IFIT5

interferon induced protein with tetratricopeptide repeats 5, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:89414568-89421605

Links

ENSG00000152778 ∙ NCBI:24138 ∙ OMIM:616135 ∙ HGNC:13328 ∙ Uniprot:Q13325 ∙ 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 IFIT5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFIT5 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			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in IFIT5

This is a list of pathogenic ClinVar variants found in the IFIT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89417359-T-C		not specified	Uncertain significance (Dec 12, 2023)
10-89417437-A-G		not specified	Uncertain significance (Aug 12, 2021)
10-89417474-G-A		not specified	Uncertain significance (Nov 10, 2022)
10-89417605-G-A		not specified	Uncertain significance (Dec 17, 2023)
10-89417633-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-89417668-C-G		not specified	Uncertain significance (Aug 30, 2021)
10-89417673-G-A			Benign (Dec 31, 2019)
10-89417810-T-G		not specified	Uncertain significance (Jul 25, 2023)
10-89417931-A-C		not specified	Uncertain significance (Mar 22, 2023)
10-89417931-A-T		not specified	Uncertain significance (Dec 26, 2023)
10-89417979-G-C		not specified	Uncertain significance (Dec 16, 2023)
10-89418116-A-G		not specified	Uncertain significance (Jun 29, 2022)
10-89418171-A-G		not specified	Uncertain significance (Jul 05, 2023)
10-89418197-G-A		not specified	Uncertain significance (Nov 08, 2022)
10-89418235-A-G		not specified	Uncertain significance (Mar 28, 2023)
10-89418238-A-G		not specified	Uncertain significance (Sep 27, 2022)
10-89418284-G-A		not specified	Likely benign (Jun 29, 2022)
10-89418296-G-A		not specified	Uncertain significance (Mar 20, 2024)
10-89418342-C-G		not specified	Uncertain significance (May 23, 2024)
10-89418391-C-T			Benign (Dec 31, 2019)
10-89418580-G-A		not specified	Uncertain significance (Dec 18, 2023)
10-89418602-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFIT5	protein_coding	protein_coding	ENST00000371795	2	6416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000118	0.957	125677	1	70	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.353	238	254	0.938	0.0000129	3172
Missense in Polyphen		72	71.687	1.0044		982
Synonymous	0.725	85	93.9	0.905	0.00000459	904
Loss of Function	1.83	9	17.2	0.524	9.18e-7	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000326	0.000326
South Asian	0.00147	0.00141
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced RNA-binding protein involved in the human innate immune response. Has a broad and adaptable RNA structure recognition important for RNA recognition specificity in antiviral defense. Binds precursor and processed tRNAs as well as poly-U-tailed tRNA fragments (PubMed:25092312, PubMed:23317505, PubMed:23774268). Specifically binds single-stranded RNA bearing a 5'-triphosphate group (PPP-RNA), thereby acting as a sensor of viral single-stranded 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 (PubMed:23334420). Also recognizes and selectively binds AT-rich dsDNA (PubMed:23774268). Additionally, as a mediator in innate immunity, regulates positively IKK-NFKB signaling by sinergizing the recruitment of IKK to MAP3K7 (PubMed:26334375). {ECO:0000269|PubMed:23317505, ECO:0000269|PubMed:23334420, ECO:0000269|PubMed:23774268, ECO:0000269|PubMed:25092312, ECO:0000269|PubMed:26334375}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.441
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.279
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of viral genome replication;innate immune response;defense response to virus
• Cellular component: cytosol;plasma membrane;IkappaB kinase complex;actin cytoskeleton;ruffle membrane;intracellular membrane-bounded organelle;apical part of cell
• Molecular function: tRNA binding;RNA cap binding;double-stranded DNA binding;RNA binding;single-stranded RNA binding;protein binding;poly(U) RNA binding