PRDX4
Basic information
Region (hg38): X:23664262-23686397
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (15 variants)
- not_provided (1 variants)
- Neurodevelopmental_delay (1 variants)
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. These statistics are base on transcript: NM_000006406.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 16 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 1 |
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