PRDX4
protein-codingperoxiredoxin 4, the group of Peroxiredoxins
Gene summary
The protein encoded by this gene is an antioxidant enzyme and belongs to the peroxiredoxin family. The protein is localized to the cytoplasm. Peroxidases of the peroxiredoxin family reduce hydrogen peroxide and alkyl hydroperoxides to water and alcohol with the use of reducing equivalents derived from thiol-containing donor molecules. This protein has been found to play a regulatory role in the activation of the transcription factor NF-kappaB. [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 ~22.1 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 PRDX4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006406.2. 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 | 6 | 6 | ||||
| missense | 48 | 1 | 49 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 15 | 15 | ||||
| Total | 0 | 0 | 72 | 0 | 1 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006397.1 | 7 | MANE Select | |
| Ensembl | ENSP00000368646.4 | 7 | MANE Select | |
| Ensembl | ENSP00000368635.3 | 3 | Standard | |
| Ensembl | ENSP00000368635.3 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Selenium Micronutrient Network
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- response to oxidative stress
- I-kappaB phosphorylation
- spermatogenesis
- male gonad development
- 4-hydroxyproline metabolic process
Molecular Function
- protein binding
- thioredoxin peroxidase activity
- protein homodimerization activity
Cellular Component
- extracellular region
- nucleus
- cytoplasm
- endoplasmic reticulum
- smooth endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379341
- Coding exons
- 7
- Length
- 22138
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 5
- Heterozygous LoFs
- 4
- Defined
- 125747
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 68 | 96.8 | 0.703 | 0.00000682 | 1720 |
| Missense (PolyPhen) | 18 | 39.478 | 0.45595 | 706 | ||
| Synonymous | -0.284 | 43 | 40.7 | 1.06 | 0.00000295 | 563 |
| Loss of Function | 1.70 | 4 | 9.71 | 0.412 | 6.72e-7 | 173 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000079 | 0.000062 | rare |
| Latino/Admixed American | 0.00019 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000075 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000025 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides and as sensor of hydrogen peroxide-mediated signaling events. Regulates the activation of NF-kappa-B in the cytosol by a modulation of I- kappa-B-alpha phosphorylation. {ECO:0000269|PubMed:9388242}.;
Recessive Scores
- pRec
- 0.302
Intolerance Scores
- LoFtool
- 0.586
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.244
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |