IFIT3

interferon induced protein with tetratricopeptide repeats 3, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:89327307-89377473

Previous symbols: [ "IFIT4" ]

Links

ENSG00000119917 ∙ NCBI:3437 ∙ OMIM:604650 ∙ HGNC:5411 ∙ Uniprot:O14879 ∙ 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 IFIT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFIT3 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			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	2

Variants in IFIT3

This is a list of pathogenic ClinVar variants found in the IFIT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89338661-T-G		not specified	Uncertain significance (Jan 19, 2022)
10-89338737-G-C		not specified	Uncertain significance (Aug 02, 2021)
10-89338781-T-G		not specified	Uncertain significance (Aug 15, 2023)
10-89338820-C-A		not specified	Uncertain significance (Jul 12, 2022)
10-89338857-G-A		not specified	Uncertain significance (Jul 30, 2024)
10-89338905-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-89338947-G-A		not specified	Uncertain significance (Dec 16, 2022)
10-89338977-G-A		not specified	Uncertain significance (Oct 07, 2022)
10-89339119-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-89339201-T-G		not specified	Uncertain significance (May 12, 2024)
10-89339271-A-G		not specified	Uncertain significance (Dec 14, 2023)
10-89339277-T-C		not specified	Uncertain significance (Nov 14, 2023)
10-89339305-T-C		not specified	Uncertain significance (Jun 29, 2023)
10-89339389-G-A		not specified	Uncertain significance (May 20, 2024)
10-89339439-G-A		not specified	Uncertain significance (Aug 10, 2023)
10-89339451-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-89339452-G-A		not specified	Uncertain significance (Jan 05, 2022)
10-89339452-G-C		not specified	Uncertain significance (Oct 26, 2022)
10-89339617-C-A		not specified	Uncertain significance (May 16, 2024)
10-89339661-G-A		not specified	Likely benign (Feb 16, 2023)
10-89339671-T-C		not specified	Uncertain significance (Jun 22, 2023)
10-89339677-C-T		not specified	Uncertain significance (Mar 25, 2024)
10-89339695-C-A			Uncertain significance (Jan 01, 2024)
10-89339709-G-C			Benign (Oct 24, 2017)
10-89339742-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFIT3	protein_coding	protein_coding	ENST00000371818	2	13078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.117	0.788	125650	0	9	125659	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.797	215	251	0.858	0.0000124	3234
Missense in Polyphen		46	59.322	0.77543		832
Synonymous	0.607	91	98.7	0.922	0.00000496	898
Loss of Function	1.32	2	5.28	0.379	2.27e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: IFN-induced antiviral protein which acts as an inhibitor of cellular as well as viral processes, cell migration, proliferation, signaling, and viral replication. Enhances MAVS- mediated host antiviral responses by serving as an adapter bridging TBK1 to MAVS which leads to the activation of TBK1 and phosphorylation of IRF3 and phosphorylated IRF3 translocates into nucleus to promote antiviral gene transcription. Exihibits an antiproliferative activity via the up-regulation of cell cycle negative regulators CDKN1A/p21 and CDKN1B/p27. Normally, CDKN1B/p27 turnover is regulated by COPS5, which binds CDKN1B/p27 in the nucleus and exports it to the cytoplasm for ubiquitin- dependent degradation. IFIT3 sequesters COPS5 in the cytoplasm, thereby increasing nuclear CDKN1B/p27 protein levels. Upregulates CDKN1A/p21 by downregulating MYC, a repressor of CDKN1A/p21. Can negatively regulate the apoptotic effects of IFIT2. {ECO:0000269|PubMed:17050680, ECO:0000269|PubMed:20686046, ECO:0000269|PubMed:21190939, ECO:0000269|PubMed:21642987, ECO:0000269|PubMed:21813773}.
• Pathway: The human immune response to tuberculosis;Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.705
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.0240
• hipred: N
• hipred_score: 0.216
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifit3b

Gene ontology

• Biological process: negative regulation of cell population proliferation;response to virus;cellular response to interferon-alpha;negative regulation of apoptotic process;defense response to virus;type I interferon signaling pathway
• Cellular component: cytoplasm;mitochondrion;cytosol
• Molecular function: molecular_function;protein binding;identical protein binding