PRDX3
peroxiredoxin 3, the group of Peroxiredoxins
Basic information
Region (hg38): 10:119167720-119178812
Previous symbols: [ "AOP1" ]
Links
Phenotypes
GenCC
Source:
- spinocerebellar ataxia, autosomal recessive 32 (Moderate), mode of inheritance: AR
- spinocerebellar ataxia, autosomal recessive 32 (Strong), mode of inheritance: AR
- corneal dystrophy, punctiform and polychromatic pre-descemet (Strong), mode of inheritance: AD
- spinocerebellar ataxia, autosomal recessive 32 (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Corneal dystrophy, punctiform and polychromatic pre-Descemet; Spinocerebellar ataxia, autosomal recessive 32 | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic; Ophthalmologic | 31782998; 33889951; 34369396; 35792670 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (38 variants)
- Spinocerebellar_ataxia,_autosomal_recessive_32 (12 variants)
- not_provided (9 variants)
- Corneal_dystrophy,_punctiform_and_polychromatic_pre-descemet (2 variants)
- Autosomal_recessive_cerebellar_ataxia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006793.5. 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 | 3 | |||||
| missense | 41 | 45 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| Total | 6 | 3 | 42 | 4 | 0 |
Highest pathogenic variant AF is 0.000074351745
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDX3 | protein_coding | protein_coding | ENST00000298510 | 7 | 11131 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00424 | 0.965 | 125721 | 0 | 27 | 125748 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0584 | 145 | 147 | 0.986 | 0.00000785 | 1660 |
| Missense in Polyphen | 44 | 52.458 | 0.83876 | 649 | ||
| Synonymous | 0.627 | 52 | 58.1 | 0.895 | 0.00000360 | 508 |
| Loss of Function | 1.89 | 6 | 13.5 | 0.445 | 8.26e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000580 | 0.0000580 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000158 | 0.000158 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000138 | 0.000131 |
| 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 (PubMed:7733872, PubMed:17707404). Acts synergistically with MAP3K13 to regulate the activation of NF-kappa-B in the cytosol (PubMed:12492477). {ECO:0000269|PubMed:12492477, ECO:0000269|PubMed:17707404, ECO:0000269|PubMed:7733872}.;
- Pathway
- Selenium Micronutrient Network;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Cellular responses to external stimuli;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.338
Intolerance Scores
- loftool
- 0.844
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.18
Haploinsufficiency Scores
- pHI
- 0.414
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.538
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.886
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdx3
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; respiratory system phenotype;
Gene ontology
- Biological process
- maternal placenta development;apoptotic process;response to oxidative stress;mitochondrion organization;positive regulation of cell population proliferation;peptidyl-cysteine oxidation;myeloid cell differentiation;response to lipopolysaccharide;negative regulation of kinase activity;cellular response to oxidative stress;cellular response to reactive oxygen species;response to hydrogen peroxide;hydrogen peroxide catabolic process;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;cell redox homeostasis;positive regulation of NF-kappaB transcription factor activity;regulation of mitochondrial membrane potential;cellular oxidant detoxification
- Cellular component
- cytoplasm;mitochondrion;mitochondrial matrix;early endosome;cytosol;protein-containing complex;myelin sheath
- Molecular function
- protein binding;protein C-terminus binding;thioredoxin peroxidase activity;alkyl hydroperoxide reductase activity;kinase binding;protein kinase binding;identical protein binding;cysteine-type endopeptidase inhibitor activity involved in apoptotic process