IFNA2

interferon alpha 2, the group of Interferons

Basic information

Region (hg38): 9:21384255-21385398

Links

ENSG00000188379NCBI:3440OMIM:147562HGNC:5423Uniprot:P01563AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFNA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNA2 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
clinvar
1
missense
11
clinvar
1
clinvar
4
clinvar
16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 11 1 5

Variants in IFNA2

This is a list of pathogenic ClinVar variants found in the IFNA2 region.

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

Position Type Phenotype Significance ClinVar
9-21384786-C-G not specified Uncertain significance (Aug 17, 2022)2308280
9-21384789-G-T not specified Uncertain significance (Nov 23, 2021)2343735
9-21384793-G-A Benign (May 15, 2018)781165
9-21384817-C-T Benign (May 21, 2018)778411
9-21384846-C-T not specified Uncertain significance (Oct 20, 2023)3108247
9-21384854-C-T not specified Uncertain significance (Apr 12, 2024)3285354
9-21384879-G-A not specified Uncertain significance (Jun 30, 2022)2391423
9-21384929-A-G not specified Uncertain significance (May 13, 2024)2286875
9-21384954-C-A not specified Uncertain significance (Nov 03, 2022)2322395
9-21384954-C-T not specified Uncertain significance (Feb 28, 2023)2491121
9-21384969-A-C not specified Uncertain significance (Mar 07, 2023)2495023
9-21385037-G-T not specified Uncertain significance (Jun 22, 2024)3285355
9-21385073-A-G not specified Likely benign (Aug 17, 2022)2308279
9-21385086-T-C not specified Uncertain significance (Aug 17, 2022)2308275
9-21385087-C-G not specified Uncertain significance (Oct 25, 2023)3108246
9-21385133-A-G not specified Uncertain significance (Feb 15, 2023)2484651
9-21385160-T-C Benign (Jun 08, 2018)783545
9-21385193-C-T Benign (Apr 04, 2018)786570
9-21385313-G-T Benign (May 21, 2018)778412

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IFNA2protein_codingprotein_codingENST00000380206 11143
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-0.99511790.41.290.000003831232
Missense in Polyphen2622.2231.1699355
Synonymous-0.8114235.81.170.00000155356
Loss of Function

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
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.;
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);Regulation of toll-like receptor signaling pathway;PI3K-Akt Signaling Pathway;Type II interferon signaling (IFNG);Toll-like Receptor 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
0.0660

Intolerance Scores

loftool
0.620
rvis_EVS
0.46
rvis_percentile_EVS
78.46

Haploinsufficiency Scores

pHI
0.0387
hipred
N
hipred_score
0.254
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.778

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
adaptive immune response;T cell activation involved in immune response;natural killer cell activation involved in immune response;apoptotic process;inflammatory response;humoral immune response;cell surface receptor signaling pathway;cell-cell signaling;blood coagulation;regulation of signaling receptor activity;negative regulation of gene expression;cytokine-mediated signaling pathway;B cell differentiation;positive regulation of peptidyl-serine phosphorylation of STAT protein;B cell proliferation;positive regulation of phosphorylation;positive regulation of tyrosine phosphorylation of STAT protein;response to exogenous dsRNA;negative regulation of T cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of viral entry into host cell;defense response to virus;type I interferon signaling pathway;negative regulation of T-helper 2 cell cytokine production;negative regulation of interleukin-5 secretion;negative regulation of interleukin-13 secretion
Cellular component
extracellular region;extracellular space;collagen-containing extracellular matrix
Molecular function
cytokine activity;type I interferon receptor binding;protein binding