IL20

protein-coding

interleukin 20, the group of Interleukins

Gene summary

The protein encoded by this gene is a cytokine structurally related to interleukin 10 (IL10). This cytokine has been shown to transduce its signal through signal transducer and activator of transcription 3 (STAT3) in keratinocytes. A specific receptor for this cytokine is found to be expressed in skin and upregulated dramatically in psoriatic skin, suggesting a role for this protein in epidermal function and psoriasis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018724.4

Inheritance

—

ClinVar variants

U:15B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr1:206,865,623-206,869,223

External References & Databases

Ensembl (ENSG00000162891)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 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 IL20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018724.4. 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			15 clinvar	2 clinvar		17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	2	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018724.4	RefSeq	NP_061194.2	5	MANE Select
ENST00000367098.6	Ensembl	ENSP00000356065.1	5	MANE Select
NM_001385165.1	RefSeq	NP_001372094.1	4	Standard
NM_001385166.1	RefSeq	NP_001372095.1	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

Biological Process

regulation of signaling receptor activity
cytokine-mediated signaling pathway
positive regulation of tyrosine phosphorylation of STAT protein
positive regulation of epidermal cell differentiation
positive regulation of keratinocyte differentiation

Molecular Function

cytokine activity
interleukin-20 receptor binding
interleukin-22 receptor binding

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367098
Coding exons: 5
Length: 3870
Individuals with no LoFs: 125433
Homozygous LoFs: 2
Heterozygous LoFs: 297
Defined: 125732
p: 0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.127	95	98.5	0.964	0.00000533	1154
Missense (PolyPhen)		34	33.497	1.015		429
Synonymous	0.204	34	35.5	0.956	0.00000183	338
Loss of Function	0.0221	9	9.07	0.992	5.47e-7	99

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0015	0.0015	notable
Latino/Admixed American	0.00069	0.00069	rare
Ashkenazi Jewish	0.0054	0.0053	notable
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00083	0.00083	rare
South Asian	0.0032	0.0032	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proinflammatory and angiogenic cytokine that may be involved in epidermal function and psoriasis. Angiogenic and proliferative activities are antagonized by IL10. May act through STAT3. {ECO:0000269|PubMed:16511554}.;

Recessive Scores

pRec: 0.179

Intolerance Scores

LoFtool: 0.764
RVIS EVS: 0.1
RVIS percentile EVS: 61.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.852

Gene Damage Prediction

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