PRDX2
peroxiredoxin 2, the group of Peroxiredoxins
Basic information
Region (hg38): 19:12796820-12801800
Previous symbols: [ "TDPX1" ]
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 PRDX2 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in PRDX2
This is a list of pathogenic ClinVar variants found in the PRDX2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-12797086-T-A | not specified | Uncertain significance (Sep 08, 2024) | ||
| 19-12799911-A-C | not specified | Uncertain significance (Feb 12, 2024) | ||
| 19-12800211-C-T | not specified | Uncertain significance (Nov 09, 2024) | ||
| 19-12800228-C-T | not specified | Uncertain significance (Sep 30, 2024) | ||
| 19-12800229-G-A | not specified | Uncertain significance (May 18, 2022) | ||
| 19-12800238-C-T | not specified | Uncertain significance (Aug 14, 2023) | ||
| 19-12800920-C-A | not specified | Uncertain significance (Dec 15, 2023) | ||
| 19-12800924-G-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 19-12800977-G-A | not specified | Uncertain significance (Jul 05, 2024) | ||
| 19-12800991-C-T | not specified | Likely benign (Jan 03, 2024) | ||
| 19-12801008-G-C | not specified | Uncertain significance (Aug 05, 2024) | ||
| 19-12801030-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 19-12801037-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
| 19-12801191-G-A | not specified | Uncertain significance (Aug 21, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDX2 | protein_coding | protein_coding | ENST00000301522 | 5 | 5061 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0865 | 0.875 | 125690 | 0 | 38 | 125728 | 0.000151 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 91 | 124 | 0.735 | 0.00000714 | 1283 |
| Missense in Polyphen | 16 | 37.609 | 0.42543 | 462 | ||
| Synonymous | -0.170 | 55 | 53.4 | 1.03 | 0.00000331 | 401 |
| Loss of Function | 1.77 | 3 | 8.59 | 0.349 | 3.64e-7 | 101 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00169 | 0.00169 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000443 | 0.0000440 |
| Middle Eastern | 0.00169 | 0.00169 |
| South Asian | 0.0000662 | 0.0000653 |
| 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. Might participate in the signaling cascades of growth factors and tumor necrosis factor-alpha by regulating the intracellular concentrations of H(2)O(2). {ECO:0000269|PubMed:9497357}.;
- Pathway
- Oxidative Stress Regulatory Pathway (Erythrocyte);Selenium Micronutrient Network;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;Detoxification of Reactive Oxygen Species;Gene expression (Transcription);Generic Transcription Pathway;Cellular responses to stress;RNA Polymerase II Transcription;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Transcriptional Regulation by TP53
(Consensus)
Recessive Scores
- pRec
- 0.599
Intolerance Scores
- loftool
- 0.427
- rvis_EVS
- -0.41
- rvis_percentile_EVS
- 26.23
Haploinsufficiency Scores
- pHI
- 0.926
- hipred
- N
- hipred_score
- 0.497
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdx2
- Phenotype
- immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- response to oxidative stress;removal of superoxide radicals;cellular response to oxidative stress;hydrogen peroxide catabolic process;regulation of apoptotic process;negative regulation of apoptotic process;leukocyte activation;cell redox homeostasis;oxidation-reduction process
- Cellular component
- cytoplasm;cytosol;extracellular exosome
- Molecular function
- protein binding;thioredoxin peroxidase activity;antioxidant activity