IFNAR1

interferon alpha and beta receptor subunit 1, the group of Interferon receptors

Basic information

Region (hg38): 21:33324387-33359864

Previous symbols: [ "IFNAR" ]

Links

ENSG00000142166

∙ NCBI:3454 ∙ OMIM:107450 ∙ HGNC:5432 ∙ Uniprot:P17181 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

immunodeficiency 106, susceptibility to viral infections (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 106, susceptibility to viral infections	AR	Allergy/Immunology/Infectious	The condition involves increased risk of viral infections as well as adverse events related to live virus vaccination, and antiinfectious prophylaxis, early and aggressive treatment of infections, and consideration of vaccination regimens may be beneficial	Allergy/Immunology/Infectious	31270247; 32960813; 33252644; 34713375; 35091979; 35442418

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFNAR1 gene.

not_provided (265 variants)
not_specified (60 variants)
Immunodeficiency_106,_susceptibility_to_viral_infections (14 variants)
IFNAR1-related_disorder (3 variants)
Susceptibility_to_severe_COVID-19 (2 variants)
IMMUNODEFICIENCY_106,_SUSCEPTIBILITY_TO_VIRAL_INFECTIONS/IMMUNODEFICIENCY_28,_DIGENIC (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNAR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000629.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	65 clinvar	6 clinvar	72
missense			132 clinvar	11 clinvar	2 clinvar	145
nonsense	5 clinvar	1 clinvar	3 clinvar			9
start loss						0
frameshift	8 clinvar	1 clinvar	4 clinvar			13
splice donor/acceptor (+/-2bp)		7 clinvar	3 clinvar			10
Total	13	9	143	76	8

Highest pathogenic variant AF is 0.0000465007

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNAR1	protein_coding	protein_coding	ENST00000270139	11	35435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.25e-12	0.155	125705	0	42	125747	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.361	270	287	0.940	0.0000140	3690
Missense in Polyphen		65	73.552	0.88372		988
Synonymous	-0.213	108	105	1.03	0.00000560	1006
Loss of Function	0.755	20	24.0	0.834	0.00000101	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000187	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000187	0.000163
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the receptor for type I interferons, including interferons alpha, IFNB1 and IFNW1 (PubMed:2153461, PubMed:7665574, PubMed:10049744, PubMed:14532120, PubMed:15337770, PubMed:21854986). Functions in general as heterodimer with IFNAR2 (PubMed:7665574, PubMed:10049744, PubMed:21854986). Type I interferon binding activates the JAK-STAT signaling cascade, and triggers tyrosine phosphorylation of a number of proteins including JAKs, TYK2, STAT proteins and the IFNR alpha- and beta- subunits themselves (PubMed:7665574, PubMed:21854986). Can form an active IFNB1 receptor by itself and activate a signaling cascade that does not involve activation of the JAK-STAT pathway (By similarity). {ECO:0000250|UniProtKB:P33896, ECO:0000269|PubMed:10049744, ECO:0000269|PubMed:14532120, ECO:0000269|PubMed:15337770, ECO:0000269|PubMed:19561067, ECO:0000269|PubMed:2153461, ECO:0000269|PubMed:7665574, ECO:0000305|PubMed:21854986}.;
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);Hepatitis B - 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;Osteoclast Signaling;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 (Consensus)

Recessive Scores

pRec: 0.0742

Intolerance Scores

loftool: 0.696
rvis_EVS: 0.04
rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

pHI: 0.0941
hipred: Y
hipred_score: 0.672
ghis: 0.495

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ifnar1
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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; renal/urinary system 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype;

Gene ontology

Biological process: JAK-STAT cascade;response to virus;cytokine-mediated signaling pathway;response to lipopolysaccharide;cellular response to interferon-alpha;type I interferon signaling pathway
Cellular component: lysosome;late endosome;plasma membrane;integral component of plasma membrane
Molecular function: cytokine receptor activity;type I interferon receptor activity;protein binding;type I interferon binding