uncertain significance (Aug 16, 2022)
1-206770913-C-T		Inflammatory bowel disease	Likely benign (Jul 19, 2022)
1-206770914-C-T		Inflammatory bowel disease	Uncertain significance (Oct 01, 2022)
1-206770915-G-A		Inflammatory bowel disease • not specified	Uncertain significance (Dec 06, 2021)
1-206770920-C-T		Inflammatory bowel disease	Uncertain significance (Jun 09, 2020)
1-206770924-G-A		Inflammatory bowel disease	Likely benign (Feb 25, 2022)
1-206770940-G-A		Inflammatory bowel disease	Likely benign (Dec 31, 2023)
1-206770942-T-A		Inflammatory bowel disease	Uncertain significance (Dec 11, 2023)
1-206770949-C-G		Inflammatory bowel disease	Likely benign (Dec 12, 2019)
1-206770951-G-A		Inflammatory bowel disease	Likely benign (Jul 19, 2022)
1-206770953-G-A		Inflammatory bowel disease	Uncertain significance (Feb 27, 2020)
1-206770958-C-T		Inflammatory bowel disease	Likely benign (Jun 08, 2022)
1-206770962-T-C		Inflammatory bowel disease	Uncertain significance (Apr 09, 2022)
1-206770964-C-T		Inflammatory bowel disease	Likely benign (Jul 16, 2023)
1-206770965-G-A		Inflammatory bowel disease	Uncertain significance (Nov 18, 2020)
1-206770965-G-T		Inflammatory bowel disease	Uncertain significance (Aug 15, 2022)
1-206770971-A-C		Inflammatory bowel disease	Uncertain significance (Nov 18, 2023)
1-206770976-T-C		Inflammatory bowel disease	Likely benign (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL19	protein_coding	protein_coding	ENST00000340758	6	44110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000433	0.652	125736	1	9	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.668	100	121	0.829	0.00000635	1417
Missense in Polyphen		20	30.375	0.65843		459
Synonymous	0.299	45	47.6	0.945	0.00000288	398
Loss of Function	0.863	8	11.1	0.721	5.70e-7	121

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)	0.0000704	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play some important roles in inflammatory responses. Up-regulates IL-6 and TNF-alpha and induces apoptosis (By similarity). {ECO:0000250}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Signaling by Interleukins;Cytokine Signaling in Immune system;Interleukin-20 family signaling;Immune System;IL23-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.483
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.0311
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.379

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il19
• Phenotype: growth/size/body region phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: apoptotic process;immune response;signal transduction;regulation of signaling receptor activity;negative regulation of low-density lipoprotein particle clearance;cytokine-mediated signaling pathway;interleukin-6 biosynthetic process;reactive oxygen species metabolic process;negative regulation of extrinsic apoptotic signaling pathway;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity