IFIT2
protein-codinginterferon induced protein with tetratricopeptide repeats 2, the group of Tetratricopeptide repeat domain containing
Gene summary
Enables RNA binding activity. Involved in positive regulation of apoptotic process and response to virus. Acts upstream of or within antiviral innate immune response. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]
- IFI54
- G10P2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IFIT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001547.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 49 | 5 | 2 | 56 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 5 | 2 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001538.4 | 2 | MANE Select | |
| Ensembl | ENSP00000360891.3 | 2 | MANE Select | |
| Ensembl | ENSP00000484770.2 | 2 | Standard | |
| Ensembl | ENSP00000490935.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Type II interferon signaling (IFNG)
- Cytokine Signaling in Immune system
- Immune System
- Interferon alpha/beta signaling
- Interferon Signaling
Biological Process
- apoptotic mitochondrial changes
- response to virus
- negative regulation of protein binding
- cellular response to interferon-alpha
- positive regulation of apoptotic process
Molecular Function
- RNA binding
- protein binding
Cellular Component
- cytoplasm
- endoplasmic reticulum
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371826
- Coding exons
- 2
- Length
- 7322
- Individuals with no LoFs
- 125370
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 43
- Defined
- 125413
- p
- 0.000171
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.522 | 227 | 250 | 0.907 | 0.0000136 | 3128 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00036 | 0.00033 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.649
- RVIS EVS
- 0.62
- RVIS percentile EVS
- 83.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.417
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |