IFIT2

interferon induced protein with tetratricopeptide repeats 2, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:89283694-89309271

Previous symbols: [ "IFI54", "G10P2" ]

Links

ENSG00000119922 ∙ NCBI:3433 ∙ OMIM:147040 ∙ HGNC:5409 ∙ Uniprot:P09913 ∙ 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 IFIT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFIT2 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			20	2	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	2

Variants in IFIT2

This is a list of pathogenic ClinVar variants found in the IFIT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89305967-A-C		not specified	Likely benign (Jul 27, 2024)
10-89305970-A-G		not specified	Uncertain significance (Oct 24, 2024)
10-89305996-C-T		not specified	Uncertain significance (Jul 21, 2021)
10-89306062-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-89306071-T-C		not specified	Uncertain significance (Jan 03, 2024)
10-89306147-A-C		not specified	Uncertain significance (Nov 08, 2022)
10-89306249-G-A		not specified	Uncertain significance (Oct 12, 2024)
10-89306282-G-A		not specified	Uncertain significance (Apr 23, 2024)
10-89306293-G-A		not specified	Uncertain significance (Jun 10, 2022)
10-89306329-G-A		not specified	Likely benign (Aug 04, 2023)
10-89306377-G-C		not specified	Uncertain significance (Oct 12, 2021)
10-89306440-G-C		not specified	Uncertain significance (Oct 12, 2021)
10-89306483-C-G		not specified	Uncertain significance (Nov 21, 2024)
10-89306525-C-A		not specified	Uncertain significance (Mar 16, 2022)
10-89306581-C-A		not specified	Uncertain significance (Dec 16, 2022)
10-89306621-T-G		not specified	Uncertain significance (May 28, 2024)
10-89306657-A-G		not specified	Likely benign (Jun 24, 2022)
10-89306689-G-C			Benign (May 21, 2018)
10-89306707-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-89306749-A-G		not specified	Uncertain significance (Jul 14, 2021)
10-89306794-A-G		not specified	Uncertain significance (Mar 28, 2023)
10-89306849-T-C			Benign (May 21, 2018)
10-89306911-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-89306945-A-G		not specified	Uncertain significance (Feb 23, 2023)
10-89306950-A-C		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFIT2	protein_coding	protein_coding	ENST00000371826	2	7322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.251	0.723	125370	0	43	125413	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.522	227	250	0.907	0.0000136	3128
Missense in Polyphen		45	60.866	0.73932		798
Synonymous	-1.16	106	91.9	1.15	0.00000473	867
Loss of Function	1.87	2	7.54	0.265	4.03e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000362	0.000326
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: IFN-induced antiviral protein which inhibits expression of viral messenger RNAs lacking 2'-O-methylation of the 5' cap. The ribose 2'-O-methylation would provide a molecular signature to distinguish between self and non-self mRNAs by the host during viral infection. 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). Binds AU-rich viral RNAs, with or without 5' triphosphorylation, RNA-binding is required for antiviral activity. Can promote apoptosis. {ECO:0000269|PubMed:21190939}.
• Pathway: Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.649
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.0853
• hipred: N
• hipred_score: 0.386

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifit2
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: apoptotic mitochondrial changes;response to virus;negative regulation of protein binding;cellular response to interferon-alpha;positive regulation of apoptotic process;defense response to virus;type I interferon signaling pathway
• Cellular component: cytoplasm;endoplasmic reticulum;cytosol
• Molecular function: RNA binding;protein binding