IFI30
protein-codingIFI30 lysosomal thiol reductase
Gene summary
The protein encoded by this gene is a lysosomal thiol reductase that at low pH can reduce protein disulfide bonds. The enzyme is expressed constitutively in antigen-presenting cells and induced by gamma-interferon in other cell types. This enzyme has an important role in MHC class II-restricted antigen processing. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.0 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 IFI30 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006332.5. 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 | 42 | 2 | 1 | 45 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 45 | 3 | 1 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006323.2 | 7 | MANE Select | |
| Ensembl | ENSP00000384886.1 | 7 | MANE Select | |
| Ensembl | ENSP00000470527.2 | 2 | Standard | |
| Ensembl | ENSP00000543953.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Antigen processing and presentation - Homo sapiens (human)
- Cytokine Signaling in Immune system
- MHC class II antigen presentation
- Immune System
- Adaptive Immune System
Biological Process
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- antigen processing and presentation of exogenous peptide antigen via MHC class I
- oxidation-reduction process
- interferon-gamma-mediated signaling pathway
Molecular Function
- protein binding
- oxidoreductase activity, acting on a sulfur group of donors
Cellular Component
- extracellular region
- lysosome
- cytosol
- cell junction
- lysosomal lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000407280
- Coding exons
- 7
- Length
- 4956
- Individuals with no LoFs
- 124590
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 124618
- p
- 0.000112
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.630 | 112 | 132 | 0.846 | 0.00000709 | 1566 |
| Missense (PolyPhen) | 41 | 48.9 | 0.83845 | 571 | ||
| Synonymous | -0.276 | 61 | 58.3 | 1.05 | 0.00000362 | 485 |
| Loss of Function | 0.203 | 12 | 12.8 | 0.939 | 5.97e-7 | 139 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000073 | 0.000065 | rare |
| Latino/Admixed American | 0.00019 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000067 | 0.000056 | rare |
| Finnish | 0.000094 | 0.000093 | rare |
| European (Non-Finnish) | 0.00014 | 0.00013 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Lysosomal thiol reductase that can reduce protein disulfide bonds. May facilitate the complete unfolding of proteins destined for lysosomal degradation. Plays an important role in antigen processing. Facilitates the generation of MHC class II- restricted epitodes from disulfide bond-containing antigen by the endocytic reduction of disulfide bonds (By similarity). Facilitates also MHC class I-restricted recognition of exogenous antigens containing disulfide bonds by CD8+ T-cells or crosspresentation (By similarity). {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.555
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 46.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.190
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |