IL22RA2

interleukin 22 receptor subunit alpha 2, the group of Interleukin receptors

Basic information

Region (hg38): 6:137143820-137173648

Links

ENSG00000164485 ∙ NCBI:116379 ∙ OMIM:606648 ∙ HGNC:14901 ∙ Uniprot:Q969J5 ∙ 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 IL22RA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL22RA2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in IL22RA2

This is a list of pathogenic ClinVar variants found in the IL22RA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-137145641-A-G		not specified	Uncertain significance (Oct 05, 2021)
6-137145679-G-A		not specified	Uncertain significance (May 03, 2023)
6-137145682-T-C		not specified	Uncertain significance (May 04, 2022)
6-137145687-T-C		not specified	Uncertain significance (Mar 15, 2024)
6-137145719-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-137145733-A-G		not specified	Uncertain significance (Feb 13, 2023)
6-137145740-C-A		not specified	Uncertain significance (Aug 21, 2023)
6-137145742-G-A		not specified	Likely benign (May 08, 2023)
6-137154943-T-G		not specified	Uncertain significance (Jan 23, 2023)
6-137154961-C-T		not specified	Uncertain significance (Jul 20, 2022)
6-137154964-G-A		not specified	Uncertain significance (Sep 30, 2022)
6-137155003-G-A		not specified	Uncertain significance (Apr 12, 2022)
6-137155016-C-T		not specified	Uncertain significance (Dec 22, 2023)
6-137155024-G-A		not specified	Uncertain significance (Jun 14, 2024)
6-137158386-A-T		not specified	Uncertain significance (Dec 27, 2023)
6-137158428-C-T		not specified	Uncertain significance (Sep 09, 2021)
6-137158429-G-A		Multisystem inflammatory syndrome in children	risk factor (Nov 14, 2021)
6-137158437-A-T		not specified	Uncertain significance (Jul 13, 2021)
6-137158467-T-C		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL22RA2	protein_coding	protein_coding	ENST00000296980	6	29818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-16	0.000786	125668	0	72	125740	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.136	145	140	1.03	0.00000685	1731
Missense in Polyphen		55	42.155	1.3047		516
Synonymous	1.10	39	48.7	0.800	0.00000260	458
Loss of Function	-1.36	21	15.3	1.38	8.20e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000437	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000320	0.000317
Middle Eastern	0.000437	0.000435
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2 is a receptor for IL22. Binds to IL22, prevents interaction with the functional IL-22R complex and blocks the activity of IL22 (in vitro). May play an important role as an IL22 antagonist in the regulation of inflammatory responses.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Ncore;Signaling by Interleukins;il22 soluble receptor signaling pathway;Cytokine Signaling in Immune system;Interleukin-20 family signaling;Immune System (Consensus)

Recessive Scores

• pRec: 0.0815

Intolerance Scores

• loftool: 0.612
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.0470
• hipred: N
• hipred_score: 0.123
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il22ra2
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype; neoplasm; immune system phenotype

Gene ontology

• Biological process: cytokine-mediated signaling pathway;regulation of tyrosine phosphorylation of STAT protein;negative regulation of inflammatory response
• Cellular component: extracellular region;extracellular space;cytosol;plasma membrane
• Molecular function: cytokine receptor activity;interleukin-22 binding;interleukin-22 receptor activity