PRDX4
peroxiredoxin 4, the group of Peroxiredoxins
Basic information
Region (hg38): X:23664262-23686397
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX4 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 | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 1 |
Variants in PRDX4
This is a list of pathogenic ClinVar variants found in the PRDX4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-23667598-A-G | not specified | Uncertain significance (Dec 09, 2023) | ||
| X-23667619-C-A | not specified | Uncertain significance (Oct 27, 2022) | ||
| X-23667754-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| X-23667759-G-C | not specified | Uncertain significance (Mar 25, 2024) | ||
| X-23667781-G-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| X-23671559-C-G | not specified | Uncertain significance (Apr 07, 2023) | ||
| X-23671600-G-A | Benign (Feb 25, 2018) | |||
| X-23671606-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
| X-23675006-A-T | not specified | Uncertain significance (Sep 26, 2022) | ||
| X-23675046-G-C | not specified | Uncertain significance (Apr 14, 2022) | ||
| X-23679223-G-C | not specified | Uncertain significance (Apr 25, 2022) | ||
| X-23682515-A-G | not specified | Uncertain significance (Mar 31, 2023) | ||
| X-23682520-G-A | Neurodevelopmental delay | Uncertain significance (Apr 03, 2017) | ||
| X-23686321-G-A | not specified | Uncertain significance (Jul 15, 2021) | ||
| X-23686328-T-G | not specified | Uncertain significance (Dec 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDX4 | protein_coding | protein_coding | ENST00000379341 | 7 | 22138 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0268 | 0.925 | 125738 | 5 | 4 | 125747 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 68 | 96.8 | 0.703 | 0.00000682 | 1720 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000270 | 0.000253 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000748 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000250 | 0.0000176 |
| Middle Eastern | 0.0000748 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Selenium Micronutrient Network;Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.302
Intolerance Scores
- loftool
- 0.586
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.28
Haploinsufficiency Scores
- pHI
- 0.207
- hipred
- Y
- hipred_score
- 0.593
- ghis
- 0.399
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.244
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdx4
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype;
Gene ontology
- Biological process
- response to oxidative stress;I-kappaB phosphorylation;spermatogenesis;male gonad development;4-hydroxyproline metabolic process;protein maturation by protein folding;extracellular matrix organization;hydrogen peroxide catabolic process;neutrophil degranulation;cell redox homeostasis;oxidation-reduction process;cellular oxidant detoxification;negative regulation of male germ cell proliferation
- Cellular component
- extracellular region;nucleus;cytoplasm;endoplasmic reticulum;smooth endoplasmic reticulum;cytosol;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
- Molecular function
- protein binding;thioredoxin peroxidase activity;protein homodimerization activity