IFNW1

Summary

IFNW1 (interferon omega 1, HGNC:5448) is a protein-coding gene on chromosome 9p21.3, encoding Interferon omega-1 (P05000).

The protein encoded by this gene is an interferon and possesses antiviral activity. The encoded protein binds to the interferon alpha/beta receptor but not to the interferon gamma receptor. This intronless gene has several pseudogenes spread throughout the genome.

Source: NCBI Gene 3467 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_002177

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5448
Approved symbol	IFNW1
Name	interferon omega 1
Location	9p21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000177047
Ensembl biotype	protein_coding
OMIM	147553
Entrez	3467

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000380229

RefSeq mRNA: 1 — MANE Select: NM_002177 NM_002177

CCDS: CCDS6496

Canonical transcript exons

ENST00000380229 — 1 exons

Exon	Start	End
ENSE00001431387	21140632	21141832

Expression profiles

Bgee: expression breadth tissue_specific, 2 present calls, max score 76.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0108 / max 11.3377, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100205	0.0108	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.25	silver quality
secondary oocyte	CL:0000655	60.82	gold quality
cerebellar vermis	UBERON:0004720	56.19	gold quality
metanephric glomerulus	UBERON:0004736	55.97	gold quality
endometrium epithelium	UBERON:0004811	54.45	gold quality
medial globus pallidus	UBERON:0002477	53.52	gold quality
globus pallidus	UBERON:0001875	51.33	gold quality
frontal pole	UBERON:0002795	50.41	gold quality
middle frontal gyrus	UBERON:0002702	50.30	gold quality
paraflocculus	UBERON:0005351	50.18	gold quality
Brodmann (1909) area 10	UBERON:0013541	50.18	gold quality
thymus	UBERON:0002370	48.50	gold quality
quadriceps femoris	UBERON:0001377	47.52	gold quality
vastus lateralis	UBERON:0001379	46.84	gold quality
bone marrow	UBERON:0002371	46.73	gold quality
substantia nigra pars reticulata	UBERON:0001966	45.93	gold quality
deltoid	UBERON:0001476	45.36	gold quality
substantia nigra pars compacta	UBERON:0001965	45.29	gold quality
adult organism	UBERON:0007023	44.22	gold quality
layer of synovial tissue	UBERON:0007616	44.13	gold quality
lateral globus pallidus	UBERON:0002476	44.07	gold quality
oocyte	CL:0000023	43.85	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
gingiva	UBERON:0001828	42.36	gold quality
trachea	UBERON:0003126	42.28	gold quality
colonic epithelium	UBERON:0000397	41.68	gold quality
oviduct epithelium	UBERON:0004804	41.57	gold quality
ventral tegmental area	UBERON:0002691	41.54	gold quality
biceps brachii	UBERON:0001507	41.38	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting IFNW1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-1264	99.25	66.81	1317
HSA-MIR-892B	98.00	67.11	821
HSA-MIR-5007-5P	97.95	64.71	614
HSA-MIR-924	97.78	66.21	681
HSA-MIR-6510-3P	84.92	61.55	36

Literature-anchored findings (GeneRIF, showing 6)

• type I interferons interact with receptor components results and have roles in the activation of a number of signaling pathways [review] (PMID:15621727)
• Data show that a novel c.1344delC mutation in AIRE and anti-IFN-omega antibodies appear very early in life are helpful to differentiate APS I from other multi-organ autoimmune diseases. (PMID:19863576)
• Single nucleotide polymorphism in ACO1 gene is associated with skin pigmentation. (PMID:20574843)
• The crystal structures of two human type I IFN ternary signaling complexes containing IFNalpha2 and IFNomega reveal recognition modes and heterotrimeric architectures that are unique among the cytokine receptor superfamily but conserved between type I IFNs. (PMID:21854986)
• Studies indicate that upregulation of the type I interferon protein signature has added additional markers of disease activity and insight into the pathogenesis of the disease. (PMID:22192711)
• a review on current status in clinical applications of interferon-omega (PMID:28957693)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	ifnphi2	ENSDARG00000069012
danio_rerio	ifnphi3	ENSDARG00000070676

Paralogs (16): IFNA6 (ENSG00000120235), IFNA8 (ENSG00000120242), IFNA21 (ENSG00000137080), IFNA5 (ENSG00000147873), IFNA16 (ENSG00000147885), IFNK (ENSG00000147896), IFNB1 (ENSG00000171855), IFNE (ENSG00000184995), IFNA10 (ENSG00000186803), IFNA2 (ENSG00000188379), IFNA1 (ENSG00000197919), IFNA7 (ENSG00000214042), IFNA14 (ENSG00000228083), IFNA13 (ENSG00000233816), IFNA17 (ENSG00000234829), IFNA4 (ENSG00000236637)

Protein

Protein identifiers

Interferon omega-1 — P05000 (reviewed: P05000)

Alternative names: Interferon alpha-II-1

All UniProt accessions (2): P05000, A0A7R8GUW6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the type-I (or alpha/beta) interferon family.

RefSeq proteins (1): NP_002168* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000471	Interferon_alpha/beta/delta	Family
IPR009079	4_helix_cytokine-like_core	Homologous_superfamily

Pfam: PF00143

UniProt features (11 total): sequence conflict 5, disulfide bond 2, signal peptide 1, chain 1, glycosylation site 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3SE4	X-RAY DIFFRACTION	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P05000-F1	83.15	0.51

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 (2): 24–122, 52–162

Glycosylation sites (1): 101

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_CELLULAR_RESPONSE_TO_VIRUS, GOBP_RESPONSE_TO_PEPTIDE, GOBP_B_CELL_ACTIVATION, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_RESPONSE_TO_TYPE_I_INTERFERON, MORF_RAD51L3, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, MORF_CTSB, GOBP_REGULATION_OF_CELL_CYCLE, MORF_IL4, MORF_PRKCA, GOBP_NATURAL_KILLER_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_HUMORAL_IMMUNE_RESPONSE

GO Biological Process (13): adaptive immune response (GO:0002250), T cell activation involved in immune response (GO:0002286), B cell activation involved in immune response (GO:0002312), natural killer cell activation involved in immune response (GO:0002323), humoral immune response (GO:0006959), response to virus (GO:0009615), response to exogenous dsRNA (GO:0043330), defense response to virus (GO:0051607), regulation of cell cycle (GO:0051726), type I interferon-mediated signaling pathway (GO:0060337), cellular response to virus (GO:0098586), defense response (GO:0006952), signal transduction (GO:0007165)

GO Molecular Function (4): cytokine activity (GO:0005125), cytokine receptor binding (GO:0005126), type I interferon receptor binding (GO:0005132), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), signaling receptor complex (GO:0043235), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
immune response	4
lymphocyte activation involved in immune response	3
response to virus	2
regulation of cellular process	2
T cell activation	1
B cell activation	1
natural killer cell activation	1
innate immune response	1
response to other organism	1
response to dsRNA	1
defense response	1
cell cycle	1
cellular response to type I interferon	1
interferon-mediated signaling pathway	1
response to stress	1
cell communication	1
cellular process	1
signaling	1
cellular response to stimulus	1
receptor ligand activity	1
signaling receptor binding	1
cytokine receptor binding	1
protein-containing complex binding	1
binding	1
protein-containing complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFNW1	MTAP	Q13126	657
IFNW1	IFNAR2	P48551	630
IFNW1	IFNAR1	P17181	587
IFNW1	AIRE	O43918	572
IFNW1	IFNL2	Q8IZJ0	461
IFNW1	IL10RB	Q08334	459
IFNW1	IFNLR1	Q8IU57	447
IFNW1	NLRP5	P59047	439
IFNW1	RACK1	P25388	428
IFNW1	IFNL3	Q8IZI9	413
IFNW1	KCNRG	Q8N5I3	400
IFNW1	CYP4F3	Q08477	398
IFNW1	PDILT	Q8N807	397
IFNW1	IL12RB1	P42701	385
IFNW1	IL17A	Q16552	374

IntAct

5 interactions, top by confidence:

A	B	Type	Score
IFNW1	ISG15	psi-mi:“MI:0915”(physical association)	0.590
IFNW1	IFNAR1	psi-mi:“MI:0407”(direct interaction)	0.440
IFNW1	SEMG1	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): ISG15 (Affinity Capture-MS), ISG15 (Affinity Capture-MS), SEMG1 (Affinity Capture-MS), SEMG2 (Affinity Capture-MS), ACPP (Affinity Capture-MS), S100P (Reconstituted Complex), S100A6 (Reconstituted Complex), APP (Reconstituted Complex)

ESM2 similar proteins: O46633, P01562, P01563, P01566, P01567, P01568, P01569, P01570, P01571, P01572, P05000, P05002, P05003, P05004, P05005, P05006, P05007, P05008, P05009, P05010, P05013, P05014, P05015, P07348, P07349, P07352, P09235, P15696, P28169, P28171, P28172, P32881, P49876, P49877, P49878, P49879, P56828, P56829, P56830, P56831

Diamond homologs: A7UHZ5, O46633, O77812, O97945, P01562, P01563, P01566, P01567, P01568, P01569, P01570, P01571, P01572, P01573, P01574, P01575, P01576, P01577, P01578, P05000, P05001, P05002, P05003, P05004, P05005, P05006, P05007, P05008, P05009, P05010, P05011, P05012, P05013, P05014, P05015, P06799, P07348, P07349, P07350, P07351

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
IFNW1	up-regulates	IFNAR1	binding
IFNW1	up-regulates	IFNAR2	binding
IFNW1	“up-regulates activity”	IFNAR	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

104 predictions. Top by Δscore:

Variant	Effect	Δscore
9:21141326:T:TG	acceptor_gain	0.8700
9:21141410:T:C	acceptor_gain	0.8100
9:21141408:CCT:C	acceptor_gain	0.7700
9:21141409:C:CC	acceptor_gain	0.6900
9:21141406:GTCC:G	acceptor_loss	0.6700
9:21141409:CTTGA:C	acceptor_loss	0.6700
9:21141410:T:A	acceptor_loss	0.6700
9:21141410:T:TC	acceptor_gain	0.6400
9:21141404:CTGTC:C	acceptor_gain	0.6200
9:21141416:C:CT	acceptor_gain	0.6200
9:21141325:CTCA:C	acceptor_gain	0.5900
9:21141327:C:A	acceptor_gain	0.5900
9:21141302:AGGCT:A	acceptor_gain	0.5300
9:21141303:GGCTG:G	acceptor_gain	0.5300
9:21141327:C:CT	acceptor_gain	0.5100
9:21141328:A:C	acceptor_gain	0.5100
9:21141417:A:T	acceptor_loss	0.5100
9:21141406:GTCCT:G	acceptor_gain	0.5000
9:21141407:TCCTT:T	acceptor_gain	0.5000
9:21141407:TC:T	acceptor_gain	0.4900
9:21141419:A:T	acceptor_gain	0.4700
9:21141304:GCT:G	acceptor_gain	0.4500
9:21141409:C:T	acceptor_gain	0.4500
9:21141401:CTT:C	acceptor_gain	0.4400
9:21141418:C:CT	acceptor_gain	0.4100
9:21141406:GTC:G	acceptor_gain	0.3600
9:21141408:CCTT:C	acceptor_gain	0.3600
9:21141411:TGAG:T	acceptor_loss	0.3500
9:21141548:A:T	acceptor_gain	0.3500
9:21141323:ATCTC:A	acceptor_gain	0.3400

AlphaMissense

1284 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:21141130:G:C	F147L	0.955
9:21141130:G:T	F147L	0.955
9:21141132:A:G	F147L	0.955
9:21141394:G:C	F59L	0.944
9:21141394:G:T	F59L	0.944
9:21141396:A:G	F59L	0.944
9:21141079:C:A	W164C	0.916
9:21141079:C:G	W164C	0.916
9:21141395:A:C	F59C	0.851
9:21141131:A:G	F147S	0.845
9:21141271:C:A	W100C	0.841
9:21141271:C:G	W100C	0.841
9:21141395:A:G	F59S	0.837
9:21141067:T:A	R168S	0.836
9:21141067:T:G	R168S	0.836
9:21141081:A:G	W164R	0.827
9:21141081:A:T	W164R	0.827
9:21141416:C:G	C52S	0.824
9:21141417:A:T	C52S	0.824
9:21141131:A:C	F147C	0.822
9:21141273:A:G	W100R	0.817
9:21141273:A:T	W100R	0.817
9:21141071:A:T	V167D	0.800
9:21141122:A:G	I150T	0.800
9:21141439:C:A	M44I	0.795
9:21141439:C:G	M44I	0.795
9:21141439:C:T	M44I	0.795
9:21141077:T:A	E165V	0.792
9:21141440:A:G	M44T	0.790
9:21141114:A:C	Y153D	0.788

dbSNP variants (sampled 300 via entrez): RS1000709534 (9:21140326 A>C), RS1000946930 (9:21140775 T>A,C), RS1001294648 (9:21140174 G>C), RS1001387544 (9:21140388 G>T), RS1001810467 (9:21140665 A>G), RS1002817109 (9:21141853 T>A), RS1004572841 (9:21143398 T>G), RS1004625118 (9:21143550 T>C), RS1006266212 (9:21140328 A>G), RS1006357169 (9:21140717 A>T), RS1006980190 (9:21141273 A>C,G), RS1007135106 (9:21143324 G>A), RS1007305855 (9:21143503 G>A), RS1008870546 (9:21142280 C>A,G,T), RS1010107894 (9:21140464 A>G)

Disease associations

OMIM: gene MIM:147553 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Resveratrol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	decreases expression	1
Copper	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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