IFNA2
Basic information
Region (hg38): 9:21384255-21385398
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 11 | 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) | ||
9-21384789-G-T | not specified | Uncertain significance (Nov 23, 2021) | ||
9-21384793-G-A | Benign (May 15, 2018) | |||
9-21384817-C-T | Benign (May 21, 2018) | |||
9-21384846-C-T | not specified | Uncertain significance (Oct 20, 2023) | ||
9-21384854-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
9-21384879-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
9-21384929-A-G | not specified | Uncertain significance (May 13, 2024) | ||
9-21384954-C-A | not specified | Uncertain significance (Nov 03, 2022) | ||
9-21384954-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
9-21384969-A-C | not specified | Uncertain significance (Mar 07, 2023) | ||
9-21385037-G-T | not specified | Uncertain significance (Jun 22, 2024) | ||
9-21385073-A-G | not specified | Likely benign (Aug 17, 2022) | ||
9-21385086-T-C | not specified | Uncertain significance (Aug 17, 2022) | ||
9-21385087-C-G | not specified | Uncertain significance (Oct 25, 2023) | ||
9-21385133-A-G | not specified | Uncertain significance (Feb 15, 2023) | ||
9-21385160-T-C | Benign (Jun 08, 2018) | |||
9-21385193-C-T | Benign (Apr 04, 2018) | |||
9-21385313-G-T | Benign (May 21, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IFNA2 | protein_coding | protein_coding | ENST00000380206 | 1 | 1143 |
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 | -0.995 | 117 | 90.4 | 1.29 | 0.00000383 | 1232 |
Missense in Polyphen | 26 | 22.223 | 1.1699 | 355 | ||
Synonymous | -0.811 | 42 | 35.8 | 1.17 | 0.00000155 | 356 |
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:
- 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
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;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