IL19

protein-coding

interleukin 19, the group of Interleukins

Gene summary

The protein encoded by this gene is a cytokine that belongs to the IL10 cytokine subfamily. This cytokine is found to be preferentially expressed in monocytes. It can bind the IL20 receptor complex and lead to the activation of the signal transducer and activator of transcription 3 (STAT3). A similar cytokine in mouse is reported to up-regulate the expression of IL6 and TNF-alpha and induce apoptosis, which suggests a role of this cytokine in inflammatory responses. Alternatively spliced transcript variants encoding the distinct isoforms have been described. [provided by RefSeq, Jul 2008]

MANE transcript

NM_153758.5

Inheritance

—

ClinVar variants

U:26B:5

Top phenotype

Inflammatory bowel disease

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr1:206,770,764-206,842,981

External References & Databases

Ensembl (ENSG00000142224)

Transcript & Mutation Effects

hg38 • Region Span ~72.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IL19 variants in ClinVar

7 Conditions Cataloged

Inflammatory bowel diseaseTotal: 47

not specifiedTotal: 42

not providedTotal: 8

Rheumatoid arthritisTotal: 1

Graft-versus-host disease, susceptibility toTotal: 1

Susceptibility to HIV infectionTotal: 1

Rheumatoid arthritis, progression ofTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153758.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			26 clinvar	5 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	5	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153758.5	RefSeq	NP_715639.2	5	MANE Select
ENST00000659997.3	Ensembl	ENSP00000499459.2	5	MANE Select
NM_001369605.1	RefSeq	NP_001356534.1	5	Standard
NM_001393490.1	RefSeq	NP_001380419.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

apoptotic process
immune response
signal transduction
regulation of signaling receptor activity
negative regulation of low-density lipoprotein particle clearance

Molecular Function

cytokine activity

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340758
Coding exons: 6
Length: 44110
Individuals with no LoFs: 125736
Homozygous LoFs: 1
Heterozygous LoFs: 9
Defined: 125746
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.668	100	121	0.829	0.00000635	1417
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000070	0.000070	rare
South Asian	0.000098	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.146

Intolerance Scores

LoFtool: 0.483
RVIS EVS: 0.5
RVIS percentile EVS: 79.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.379

Gene Damage Prediction

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