IFNL2

interferon lambda 2, the group of Interferons

Basic information

Region (hg38): 19:39268396-39270188

Previous symbols: [ "IL28A" ]

Links

ENSG00000183709 ∙ NCBI:282616 ∙ OMIM:607401 ∙ HGNC:18364 ∙ Uniprot:Q8IZJ0 ∙ 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 IFNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNL2 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			15	3	3	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	15	3	5

Variants in IFNL2

This is a list of pathogenic ClinVar variants found in the IFNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39268684-T-C			Benign (Dec 31, 2019)
19-39268695-C-A		not specified	Uncertain significance (Nov 17, 2023)
19-39268695-C-T			Benign (Dec 31, 2019)
19-39268763-G-A		not specified	Likely benign (Nov 13, 2024)
19-39268763-G-C		not specified	Likely benign (Feb 28, 2024)
19-39268773-C-T		not specified	Uncertain significance (May 12, 2024)
19-39268818-C-T		not specified	Uncertain significance (Aug 01, 2024)
19-39269162-T-G		not specified	Uncertain significance (Aug 14, 2024)
19-39269180-G-A		not specified	Uncertain significance (Jun 23, 2023)
19-39269186-A-G			Benign (Feb 26, 2018)
19-39269497-C-T		not specified	Uncertain significance (May 26, 2022)
19-39269531-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-39269557-G-A		not specified	Uncertain significance (Jul 22, 2024)
19-39269576-T-G		not specified	Likely benign (Dec 16, 2022)
19-39269594-C-T		not specified	Uncertain significance (Nov 08, 2024)
19-39269767-G-T		not specified	Uncertain significance (Nov 19, 2022)
19-39269778-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-39269795-T-C			Benign (Aug 16, 2017)
19-39269799-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-39269933-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-39269954-C-T		not specified	Uncertain significance (Sep 10, 2024)
19-39269964-T-A		not specified	Uncertain significance (Jun 01, 2023)
19-39269972-C-T		Susceptibility to severe COVID-19	Likely risk allele (Jul 01, 2022)
19-39269998-G-A			Benign (Apr 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNL2	protein_coding	protein_coding	ENST00000331982	6	1579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.99e-8	0.0672	125682	0	27	125709	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	129	121	1.06	0.00000733	1262
Missense in Polyphen		16	25.439	0.62895		327
Synonymous	0.117	54	55.1	0.980	0.00000340	432
Loss of Function	-0.689	10	7.91	1.26	3.35e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000237	0.000236
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000544	0.000544
South Asian	0.0000662	0.0000653
Other	0.00	0.00

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. 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. Exerts an immunomodulatory effect by up-regulating MHC class I antigen expression. {ECO:0000269|PubMed:12469119, ECO:0000269|PubMed:12483210, ECO:0000269|PubMed:16539846}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Type III interferon signaling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.19

Haploinsufficiency Scores

• pHI: 0.0755
• hipred: N
• hipred_score: 0.112

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: mucosal immune response;JAK-STAT cascade;regulation of signaling receptor activity;cytokine-mediated signaling pathway;innate immune response;positive regulation of immune response;defense response to virus
• Cellular component: extracellular region;extracellular space
• Molecular function: signaling receptor binding;cytokine activity