IFNA1

interferon alpha 1, the group of Interferons

Basic information

Region (hg38): 9:21440439-21441316

Links

ENSG00000197919 ∙ NCBI:3439 ∙ OMIM:147660 ∙ HGNC:5417 ∙ Uniprot:P01562 ∙ 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 IFNA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNA1 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					1	1
missense			1	1	3	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	4

Variants in IFNA1

This is a list of pathogenic ClinVar variants found in the IFNA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-21440536-T-C			Benign (Dec 31, 2019)
9-21440549-C-T			Benign (Dec 31, 2019)
9-21440905-C-T		not specified	Uncertain significance (Aug 01, 2023)
9-21440917-C-T			Benign (Dec 31, 2019)
9-21440938-A-G		not specified	Likely benign (Jun 12, 2023)
9-21440965-A-G		not specified	Uncertain significance (May 13, 2024)
9-21440995-C-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNA1	protein_coding	protein_coding	ENST00000276927	1	876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0391	86	87.0	0.988	0.00000385	1236
Missense in Polyphen		19	18.691	1.0165		288
Synonymous	0.340	34	36.6	0.928	0.00000181	364
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase. {ECO:0000269|PubMed:1634550}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Influenza A - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Cytosolic DNA-sensing pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;Regulation of toll-like receptor signaling pathway;RIG-I-like Receptor Signaling;PI3K-Akt Signaling Pathway;Toll-like Receptor Signaling Pathway;double stranded rna induced gene expression;signal transduction through il1r;ifn alpha signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;IFN alpha signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i;Regulation of IFNA signaling;Interferon alpha/beta signaling;Downstream signaling in naïve CD8+ T cells;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0761

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.0350
• hipred: N
• hipred_score: 0.337

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: adaptive immune response;T cell activation involved in immune response;natural killer cell activation involved in immune response;humoral immune response;blood coagulation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;B cell differentiation;positive regulation of peptidyl-serine phosphorylation of STAT protein;B cell proliferation;response to exogenous dsRNA;defense response to virus;type I interferon signaling pathway
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;type I interferon receptor binding