IFNAR2

interferon alpha and beta receptor subunit 2, the group of Interferon receptors

Basic information

Region (hg38): 21:33205281-33265675

Previous symbols: [ "IFNABR" ]

Links

ENSG00000159110 ∙ NCBI:3455 ∙ OMIM:602376 ∙ HGNC:5433 ∙ Uniprot:P48551 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 45 (Strong), mode of inheritance: AR
• immunodeficiency 45 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 45	AR	Allergy/Immunology/Infectious	Individuals have immunodeficiency, and related adverse reactions to vaccinations have been reported such that awareness may help prevent morbidity	Allergy/Immunology/Infectious	26424569

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFNAR2 gene.

• not provided (204 variants)
• Inborn genetic diseases (20 variants)
• Immunodeficiency 45 (11 variants)
• not specified (9 variants)
• Mortality risk in patients with severe coronavirus disease (COVID-19) (4 variants)
• Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (2 variants)
• Multisystem inflammatory syndrome in children (1 variants)
• Susceptibility to severe COVID-19 (1 variants)
• Hepatitis B virus, susceptibility to;Immunodeficiency 45 (1 variants)
• Hepatitis B virus, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNAR2 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				48	7	55
missense			105	5	6	116
nonsense	2					2
start loss						0
frameshift	3		1			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2	1			3
splice region			3	1	1	5
non coding			2	22	8	32
Total	5	2	110	75	21

Highest pathogenic variant AF is 0.0000526

Variants in IFNAR2

This is a list of pathogenic ClinVar variants found in the IFNAR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-33237200-G-A		Mortality risk in patients with severe coronavirus disease (COVID-19) • Associated with severe COVID-19 disease	Uncertain significance; association (Jul 01, 2023)
21-33241936-A-G			Uncertain significance (Jul 26, 2022)
21-33241945-T-C		Hepatitis B virus, susceptibility to • Immunodeficiency 45 • Mortality risk in patients with severe coronavirus disease (COVID-19) • not specified	Benign (Feb 01, 2024)
21-33241949-C-G		not specified	Uncertain significance (Jul 12, 2023)
21-33241950-T-A		Associated with severe COVID-19 disease	Uncertain significance (Jul 01, 2023)
21-33241950-T-G		Immunodeficiency 45 • Mortality risk in patients with severe coronavirus disease (COVID-19) • not specified	Benign (Feb 01, 2024)
21-33241955-A-T			Uncertain significance (Aug 19, 2022)
21-33241958-A-G			Likely benign (Jul 19, 2022)
21-33241958-A-T			Likely benign (Sep 27, 2023)
21-33241961-T-G			Likely benign (Nov 21, 2023)
21-33241966-T-G			Uncertain significance (Feb 17, 2022)
21-33241975-T-C			Uncertain significance (Jul 04, 2022)
21-33241987-G-A			Likely benign (Dec 27, 2023)
21-33241987-G-C			Likely benign (Jan 19, 2024)
21-33241988-C-T			Likely benign (Nov 18, 2023)
21-33241994-A-G			Likely benign (Sep 21, 2021)
21-33241994-A-T			Likely benign (Mar 06, 2022)
21-33241995-T-C			Likely benign (Jun 06, 2023)
21-33241996-C-T			Likely benign (Nov 19, 2022)
21-33243657-G-A			Likely benign (Feb 09, 2022)
21-33243676-A-G			Uncertain significance (Oct 03, 2023)
21-33243682-G-T		not specified	Uncertain significance (Sep 09, 2022)
21-33243683-C-T			Likely benign (Dec 24, 2020)
21-33243686-C-T			Likely benign (Sep 30, 2023)
21-33243687-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNAR2	protein_coding	protein_coding	ENST00000342136	8	35775

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000853	0.776	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.258	265	277	0.956	0.0000141	3411
Missense in Polyphen		86	105.39	0.81604		1325
Synonymous	0.135	110	112	0.984	0.00000668	967
Loss of Function	1.22	10	15.1	0.662	7.16e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000644	0.000642
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with IFNAR1 to form the type I interferon receptor. Receptor for interferons alpha and beta. Involved in IFN-mediated STAT1, STAT2 and STAT3 activation (PubMed:26424569). Isoform 1 and isoform 2 are directly involved in signal transduction due to their association with the TYR kinase, JAK1 (PubMed:8181059, PubMed:7665574, PubMed:7759950). Isoform 3 is a potent inhibitor of type I IFN receptor activity (PubMed:7759950). {ECO:0000269|PubMed:10049744, ECO:0000269|PubMed:11682488, ECO:0000269|PubMed:12105218, ECO:0000269|PubMed:26424569, ECO:0000269|PubMed:7665574, ECO:0000269|PubMed:7759950, ECO:0000269|PubMed:8181059}.
• Disease: DISEASE: Immunodeficiency 45 (IMD45) [MIM:616669]: An autosomal recessive disorder characterized by increased susceptibility to viral infection due to impaired antiviral immunity, resulting in infection-associated encephalopathy. Affected individuals are at risk for developing fatal encephalitis after routine measles/mumps/rubella (MMR) vaccination. {ECO:0000269|PubMed:26424569}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Influenza A - Homo sapiens (human);Necroptosis - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Measles - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;Regulation of toll-like receptor signaling pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;The human immune response to tuberculosis;Interferon type I signaling pathways;Toll-like Receptor Signaling Pathway;ifn alpha signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;IFN alpha signaling;JAK STAT MolecularVariation 2;bone remodeling;JAK STAT pathway and regulation;Regulation of IFNA signaling;Interferon alpha/beta signaling;Downstream signaling in naïve CD8+ T cells;Interferon Signaling;Regulation of Telomerase (Consensus)

Recessive Scores

• pRec: 0.318

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.82

Haploinsufficiency Scores

• pHI: 0.0738
• hipred: Y
• hipred_score: 0.539
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.836

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifnar2
• 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); hematopoietic system phenotype; neoplasm; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;JAK-STAT cascade;response to virus;cytokine-mediated signaling pathway;response to interferon-alpha;response to interferon-beta;defense response to virus;type I interferon signaling pathway;regulation of type I interferon-mediated signaling pathway
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane
• Molecular function: cytokine receptor activity;type I interferon receptor activity;protein binding;protein kinase binding