IFNL4

gene
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Also known as IFNAN

Summary

IFNL4 (interferon lambda 4 (gene/pseudogene), HGNC:44480) is a protein-coding gene on chromosome 19q13.2, encoding Interferon lambda-4 (K9M1U5). Cytokine that may trigger an antiviral response activating the JAK-STAT pathway and up-regulating specifically some interferon-stimulated genes.

This gene is a polymorphic pseudogene which, in some humans, encodes the interferon (IFN) lambda 4 protein. Humans are polymorphic for the dinucleotide TT/deltaG allele. Compared to the ancestral state in non-human primates, the TT allele produces a frameshift in the coding region of this gene which is predicted to induce nonsense-mediated mRNA decay. This allele, and an allele in the first intron of this gene, have experienced a rapid increase in frequency and show indications of positive selection. The ancestral states of these alleles are associated with an impaired ability to clear hepatitis C virus. This gene, like other type III interferons (IFNs), interacts with the IFN lambda receptor complex (IFNLR) whose signaling is generally restricted to epithelial cells. This gene resides in a cluster of four type III IFN genes and at least two pseudogenes on chromosome 19q13.2. In general, interferons are produced in response to viral infection and block viral replication and propagation to uninfected cells by activating the JAK-STAT pathway and up-regulating antiviral genes. Multiple alternatively spliced transcripts have been described for this gene but their biological validity and protein coding status is still being ascertained.

Source: NCBI Gene 101180976 — RefSeq curated summary.

At a glance

  • GWAS associations: 11

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:44480
Approved symbolIFNL4
Nameinterferon lambda 4 (gene/pseudogene)
Location19q13.2
Locus typegene with protein product
StatusApproved
AliasesIFNAN
Ensembl geneENSG00000272395
Ensembl biotypeprotein_coding
OMIM615090
Entrez101180976

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding_LoF

ENST00000606380, ENST00000634680, ENST00000634967

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000606380 — 5 exons

ExonStartEnd
ENSE000036975333924631439247231
ENSE000036995363924738939247463
ENSE000037005263924792439247995
ENSE000037005713924770839247851
ENSE000037530563924842939248856

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 85.96.

Top tissues by expression

107 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.96gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099147.23gold quality
prefrontal cortexUBERON:000045145.49gold quality
superior frontal gyrusUBERON:000266141.36silver quality
frontal cortexUBERON:000187040.41gold quality
bone marrow cellCL:000209240.20gold quality
hypothalamusUBERON:000189839.67gold quality
granulocyteCL:000009439.22gold quality
cerebral cortexUBERON:000095637.90gold quality
cerebellumUBERON:000203737.44gold quality
cerebellar cortexUBERON:000212937.31gold quality
colonic epitheliumUBERON:000039737.20gold quality
cerebellar hemisphereUBERON:000224537.06gold quality
sural nerveUBERON:001548836.93gold quality
ventricular zoneUBERON:000305336.48gold quality
right hemisphere of cerebellumUBERON:001489035.91gold quality
substantia nigraUBERON:000203835.89silver quality
hindlimb stylopod muscleUBERON:000425235.77gold quality
anterior cingulate cortexUBERON:000983535.77silver quality
temporal lobeUBERON:000187135.56silver quality
ganglionic eminenceUBERON:000402335.49gold quality
amygdalaUBERON:000187635.24silver quality
Ammon’s hornUBERON:000195435.24silver quality
bone marrowUBERON:000237135.03gold quality
myometriumUBERON:000129634.70silver quality
leukocyteCL:000073834.44gold quality
monocyteCL:000057634.41gold quality
body of uterusUBERON:000985334.38silver quality
brainUBERON:000095534.32silver quality
body of pancreasUBERON:000115031.82gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.65

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

  • A new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. (PMID:23291588)
  • IFNL4-DeltaG is strongly associated with impaired spontaneous hepatitis C virus clearance. (PMID:23956438)
  • IFNL4 improves prediction of response to interferon-based hepatitis C therapies, if SNP rs8099917 is used. (PMID:24205831)
  • Its polymorphisms are strongly associated with responses to pegylated interferon (PEG-IFN) and ribavirin (RBV) therapy in patients chronically infected with hepatitis C virus. (PMID:24325405)
  • genetic polymorphism is associated with antiviral therapy outcome in the Japanese population (PMID:24355007)
  • It was reported that in patients treated with sofosbuvir along with ribavirin, IFNL4-DeltaG is associated with slower early viral decay, due to slower loss of free virus and decreased drug efficacy. (PMID:24367041)
  • HCV infection in particular might activate IFNL4 transcription in the liver (PMID:24376784)
  • Intrahepatic lymphocyte degranulation activity in HCV-infected patients is associated with IFNL4 polymorphisms and contributes to the clearance of HCV in patients with favorable genotypes under antiviral therapy. (PMID:24415789)
  • could not find any difference in the predictive impact of any of three SNPs of IFNL4 or IL-28B with regard to susceptibility to HCV or treatment response (PMID:24646752)
  • IFNL3 and IFNL4 single nucleotide polymorphisms correlate with treatment response in hepatitis C patients depending on virus genotype. (PMID:24782280)
  • this review summarizes the current knowledge of IFN-l4 and discusses questions that should be addressed to resolve its paradoxical biologic activities.[review] (PMID:24786669)
  • This study demonstrates that IFNL4 rs368234815 polymorphism is an important predictor of response to antiviral treatment in the liver transplantation setting. (PMID:25130512)
  • Authors report for the first time an association between an IFNL3/4 polymorphism and susceptibility to AIDS-related cytomegalovirus retinitis. (PMID:25259701)
  • Polymorphisms in the IFNL3/4 region influence susceptibility to cytomegalovirus replication in solid-organ transplant recipients. (PMID:25301956)
  • Natural selection history of IFNL4-inactivating allele has thus shaped present-day heterogeneity across populations not only in genetic variation, but also in relevant phenotypes and susceptibility to hepatitis C. (PMID:25329461)
  • IFNL4 gene polymorphisms can predict treatment response in chronic hepatitis C. (PMID:25393304)
  • Patients harbouring the impaired IFNlambda4-S70 variant display lower interferon-stimulated gene (ISG) expression levels. (PMID:25534433)
  • Among Puerto Rican hepatitis C patients, SNP frequencies of IFNL4 locus ss469415590 were 26% (TT/TT), 48% (TT/DeltaG), and 26% (DeltaG/DeltaG). (PMID:25563035)
  • Genetic analysis revealed associations of rs368234815 of IFNL4 with sustained virological response and pre-treatment viral load. (PMID:25577150)
  • Overexpression of IFNlambda4 suppressed IL28B induction and promoter activation. (PMID:25611696)
  • We found an independent association of the IFNL4 ss469415590 polymorphism with higher prevalence of AIDS-defining illnesses and lower CD4 T cell numbers. (PMID:25658540)
  • IFNL4 and IFNL3 associated polymorphisms strongly influence the spontaneous IFN-alpha receptor-1 expression in HCV-infected patients (PMID:25675103)
  • Interferon-lambda rs12979860 genotype is a strong aetiology-independent predictor of tissue inflammation and fibrosis in viral and non-viral chronic liver disease. (PMID:25740255)
  • The IFNL3.rs12979860 and IFNL4.ss469415590 variants have comparable effects on spontaneous resolution of hepatitis C virus infection among Egyptians. (PMID:25788203)
  • HCV infection is proposed to induce a more efficient antiviral response in individuals with the IFNL4 TT/TT genotype that results either in viral clearance or selection for viral adaptations. (PMID:25849245)
  • Females with the IFNL4 genotype detected were more likely to have HCV reclearance. (PMID:25883387)
  • IFNL4 polymorphisms were predictive of treatment outcome only for patients infected with HCV-1. (PMID:25938236)
  • Transcriptome analysis reveals a classical interferon signature induced by IFNlambda4 in human primary cells (PMID:26066369)
  • The current study is the first to investigate the effect of IFNL3 and IFNL4 polymorphisms on liver-related mortality. The lower risk of death among African American HIV/HCV-coinfected women is not explained by genetic variation in the IFN-lambda region. (PMID:26115445)
  • IFN-l4 may have at least 3 functions in human hepatic cells-activation of interferon signaling, inhibition of cell proliferation, and induction of cell death (PMID:26134097)
  • IFNL3 and IFNL4 genotyping could identify those likely to clear naturally and in whom treatment could be delayed, or help prioritize Directly-acting antivirals treatment to those less likely to respond to interferon-containing regimens. (PMID:26150150)
  • IFNL4-DeltaG/TT is the primary IFN-lambda region polymorphism for impaired HCV clearance (PMID:26186989)
  • Studies indicate that the type III interferons (IFNs) or IFN-lambdas consists of four members: IFN-lambda1 (IL-29), IFN-lambda2 (IL28A), IFN-lambda3 (IL-28B) and IFN-lambda4. (PMID:26194286)
  • Single Nucleotide Polymorphism of Interferon Lambda-4 Gene is not Associated with Treatment Response to Pegylated Interferon in Chronic Hepatitis B. (PMID:26225703)
  • Despite differences in protein sequences, functional properties of the recombinant human and nonhuman IFN-l4 proteins are comparable-they are all biologically active for induction of interferon signaling. (PMID:26308395)
  • The hepatitis C protective allele TT was associated with decreased likelihood of HIV-1 infection in male intravenous drug users [odds ratio (OR): 0.3; P = 0.006], and this association was not modified by the genotype of CCR5. (PMID:26372394)
  • Single-nucleotide polymorphisms (SNPs) in the interferon lambda 4 (IFNL4) gene are predictors for treatment success in patients with hepatitis C virus (HCV) infection (PMID:26406534)
  • IFNL4-DeltaG/TT genotype was not associated with HSV-related outcomes, including episodes of oral or genital herpes (PMID:26431156)
  • Single-nucleotide polymorphisms (rs12979860) in the intronic region of the interferon-lambda4 (IFNL4) gene modulate liver inflammation and fibrosis, in an etiology independent manner. (PMID:26592354)
  • data on ex vivo derived liver tissue samples argue against an attenuating impact of IFNL3 rs4803217 or IFNL4 rs368234815 minor alleles on hepatic IFNL3 gene expression in vivo. (PMID:26606750)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Interferon lambda-4K9M1U5 (reviewed: K9M1U5)

All UniProt accessions (1): K9M1I6

UniProt curated annotations — full annotation on UniProt →

Function. Cytokine that may trigger an antiviral response activating the JAK-STAT pathway and up-regulating specifically some interferon-stimulated genes.

Subcellular location. Cytoplasm. Secreted.

Induction. Up-regulated by polyinosinic:polycytidylic acid (polyI:C) which mimics the double-stranded hepatitis C virus.

Polymorphism. A one-base insertion, introducing a frameshift at position 22, results in inactivation of the gene in a majority of the population. That polymorphism is a good marker for predicting spontaneous hepatitis C virus (HCV) clearance and the response to treatment of chronic hepatitis C. The allele producing a functional protein able to induce an antiviral response and to prevent HCV replication in cell cultures, is less frequent in human populations and is associated with impaired spontaneous clearance of HCV.

Miscellaneous. Active form which is able to induce an antiviral response and prevent hepatitis C virus (HCV) replication in cell cultures. Inactive form. Inactive form unable to elicit an antiviral response. Inactive form unable to elicit an antiviral response.

Similarity. Belongs to the type-III (or lambda) interferon family.

Isoforms (4)

UniProt IDNamesCanonical?
K9M1U5-11, IFNL4, p179yes
K9M1U5-22, p170
K9M1U5-33, p131
K9M1U5-44, p107

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029177INF_lambdaFamily
IPR038326IFN-lambda_sfHomologous_superfamily

Pfam: PF15177

UniProt features (16 total): helix 6, disulfide bond 3, splice variant 3, signal peptide 1, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9BPUELECTRON MICROSCOPY3.26

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-K9M1U5-F177.090.26

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 27–122, 62–152, 76–178

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GOBP_CELLULAR_RESPONSE_TO_VIRUS, GOBP_RESPONSE_TO_PEPTIDE, GOBP_CELL_SURFACE_RECEPTOR_SIGNALING_PATHWAY_VIA_JAK_STAT, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_DEFENSE_RESPONSE_TO_VIRUS, GOMF_CYTOKINE_ACTIVITY, GOMF_SIGNALING_RECEPTOR_BINDING, GOBP_RESPONSE_TO_VIRUS, GOMF_SIGNALING_RECEPTOR_REGULATOR_ACTIVITY, GOBP_PEPTIDYL_TYROSINE_MODIFICATION, GOBP_CELL_SURFACE_RECEPTOR_SIGNALING_PATHWAY_VIA_STAT, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_CALU3_CELLS_UP, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_UP, GOBP_PEPTIDYL_AMINO_ACID_MODIFICATION

GO Biological Process (6): tyrosine phosphorylation of STAT protein (GO:0007260), type III interferon-mediated signaling pathway (GO:0038196), innate immune response (GO:0045087), positive regulation of immune response (GO:0050778), defense response to virus (GO:0051607), cellular response to virus (GO:0098586)

GO Molecular Function (2): signaling receptor binding (GO:0005102), cytokine activity (GO:0005125)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
immune response2
response to virus2
cell surface receptor signaling pathway via JAK-STAT1
peptidyl-tyrosine phosphorylation1
cellular response to type III interferon1
interferon-mediated signaling pathway1
defense response to symbiont1
positive regulation of immune system process1
positive regulation of response to stimulus1
regulation of immune response1
defense response1
protein binding1
receptor ligand activity1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

BioGRID (1): RIOK2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A140LIA7, A0A1B0GTL2, A2VDX9, A3FFS8, A6NCS6, A8MVW0, K9M1U5, O43541, P01588, P03971, P03972, P07321, P07865, P0C7N4, P0DPE3, P13725, P27106, P29676, P33707, P33708, P33709, P48617, P49000, P49157, P53346, P79295, Q02011, Q0Z956, Q16619, Q1HCM0, Q28513, Q29RM6, Q5BLP8, Q5S1V9, Q60753, Q63086, Q65Z15, Q6H8S9, Q6H8T0, Q6H8T1

Diamond homologs: B4ER10, K9M1U5, Q4VK74, Q8CGK6, Q8IU54, Q8IZI9, Q8IZJ0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

579 predictions. Top by Δscore:

VariantEffectΔscore
19:39247852:C:CCacceptor_gain1.0000
19:39248427:A:ACdonor_gain1.0000
19:39248428:C:CCdonor_gain1.0000
19:39248428:CGTAG:Cdonor_gain1.0000
19:39247722:C:Adonor_gain0.9900
19:39247847:CAGGA:Cacceptor_gain0.9900
19:39247848:AGGA:Aacceptor_gain0.9900
19:39247849:GGA:Gacceptor_gain0.9900
19:39247850:GA:Gacceptor_gain0.9900
19:39247850:GAC:Gacceptor_loss0.9900
19:39247852:C:Tacceptor_loss0.9900
19:39247944:T:TAdonor_gain0.9900
19:39248422:GACTT:Gdonor_loss0.9900
19:39248423:ACTTA:Adonor_loss0.9900
19:39248424:CTTA:Cdonor_loss0.9900
19:39248425:TTACG:Tdonor_loss0.9900
19:39248426:TACG:Tdonor_loss0.9900
19:39248427:A:AGdonor_loss0.9900
19:39248428:C:Adonor_loss0.9900
19:39248432:G:Cdonor_gain0.9900
19:39247239:C:CTacceptor_gain0.9800
19:39247706:A:ACdonor_gain0.9800
19:39247707:C:CCdonor_gain0.9800
19:39247707:CG:Cdonor_gain0.9800
19:39248428:CG:Cdonor_gain0.9800
19:39248428:CGT:Cdonor_gain0.9800
19:39248428:CGTA:Cdonor_gain0.9800
19:39248421:TGAC:Tdonor_loss0.9700
19:39248442:AGCG:Adonor_gain0.9700
19:39247388:CCG:Cdonor_gain0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000085840 (19:39248277 T>C), RS1001485874 (19:39249500 T>C), RS1001585285 (19:39248316 G>A), RS1001953072 (19:39249462 T>C,G), RS1002384269 (19:39249178 A>G), RS1003426909 (19:39246228 C>T), RS1003660380 (19:39250355 G>A), RS1003888415 (19:39245982 A>G), RS1004129451 (19:39250073 G>T), RS1004348645 (19:39249106 G>A), RS1004683763 (19:39250257 C>T), RS1004936794 (19:39246689 T>C,G), RS1005397451 (19:39246328 G>A), RS1005887188 (19:39247655 G>A), RS1005945581 (19:39247570 C>A,G,T)

Disease associations

OMIM: gene MIM:615090 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

11 associations (top):

StudyTraitp-value
GCST002967_3Mucinous ovarian carcinoma7.000000e-13
GCST002967_6Mucinous ovarian carcinoma1.000000e-08
GCST005017_16Hepatitis A6.000000e-08
GCST007631_2Hepatitis C (spontaneous viral clearance)6.000000e-50
GCST007632_1Hepatitis C (spontaneous viral clearance)1.000000e-15
GCST007633_1Hepatitis C (spontaneous viral clearance)7.000000e-24
GCST007634_1Hepatitis C (spontaneous viral clearance)3.000000e-12
GCST009439_25Age-related cognitive decline (language) (slope of z-scores)6.000000e-06
GCST011878_7Mitochondrial heteroplasmy measurement6.000000e-13
GCST011999_13Hepatitis C (spontaneous viral clearance)5.000000e-21
GCST011999_5Hepatitis C (spontaneous viral clearance)4.000000e-25

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0008415susceptibility to hepatitis A infection measurement
EFO:0009785remission
EFO:0007710cognitive decline measurement
EFO:0600008mitochondrial heteroplasmy measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

21 annotations.

VariantTypeLevelDrugsPhenotypes
rs11322783Efficacy1Bpeginterferon alfa-2a;peginterferon alfa-2b;ribavirinChronic hepatitis C virus infection
rs11322783Efficacy3peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;simeprevirChronic hepatitis C virus infection
rs11322783Efficacy3direct acting antiviralsSustained virological response (SVR)
rs11322783Efficacy3sofosbuvirChronic hepatitis C virus infection
rs117648444Efficacy3peginterferon alfa-2a;peginterferon alfa-2b;ribavirinChronic hepatitis C virus infection
rs12979860Efficacy1Apeginterferon alfa-2a;peginterferon alfa-2b;ribavirin;telaprevirChronic hepatitis C virus infection
rs12979860Efficacy3interferonsHepatitis C virus infection
rs12979860Efficacy3peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;simeprevirChronic hepatitis C virus infection
rs12979860Efficacy3daclatasvir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirinChronic hepatitis C virus infection
rs12979860Efficacy3ledipasvir;sofosbuvirChronic hepatitis C virus infection
rs12979860Metabolism/PK3tenofovirHIV infectious disease
rs12979860Efficacy1Apeginterferon alfa-2a;peginterferon alfa-2b;ribavirinHepatitis C virus infection
rs12979860Efficacy1Aboceprevir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirinChronic hepatitis C virus infection
rs12979860Efficacy3deleobuvir;faldaprevirChronic hepatitis C virus infection
rs12979860Efficacy3ledipasvir;sofosbuvirChronic hepatitis C virus infection;Recurrence
rs12979860Efficacy3sofosbuvir;velpatasvir;voxilaprevirChronic hepatitis C virus infection
rs12979860Efficacy3peginterferon alfa-2a;peginterferon alfa-2bMyeloproliferative Disorder
rs12979860Efficacy3peginterferon alfa-2aHepatitis B;Chronic
rs12979860Efficacy3sofosbuvirChronic hepatitis C virus infection
rs8099917Efficacy3ledipasvir;sofosbuvirChronic hepatitis C virus infection

PharmGKB variants

4 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs8099917IFNL3, IFNL41B93.254interferons;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;telaprevir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;simeprevir;ledipasvir;sofosbuvir
rs12979860IFNL3, IFNL41A350.5015boceprevir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;telaprevir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;simeprevir;ledipasvir;sofosbuvir;daclatasvir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;sofosbuvir;velpatasvir;voxilaprevir;peginterferon alfa-2a;peginterferon alfa-2b;peginterferon alfa-2a;sofosbuvir
rs117648444IFNL3, IFNL433.501peginterferon alfa-2a;peginterferon alfa-2b;ribavirin
rs11322783IFNL41B65.004sofosbuvir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;simeprevir;peginterferon alfa-2a;peginterferon alfa-2b;ribavirin;direct acting antivirals

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.