IFNA13

Summary

IFNA13 (interferon alpha 13, HGNC:5419) is a protein-coding gene on chromosome 9p21.3, encoding Interferon alpha-13 (A0A087WWS6). Produced by macrophages, IFN-alpha have antiviral activities.

Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including lymphocyte activation involved in immune response; response to exogenous dsRNA; and type I interferon-mediated signaling pathway. Predicted to act upstream of or within defense response to virus. Predicted to be located in extracellular region. Predicted to be active in extracellular space.

Source: NCBI Gene 3447 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total — 1 pathogenic
• MANE Select transcript: NM_006900

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5419
Approved symbol	IFNA13
Name	interferon alpha 13
Location	9p21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000233816
Ensembl biotype	protein_coding
OMIM	147578
Entrez	3447

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000449498, ENST00000610660

RefSeq mRNA: 1 — MANE Select: NM_006900 NM_006900

CCDS: CCDS6505

Canonical transcript exons

ENST00000610660 — 1 exons

Exon	Start	End
ENSE00003978262	21367372	21368057

Expression profiles

Bgee: expression breadth broad, 40 present calls, max score 55.42.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	55.42	gold quality
putamen	UBERON:0001874	48.76	gold quality
primary visual cortex	UBERON:0002436	47.26	gold quality
caudate nucleus	UBERON:0001873	46.05	gold quality
Brodmann (1909) area 9	UBERON:0013540	43.87	gold quality
amygdala	UBERON:0001876	42.56	gold quality
Ammon’s horn	UBERON:0001954	42.52	gold quality
temporal lobe	UBERON:0001871	42.38	gold quality
mucosa of stomach	UBERON:0001199	41.74	silver quality
stromal cell of endometrium	CL:0002255	41.60	silver quality
substantia nigra	UBERON:0002038	41.29	gold quality
right frontal lobe	UBERON:0002810	41.20	gold quality
lower esophagus mucosa	UBERON:0035834	41.11	silver quality
frontal cortex	UBERON:0001870	40.59	gold quality
superior frontal gyrus	UBERON:0002661	40.29	silver quality
prefrontal cortex	UBERON:0000451	40.27	gold quality
granulocyte	CL:0000094	39.99	gold quality
nucleus accumbens	UBERON:0001882	39.68	gold quality
brain	UBERON:0000955	39.27	gold quality
cerebral cortex	UBERON:0000956	39.15	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	38.68	gold quality
cerebellum	UBERON:0002037	38.61	silver quality
cerebellar cortex	UBERON:0002129	38.47	silver quality
cerebellar hemisphere	UBERON:0002245	38.19	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	37.87	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
urinary bladder	UBERON:0001255	36.91	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.46

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• IFNA1 and IFNA13 Genes Confer Genetic Predisposition to Ankylosing Spondylitis-Associated Uveitis in a Chinese Population. (PMID:32990094)
• Alpha interferon suppresses the cyclin D3 and cdc25A genes, leading to a reversible G0-like arrest. (PMID:8668211)

Cross-species orthologs

34 orthologs

Organism	Symbol	Gene ID
danio_rerio	ifnphi2	ENSDARG00000069012
danio_rerio	ifnphi3	ENSDARG00000070676
mus_musculus	Ifna13	ENSMUSG00000063376
mus_musculus	Ifna4	ENSMUSG00000070904
mus_musculus	Ifna12	ENSMUSG00000073811
mus_musculus	Ifna2	ENSMUSG00000078354
mus_musculus	Ifna16	ENSMUSG00000078355
mus_musculus	Ifna9	ENSMUSG00000095270
mus_musculus	Ifna1	ENSMUSG00000095498
mus_musculus	Ifna14	ENSMUSG00000095896
mus_musculus	Ifna15	ENSMUSG00000096011
mus_musculus	Ifna5	ENSMUSG00000096682
mus_musculus	Ifnab	ENSMUSG00000100079
mus_musculus	Ifna11	ENSMUSG00000100549
mus_musculus	Ifna7	ENSMUSG00000100713
mus_musculus	Ifna6	ENSMUSG00000101252
rattus_norvegicus		ENSRNOG00000071845
rattus_norvegicus	Ifna12l	ENSRNOG00000072681
rattus_norvegicus	Ifna16l1	ENSRNOG00000074841
rattus_norvegicus		ENSRNOG00000075722
rattus_norvegicus		ENSRNOG00000076372
rattus_norvegicus	Ifna4	ENSRNOG00000077072
rattus_norvegicus	Ifna2	ENSRNOG00000078310
rattus_norvegicus	Ifna5	ENSRNOG00000079725
rattus_norvegicus	Ifna1l1	ENSRNOG00000079800
rattus_norvegicus		ENSRNOG00000079804
rattus_norvegicus		ENSRNOG00000081823
rattus_norvegicus		ENSRNOG00000082441
rattus_norvegicus		ENSRNOG00000082845
rattus_norvegicus		ENSRNOG00000083047
rattus_norvegicus	Ifna1	ENSRNOG00000084770
rattus_norvegicus		ENSRNOG00000085373
rattus_norvegicus		ENSRNOG00000085882
rattus_norvegicus		ENSRNOG00000086565

Paralogs (16): IFNA6 (ENSG00000120235), IFNA8 (ENSG00000120242), IFNA21 (ENSG00000137080), IFNA5 (ENSG00000147873), IFNA16 (ENSG00000147885), IFNK (ENSG00000147896), IFNB1 (ENSG00000171855), IFNW1 (ENSG00000177047), IFNE (ENSG00000184995), IFNA10 (ENSG00000186803), IFNA2 (ENSG00000188379), IFNA1 (ENSG00000197919), IFNA7 (ENSG00000214042), IFNA14 (ENSG00000228083), IFNA17 (ENSG00000234829), IFNA4 (ENSG00000236637)

Protein

Protein identifiers

Interferon alpha-13 — A0A087WWS6 (reviewed: A0A087WWS6)

All UniProt accessions (2): A0A087WWS6, P01562

UniProt curated annotations — full annotation on UniProt →

Function. Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase.

Subcellular location. Secreted.

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

RefSeq proteins (1): NP_008831* (*=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 (4 total): disulfide bond 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3UX9	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

No AlphaFold model available for A0A087WWS6 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Antibody-complex structures (SAbDab): 1 — 3UX9

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): 25–123, 53–163

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-933541	TRAF6 mediated IRF7 activation
R-HSA-983231	Factors involved in megakaryocyte development and platelet production

MSigDB gene sets: 62 (showing top): REACTOME_DDX58_IFIH1_MEDIATED_INDUCTION_OF_INTERFERON_ALPHA_BETA, REACTOME_INNATE_IMMUNE_SYSTEM, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY, KEGG_AUTOIMMUNE_THYROID_DISEASE, KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY, KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION, KEGG_JAK_STAT_SIGNALING_PATHWAY, WORSCHECH_TUMOR_REJECTION_UP, RAO_BOUND_BY_SALL4_ISOFORM_B, E2F3_UP.V1_DN, REACTOME_INFECTIOUS_DISEASE, PDGF_ERK_DN.V1_UP, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_DN

GO Biological Process (13): defense response to virus (GO:0051607), 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), defense response (GO:0006952), humoral immune response (GO:0006959), signal transduction (GO:0007165), response to exogenous dsRNA (GO:0043330), symbiont entry into host cell (GO:0046718), type I interferon-mediated signaling pathway (GO:0060337), cellular response to virus (GO:0098586), antiviral innate immune response (GO:0140374)

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 (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
DDX58/IFIH1-mediated induction of interferon-alpha/beta	1
Hemostasis	1

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
innate immune response	2
defense response	1
T cell activation	1
B cell activation	1
natural killer cell activation	1
response to stress	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
response to dsRNA	1
viral life cycle	1
symbiont entry into host	1
cellular response to type I interferon	1
interferon-mediated signaling pathway	1
defense response to virus	1
receptor ligand activity	1
signaling receptor binding	1
cytokine receptor binding	1
protein-containing complex binding	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFNA13	IL2	P01585	855
IFNA13	IFNAR1	P17181	817
IFNA13	IFNG	P01579	800
IFNA13	CR2	P20023	668
IFNA13	IFNL3	Q8IZI9	665
IFNA13	IL6	P05231	664
IFNA13	ABL1	P00519	624
IFNA13	GPT	P24298	621
IFNA13	ISG15	P05161	621
IFNA13	CD4	P01730	620
IFNA13	TNF	P01375	620
IFNA13	TLR3	O15455	605
IFNA13	IFIT2	P09913	593
IFNA13	CD8A	P01732	583
IFNA13	IL1B	P01584	582

IntAct

0 interactions, top by confidence:

BioGRID (18): IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Two-hybrid), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS), IFNA13 (Affinity Capture-MS)

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
395707	GRCh37/hg19 9p24.3-q34.3(chr9:62525-141006407)	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1256 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:21367567:G:C	F147L	0.950
9:21367567:G:T	F147L	0.950
9:21367569:A:G	F147L	0.950
9:21367831:A:C	F59L	0.941
9:21367831:A:T	F59L	0.941
9:21367833:A:G	F59L	0.941
9:21367516:C:A	W164C	0.930
9:21367516:C:G	W164C	0.930
9:21367735:A:C	F91L	0.861
9:21367735:A:T	F91L	0.861
9:21367737:A:G	F91L	0.861
9:21367504:T:A	R168S	0.860
9:21367504:T:G	R168S	0.860
9:21367708:C:A	W100C	0.846
9:21367708:C:G	W100C	0.846
9:21367518:A:G	W164R	0.828
9:21367518:A:T	W164R	0.828
9:21367547:A:G	L154P	0.819
9:21367571:T:C	Y146C	0.818
9:21367571:T:G	Y146S	0.815
9:21367508:A:T	V167D	0.814
9:21367832:A:C	F59C	0.814
9:21367572:A:G	Y146H	0.812
9:21367551:A:C	Y153D	0.804
9:21367661:A:G	L116P	0.800
9:21367568:A:G	F147S	0.797
9:21367520:G:T	A163D	0.784
9:21367825:A:C	F61L	0.782
9:21367825:A:T	F61L	0.782
9:21367827:A:G	F61L	0.782

dbSNP variants (sampled 300 via entrez): RS1000103218 (9:21367253 A>G,T), RS1001316845 (9:21367661 A>G), RS1004043238 (9:21366888 T>C,G), RS1004066783 (9:21368630 G>A), RS1005339914 (9:21367005 G>T), RS1005672905 (9:21369140 T>C), RS1006010047 (9:21368181 A>C), RS1007661703 (9:21368564 T>A), RS1007797416 (9:21368333 G>A,C,T), RS1009575861 (9:21368598 A>C), RS1010324390 (9:21367629 C>T), RS1010544013 (9:21369443 C>G), RS1010858374 (9:21369849 A>G), RS1010992116 (9:21369591 A>G), RS10116363 (9:21368667 A>C,G)

Disease associations

OMIM: gene MIM:147578 | 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

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Cadmium	increases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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