IFNA16

interferon alpha 16, the group of Interferons

Basic information

Region (hg38): 9:21216372-21217311

Links

ENSG00000147885 ∙ NCBI:3449 ∙ OMIM:147580 ∙ HGNC:5421 ∙ Uniprot:P05015 ∙ 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 IFNA16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFNA16 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						0
missense			10	1	2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	2

Variants in IFNA16

This is a list of pathogenic ClinVar variants found in the IFNA16 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-21216762-G-T		not specified	Uncertain significance (Aug 02, 2021)
9-21216766-G-C		not specified	Uncertain significance (Apr 04, 2023)
9-21216783-A-G		not specified	Uncertain significance (May 28, 2024)
9-21216822-A-T		not specified	Uncertain significance (Oct 26, 2021)
9-21216840-C-T		not specified	Uncertain significance (May 15, 2024)
9-21216892-G-T		not specified	Uncertain significance (Feb 07, 2023)
9-21216935-G-A			Benign (Dec 31, 2019)
9-21216944-G-A		not specified	Uncertain significance (Jun 07, 2024)
9-21216984-A-G		not specified	Likely benign (May 01, 2022)
9-21217011-C-T		not specified	Uncertain significance (May 03, 2023)
9-21217067-A-G		not specified	Uncertain significance (Jan 04, 2024)
9-21217108-A-C		not specified	Uncertain significance (Jun 10, 2024)
9-21217148-A-G		not specified	Uncertain significance (Nov 14, 2023)
9-21217154-G-A		not specified	Uncertain significance (Aug 02, 2022)
9-21217160-T-G			Benign (Dec 31, 2019)
9-21217181-G-A		not specified	Uncertain significance (May 06, 2022)
9-21217193-A-G		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFNA16	protein_coding	protein_coding	ENST00000380216	1	939

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	-2.74	166	92.0	1.80	0.00000412	1234
Missense in Polyphen		25	17.069	1.4647		266
Synonymous	-4.73	75	37.9	1.98	0.00000180	363
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.
• 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;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: 0.0748

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.56

Haploinsufficiency Scores

• pHI: 0.0236
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0414

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