PRDX6
peroxiredoxin 6, the group of Peroxiredoxins
Basic information
Region (hg38): 1:173477330-173488815
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 PRDX6 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in PRDX6
This is a list of pathogenic ClinVar variants found in the PRDX6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-173477402-C-T | not specified | Uncertain significance (Feb 03, 2022) | ||
| 1-173477431-C-T | not specified | Uncertain significance (Jun 03, 2024) | ||
| 1-173477439-T-G | not specified | Uncertain significance (Aug 30, 2021) | ||
| 1-173477447-A-G | not specified | Uncertain significance (May 09, 2024) | ||
| 1-173481318-C-G | Benign (May 18, 2018) | |||
| 1-173481351-C-G | not specified | Uncertain significance (May 09, 2023) | ||
| 1-173481352-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 1-173481421-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-173481477-A-G | not specified | Uncertain significance (Jun 20, 2024) | ||
| 1-173485389-C-T | not specified | Uncertain significance (Dec 15, 2023) | ||
| 1-173485421-G-C | not specified | Uncertain significance (Jan 11, 2023) | ||
| 1-173485483-G-C | not specified | Uncertain significance (May 10, 2024) | ||
| 1-173486377-G-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 1-173487763-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
| 1-173487796-C-T | not specified | Uncertain significance (May 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDX6 | protein_coding | protein_coding | ENST00000340385 | 5 | 11542 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000482 | 0.439 | 125717 | 0 | 31 | 125748 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.47 | 78 | 124 | 0.630 | 0.00000602 | 1465 |
| Missense in Polyphen | 20 | 45.269 | 0.4418 | 572 | ||
| Synonymous | 0.134 | 44 | 45.1 | 0.975 | 0.00000209 | 455 |
| Loss of Function | 0.341 | 7 | 8.04 | 0.870 | 3.46e-7 | 104 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000300 | 0.000277 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000205 | 0.000202 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| 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. Can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. Also has phospholipase activity, and can therefore either reduce the oxidized sn-2 fatty acyl grup of phospholipids (peroxidase activity) or hydrolyze the sn-2 ester bond of phospholipids (phospholipase activity). These activities are dependent on binding to phospholipids at acidic pH and to oxidized phospholipds at cytosolic pH. Plays a role in cell protection against oxidative stress by detoxifying peroxides and in phospholipid homeostasis. {ECO:0000269|PubMed:10893423, ECO:0000269|PubMed:9497358}.;
- Pathway
- Nuclear Receptors Meta-Pathway;NRF2 pathway;Neutrophil degranulation;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Purine metabolism;Innate Immune System;Immune System;Cellular responses to external stimuli;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.519
Intolerance Scores
- loftool
- 0.589
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.423
- hipred
- N
- hipred_score
- 0.456
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdx6
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype;
Gene ontology
- Biological process
- response to oxidative stress;cellular response to oxidative stress;hydrogen peroxide catabolic process;neutrophil degranulation;cell redox homeostasis;glycerophospholipid catabolic process;positive regulation of mRNA splicing, via spliceosome;oxidation-reduction process;cellular oxidant detoxification
- Cellular component
- extracellular region;extracellular space;nucleus;cytoplasm;cytosol;membrane;azurophil granule lumen;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- peroxidase activity;glutathione peroxidase activity;protein binding;ubiquitin protein ligase binding;protein homodimerization activity;cadherin binding;calcium-independent phospholipase A2 activity;peroxiredoxin activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)