IFNL1

interferon lambda 1, the group of Interferons

Basic information

Region (hg38): 19:39296407-39298673

Previous symbols: [ "IL29" ]

Links

ENSG00000182393 ∙ NCBI:282618 ∙ OMIM:607403 ∙ HGNC:18363 ∙ Uniprot:Q8IU54 ∙ 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 IFNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNL1 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					2	2
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	3

Variants in IFNL1

This is a list of pathogenic ClinVar variants found in the IFNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39296426-C-A		not specified	Uncertain significance (Sep 02, 2024)
19-39296443-G-A		not specified	Uncertain significance (Mar 24, 2023)
19-39296501-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-39296503-A-G			Benign (Dec 31, 2019)
19-39296513-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-39296517-G-C		not specified	Uncertain significance (Nov 17, 2023)
19-39296557-G-C		not specified	Uncertain significance (Dec 28, 2022)
19-39296820-C-A		not specified	Uncertain significance (Feb 07, 2023)
19-39297974-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-39297975-C-T			Benign (Sep 05, 2018)
19-39298008-G-A			Benign (Dec 31, 2019)
19-39298051-G-A		not specified	Likely benign (Jul 20, 2021)
19-39298078-C-A		not specified	Uncertain significance (May 06, 2024)
19-39298087-C-T		not specified	Uncertain significance (Jul 05, 2024)
19-39298096-C-T		not specified	Uncertain significance (Feb 17, 2024)
19-39298228-A-G		not specified	Uncertain significance (Oct 03, 2022)
19-39298237-C-T		not specified	Uncertain significance (Nov 06, 2023)
19-39298246-C-T		not specified	Uncertain significance (May 02, 2024)
19-39298273-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-39298274-G-C		not specified	Uncertain significance (Sep 07, 2022)
19-39298283-A-C		not specified	Uncertain significance (Dec 10, 2024)
19-39298295-A-T		not specified	Uncertain significance (Feb 28, 2023)
19-39298419-T-A		not specified	Uncertain significance (Dec 07, 2024)
19-39298446-C-T		not specified	Uncertain significance (Jan 20, 2023)
19-39298449-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNL1	protein_coding	protein_coding	ENST00000333625	5	2349

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000285	0.577	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.118	122	118	1.03	0.00000689	1261
Missense in Polyphen		26	29.703	0.87534		349
Synonymous	-0.189	57	55.2	1.03	0.00000330	453
Loss of Function	0.552	6	7.65	0.784	3.24e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000538	0.000537
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine with antiviral, antitumour and immunomodulatory activities. Plays a critical role in the antiviral host defense, predominantly in the epithelial tissues. Acts as a ligand for the heterodimeric class II cytokine receptor composed of IL10RB and IFNLR1, and receptor engagement leads to the activation of the JAK/STAT signaling pathway resulting in the expression of IFN- stimulated genes (ISG), which mediate the antiviral state. Has a restricted receptor distribution and therefore restricted targets: is primarily active in epithelial cells and this cell type- selective action is because of the epithelial cell-specific expression of its receptor IFNLR1. Exerts an immunomodulatory effect by up-regulating MHC class I antigen expression.
• 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)

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0682
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

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: Ifnl3
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of type 2 immune response;JAK-STAT cascade;negative regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;negative regulation of interleukin-13 production;negative regulation of interleukin-5 production;positive regulation of interferon-gamma production;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of memory T cell differentiation;innate immune response;positive regulation of MHC class I biosynthetic process;negative regulation of T cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of JAK-STAT cascade;positive regulation of immune response;defense response to virus
• Cellular component: extracellular region;extracellular space;interleukin-28 receptor complex
• Molecular function: signaling receptor binding;cytokine activity;interleukin-28 receptor binding