PRDX1
protein-codingperoxiredoxin 1, the group of Peroxiredoxins
Gene summary
This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein may play an antioxidant protective role in cells, and may contribute to the antiviral activity of CD8(+) T-cells. This protein may have a proliferative effect and play a role in cancer development or progression. Four transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jan 2011]
- PAGA
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0010184
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Dermatologic; Hematologic; Neurologic; Ophthalmologic; Renal
Intervention: Biochemical
Rationale: While no treatment is completely effective, specific dietary (eg, high-calorie, low protein diet and avoidance of fasting, with measures taken to avoid/treat decompensation) and other medical measures (eg, cofactor therapy) may be beneficial to treat and prevent sequelae in the acute and chronic states
Comments: Compound heterozygosity and digenic inheritance (with MMACHC) has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRDX1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_181697.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 14 | 1 | 16 | ||
| missense | 31 | 31 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 3 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 6 | 8 | ||
| Total | 1 | 2 | 42 | 14 | 1 | 60 |
Highest pathogenic variant AF is 0.00002877197
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_859048.1 | 5 | MANE Select | |
| Ensembl | ENSP00000361152.5 | 5 | MANE Select | |
| RefSeq | NP_001189360.1 | 5 | Standard | |
| RefSeq | NP_002565.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Androgen receptor signaling pathway
- Selenium Micronutrient Network
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
Biological Process
- skeletal system development
- retina homeostasis
- response to oxidative stress
- cell population proliferation
- removal of superoxide radicals
Molecular Function
- RNA binding
- peroxidase activity
- protein binding
- thioredoxin peroxidase activity
- identical protein binding
Cellular Component
- extracellular space
- nucleus
- cytoplasm
- cytosol
- melanosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262746
- Coding exons
- 5
- Length
- 12012
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 60
- Defined
- 125747
- p
- 0.000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.200 | 103 | 109 | 0.946 | 0.00000536 | 1320 |
| Missense (PolyPhen) | 35 | 41.196 | 0.8496 | 513 | ||
| Synonymous | -0.129 | 40 | 39.0 | 1.03 | 0.00000193 | 373 |
| Loss of Function | -1.08 | 12 | 8.59 | 1.40 | 3.63e-7 | 107 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00024 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00070 | 0.00069 | rare |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00030 | 0.00029 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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) (PubMed:9497357). Reduces an intramolecular disulfide bond in GDPD5 that gates the ability to GDPD5 to drive postmitotic motor neuron differentiation (By similarity). {ECO:0000250|UniProtKB:P0CB50, ECO:0000269|PubMed:9497357}.;
Recessive Scores
- pRec
- 0.732
Intolerance Scores
- LoFtool
- 0.944
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Indispensability pred.
- E
- Indispensability score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |