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IFNL4 interferon lambda 4 (gene/pseudogene) [ Homo sapiens (human) ]

Gene ID: 101180976, updated on 22-Sep-2022

Summary

Official Symbol
IFNL4provided by HGNC
Official Full Name
interferon lambda 4 (gene/pseudogene)provided by HGNC
Primary source
HGNC:HGNC:44480
See related
Ensembl:ENSG00000272395 MIM:615090; AllianceGenome:HGNC:44480
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IFNAN
Summary
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. [provided by RefSeq, May 2017]
Annotation information
Annotation category: suggests misassembly
Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression
Low expression observed in reference dataset See more
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Genomic context

See IFNL4 in Genome Data Viewer
Location:
19q13.2
Exon count:
5
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39246314..39248856, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42050583..42053125, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39736954..39739496, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904717 Neighboring gene interferon lambda 3 pseudogene 1 Neighboring gene interferon lambda 3 Neighboring gene methionine sulfoxide reductase B1 pseudogene 1 Neighboring gene CRISPRi-validated cis-regulatory element chr19.4063

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Sofosbuvir response
MedGen: CN238522 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance.
EBI GWAS Catalog
Genome-wide association study of spontaneous resolution of hepatitis C virus infection: data from multiple cohorts.
EBI GWAS Catalog

Pathways from PubChem

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables signaling receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
interferon lambda-4
Names
IFN-lambda-4
interferon, lambda 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_055295.1 RefSeqGene

    Range
    5001..7543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001276254.2NP_001263183.2  interferon lambda-4 precursor

    See identical proteins and their annotated locations for NP_001263183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents a protein coding transcript of this gene. Human populations are polymorphic for a frameshifting single nucleotide insertion in this transcript and thus transcripts with the alternate allele are non-coding.
    Source sequence(s)
    JN806234
    UniProtKB/Swiss-Prot
    K9M1U5, K9M2P7
    UniProtKB/TrEMBL
    A0A7R8C3A5
    Conserved Domains (1) summary
    pfam15177
    Location:24175
    IL28A; Interleukin-28A

RNA

  1. NR_074079.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, non-coding) has a single frameshifting nucleotide insertion, compared to variant 1, which renders this transcript subject to nonsense-mediated mRNA decay (NMD). Human populations are polymorphic for a frameshifting single nucleotide insertion in this transcript and thus transcripts with the alternate allele are protein coding. The non-coding allele is represented in GRCh38.
    Source sequence(s)
    JN806227
    Related
    ENST00000606380.2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    39246314..39248856 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791808.1 Reference GRCh38.p14 PATCHES

    Range
    26697..29238 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    42050583..42053125 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)