IFNLR1

interferon lambda receptor 1, the group of Interferon receptors

Basic information

Region (hg38): 1:24154168-24187959

Previous symbols: [ "IL28RA" ]

Links

ENSG00000185436 ∙ NCBI:163702 ∙ OMIM:607404 ∙ HGNC:18584 ∙ Uniprot:Q8IU57 ∙ 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 IFNLR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNLR1 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				1	4	5
missense			26	6	2	34
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	1	2
Total	0	0	27	8	7

Variants in IFNLR1

This is a list of pathogenic ClinVar variants found in the IFNLR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24157153-A-G		IFNLR1-related disorder	Benign (Jul 15, 2019)
1-24157158-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-24157159-G-A		not specified	Uncertain significance (May 26, 2024)
1-24157171-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-24157196-C-T			Uncertain significance (Aug 01, 2022)
1-24157206-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-24157206-G-C		IFNLR1-related disorder	Uncertain significance (Jan 23, 2023)
1-24157212-C-G		not specified	Uncertain significance (Mar 20, 2024)
1-24157214-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-24157392-G-A		not specified	Likely benign (May 24, 2024)
1-24157440-C-T		not specified	Uncertain significance (Apr 17, 2024)
1-24157480-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-24157510-C-G		not specified	Uncertain significance (May 23, 2023)
1-24157549-C-G		not specified	Uncertain significance (Oct 04, 2022)
1-24157557-C-A		not specified	Uncertain significance (Nov 27, 2024)
1-24157566-G-T		not specified	Likely benign (Apr 09, 2024)
1-24157593-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-24157609-C-G		IFNLR1-related disorder	Likely benign (Sep 17, 2021)
1-24157616-G-C		not specified	Uncertain significance (Feb 10, 2022)
1-24157624-G-A		not specified	Uncertain significance (Oct 08, 2024)
1-24157659-T-C		not specified	Uncertain significance (Nov 15, 2021)
1-24157681-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-24157705-C-T		IFNLR1-related disorder	Benign (Jul 30, 2019)
1-24157730-G-T		IFNLR1-related disorder	Likely benign (Oct 28, 2019)
1-24157747-T-C		not specified	Likely benign (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNLR1	protein_coding	protein_coding	ENST00000327535	7	33803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0625	0.923	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.770	257	294	0.874	0.0000166	3345
Missense in Polyphen		43	60.377	0.7122		777
Synonymous	1.07	113	128	0.880	0.00000803	1070
Loss of Function	2.14	4	12.0	0.334	5.11e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000968	0.0000879
Middle Eastern	0.000114	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The IFNLR1/IL10RB dimer is a receptor for the cytokine ligands IFNL2 and IFNL3 and mediates their antiviral activity. The ligand/receptor complex stimulate the activation of the JAK/STAT signaling pathway leading to the expression of IFN-stimulated genes (ISG), which contribute to the antiviral state. Determines the cell type specificity of the lambda interferon action. Shows a more restricted pattern of expression in the epithelial tissues thereby limiting responses to lambda interferons primarily to epithelial cells of the respiratory, gastrointestinal, and reproductive tracts. Seems not to be essential for early virus- activated host defense in vaginal infection, but plays an important role in Toll-like receptor (TLR)-induced antiviral defense. Plays a significant role in the antiviral immune defense in the intestinal epithelium. {ECO:0000269|PubMed:12469119, ECO:0000269|PubMed:12483210, ECO:0000269|PubMed:12521379}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Type III interferon signaling;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Interleukin-20 family signaling;Immune System (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.316
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifnlr1
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: mucosal immune response;negative regulation of cell population proliferation;cytokine-mediated signaling pathway;response to type III interferon;regulation of defense response to virus by host;defense response to virus
• Cellular component: plasma membrane;integral component of membrane;interleukin-28 receptor complex
• Molecular function: cytokine receptor activity;protein binding