IL22RA1

interleukin 22 receptor subunit alpha 1, the group of Interleukin receptors

Basic information

Region (hg38): 1:24119770-24143140

Previous symbols: [ "IL22R" ]

Links

ENSG00000142677 ∙ NCBI:58985 ∙ OMIM:605457 ∙ HGNC:13700 ∙ Uniprot:Q8N6P7 ∙ 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 IL22RA1 gene.

• Inborn genetic diseases (30 variants)
• not specified (9 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL22RA1 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					4	4
missense			28	2	4	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	28	2	12

Variants in IL22RA1

This is a list of pathogenic ClinVar variants found in the IL22RA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24120724-G-A		not specified	Benign (Jan 24, 2024)
1-24120810-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-24120962-G-A		not specified	Uncertain significance (May 16, 2023)
1-24120978-G-C		not specified	Benign (Jan 24, 2024)
1-24121004-A-T		not specified	Uncertain significance (Jul 25, 2023)
1-24121031-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-24121035-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-24121067-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-24121178-G-T		not specified	Uncertain significance (Dec 16, 2021)
1-24121235-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-24121241-T-G		not specified	Uncertain significance (Feb 27, 2024)
1-24121256-A-T		not specified	Uncertain significance (Jan 23, 2024)
1-24121311-T-C			Benign (May 31, 2018)
1-24121317-C-T		not specified	Uncertain significance (Feb 17, 2023)
1-24121342-C-T			Benign (May 31, 2018)
1-24121377-C-A		not specified	Uncertain significance (Oct 17, 2023)
1-24121449-G-A		not specified	Uncertain significance (Sep 20, 2023)
1-24121498-C-A		not specified	Uncertain significance (Dec 05, 2022)
1-24121512-C-T		not specified	Likely benign (May 27, 2022)
1-24121577-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-24121594-G-A		not specified	Benign (Jan 24, 2024)
1-24121611-A-G		not specified	Uncertain significance (Dec 01, 2022)
1-24121621-C-A		not specified	Uncertain significance (Mar 02, 2023)
1-24121686-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-24121697-A-C		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL22RA1	protein_coding	protein_coding	ENST00000270800	7	23351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00569	0.993	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.179	320	329	0.972	0.0000187	3669
Missense in Polyphen		53	66.615	0.79561		872
Synonymous	0.0442	142	143	0.995	0.00000862	1218
Loss of Function	2.90	8	23.0	0.348	0.00000121	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000156	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the receptor for IL20, IL22 and IL24. Component of IL22 receptor formed by IL22RA1 and IL10RB enabling IL22 signaling via JAK/STAT pathways. IL22 also induces activation of MAPK1/MAPK3 and Akt kinases pathways. Component of one of the receptor for IL20 and IL24 formed by IL22RA1 and IL20RB also signaling through STATs activation. Mediates IL24 antiangiogenic activity as well as IL24 inhibitory effect on endothelial cell tube formation and differentiation. {ECO:0000269|PubMed:11035029, ECO:0000269|PubMed:11564763, ECO:0000269|PubMed:11706020, ECO:0000269|PubMed:12351624, ECO:0000269|PubMed:12941841, ECO:0000269|PubMed:17204547}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Signaling by Interleukins;il22 soluble receptor signaling pathway;Cytokine Signaling in Immune system;Interleukin-20 family signaling;Immune System (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.631
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.82

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.313

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Il22ra1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: biological_process;cytokine-mediated signaling pathway;defense response to Gram-negative bacterium
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: cytokine receptor activity;interferon receptor activity;protein binding;interleukin-20 binding