GPX1
protein-codingglutathione peroxidase 1, the group of Selenoproteins
Gene summary
The protein encoded by this gene belongs to the glutathione peroxidase family, members of which catalyze the reduction of organic hydroperoxides and hydrogen peroxide (H2O2) by glutathione, and thereby protect cells against oxidative damage. Other studies indicate that H2O2 is also essential for growth-factor mediated signal transduction, mitochondrial function, and maintenance of thiol redox-balance; therefore, by limiting H2O2 accumulation, glutathione peroxidases are also involved in modulating these processes. Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. This isozyme is the most abundant, is ubiquitously expressed and localized in the cytoplasm, and whose preferred substrate is hydrogen peroxide. It is also a selenoprotein, containing the rare amino acid selenocysteine (Sec) at its active site. Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. This gene contains an in-frame GCG trinucleotide repeat in the coding region, and three alleles with 4, 5 or 6 repeats have been found in the human population. The allele with 4 GCG repeats has been significantly associated with breast cancer risk in premenopausal women. Alternatively spliced transcript variants have been found for this gene. Pseudogenes of this locus have been identified on chromosomes X and 21. [provided by RefSeq, Aug 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013601
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GPX1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000581.4. 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 | 1 | 2 | |||
| missense | 52 | 2 | 54 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 56 | 1 | 3 | 60 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000572.2 | 2 | MANE Select | |
| Ensembl | ENSP00000407375.1 | 2 | MANE Select | |
| RefSeq | NP_001316384.1 | 2 | Standard | |
| RefSeq | NP_001316431.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Doxorubicin Pathway (Cancer Cell), Pharmacodynamics
- Thyroid hormone synthesis - Homo sapiens (human)
- Glutathione metabolism - Homo sapiens (human)
- Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human)
- Huntington,s disease - Homo sapiens (human)
Biological Process
- temperature homeostasis
- endothelial cell development
- negative regulation of inflammatory response to antigenic stimulus
- purine nucleotide catabolic process
- triglyceride metabolic process
Molecular Function
- peroxidase activity
- glutathione peroxidase activity
- SH3 domain binding
Cellular Component
- cytoplasm
- mitochondrion
- mitochondrial matrix
- cytosol
- Lewy body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000419783
- Coding exons
- 2
- Length
- 1425
- Individuals with no LoFs
- 124741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 124763
- p
- 0.0000882
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.298 | 135 | 126 | 1.07 | 0.00000621 | 1289 |
| Missense (PolyPhen) | 43 | 40.123 | 1.0717 | 473 | ||
| Synonymous | -1.53 | 73 | 58.1 | 1.26 | 0.00000304 | 450 |
| Loss of Function | -0.512 | 6 | 4.79 | 1.25 | 2.05e-7 | 50 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.000082 | 0.000079 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00052 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protects the hemoglobin in erythrocytes from oxidative breakdown.;
Intolerance Scores
- LoFtool
- 0.717
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 68.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |