IFIT1

interferon induced protein with tetratricopeptide repeats 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:89392546-89406487

Previous symbols: [ "G10P1", "IFI56", "IFNAI1" ]

Links

ENSG00000185745 ∙ NCBI:3434 ∙ OMIM:147690 ∙ HGNC:5407 ∙ Uniprot:P09914 ∙ 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 IFIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFIT1 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			27			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	27	0	1

Variants in IFIT1

This is a list of pathogenic ClinVar variants found in the IFIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89402282-A-C		not specified	Uncertain significance (Jan 09, 2024)
10-89402292-A-T		not specified	Uncertain significance (Aug 29, 2023)
10-89402306-A-G		not specified	Uncertain significance (Feb 12, 2024)
10-89402318-G-C		not specified	Uncertain significance (Sep 13, 2023)
10-89402416-C-T			Benign (Jul 25, 2018)
10-89402424-A-G		not specified	Uncertain significance (Mar 02, 2023)
10-89402438-C-T		not specified	Uncertain significance (May 04, 2023)
10-89402565-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-89402616-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-89402618-C-G		not specified	Uncertain significance (Nov 11, 2024)
10-89402639-G-A		not specified	Uncertain significance (Sep 03, 2024)
10-89402640-A-G		not specified	Uncertain significance (Aug 08, 2022)
10-89402673-G-A		not specified	Uncertain significance (Mar 20, 2024)
10-89402702-T-C		not specified	Uncertain significance (Jun 05, 2023)
10-89402751-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-89402783-G-A		not specified	Uncertain significance (Mar 15, 2024)
10-89402820-C-T		not specified	Uncertain significance (Apr 11, 2023)
10-89402888-C-T		not specified	Uncertain significance (Aug 23, 2021)
10-89402930-A-G		not specified	Uncertain significance (Sep 04, 2024)
10-89402936-G-T		not specified	Uncertain significance (Oct 04, 2024)
10-89402940-T-G		not specified	Uncertain significance (Oct 25, 2023)
10-89403005-C-G		not specified	Uncertain significance (Mar 02, 2023)
10-89403023-C-G		not specified	Uncertain significance (Dec 20, 2023)
10-89403045-C-T		not specified	Uncertain significance (Sep 23, 2023)
10-89403054-T-A		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFIT1	protein_coding	protein_coding	ENST00000371804	2	11443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000278	0.572	125727	0	13	125740	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.335	234	249	0.940	0.0000123	3160
Missense in Polyphen		39	54.637	0.7138		759
Synonymous	-0.397	97	92.2	1.05	0.00000443	873
Loss of Function	0.540	6	7.61	0.789	3.16e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced antiviral RNA-binding protein that specifically binds single-stranded RNA bearing a 5'-triphosphate group (PPP-RNA), thereby acting as a sensor of viral single- stranded RNAs and inhibiting expression of viral messenger RNAs. Single-stranded PPP-RNAs, which lack 2'-O-methylation of the 5' cap and bear a 5'-triphosphate group instead, are specific from viruses, providing a molecular signature to distinguish between self and non-self mRNAs by the host during viral infection. Directly binds PPP-RNA in a non-sequence-specific manner. Viruses evolved several ways to evade this restriction system such as encoding their own 2'-O-methylase for their mRNAs or by stealing host cap containing the 2'-O-methylation (cap snatching mechanism). Exhibits antiviral activity against several viruses including human papilloma and hepatitis C viruses. {ECO:0000269|PubMed:19008854, ECO:0000269|PubMed:19416887, ECO:0000269|PubMed:21976647, ECO:0000269|PubMed:23334420}.
• Pathway: Hepatitis C - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);The human immune response to tuberculosis;Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.386
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifit1bl2

Gene ontology

• Biological process: response to virus;viral process;intracellular transport of viral protein in host cell;negative regulation of protein binding;positive regulation of viral genome replication;negative regulation of viral genome replication;negative regulation of defense response to virus by host;negative regulation of helicase activity;defense response to virus;type I interferon signaling pathway;cellular response to type I interferon;cellular response to exogenous dsRNA
• Cellular component: cytoplasm;cytosol;host cell
• Molecular function: RNA binding;protein binding