GPX3
glutathione peroxidase 3, the group of Selenoproteins
Basic information
Region (hg38): 5:151020591-151028988
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 GPX3 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in GPX3
This is a list of pathogenic ClinVar variants found in the GPX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-151020674-C-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 5-151020674-C-G | not specified | Uncertain significance (Jun 30, 2022) | ||
| 5-151020710-T-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 5-151020734-A-T | not specified | Uncertain significance (Jun 30, 2022) | ||
| 5-151025420-C-A | not specified | Uncertain significance (Sep 14, 2023) | ||
| 5-151025433-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
| 5-151025455-A-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 5-151026942-T-A | not specified | Uncertain significance (Apr 28, 2023) | ||
| 5-151027464-A-G | not specified | Uncertain significance (May 18, 2022) | ||
| 5-151027476-T-G | not specified | Uncertain significance (Oct 13, 2021) | ||
| 5-151027952-G-A | not specified | Uncertain significance (Feb 03, 2022) | ||
| 5-151027987-C-T | not specified | Uncertain significance (May 03, 2023) | ||
| 5-151028068-G-A | not specified | Uncertain significance (Apr 20, 2024) | ||
| 5-151028072-A-G | not specified | Uncertain significance (Nov 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GPX3 | protein_coding | protein_coding | ENST00000388825 | 5 | 8431 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0510 | 0.930 | 124822 | 0 | 41 | 124863 | 0.000164 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.566 | 114 | 132 | 0.862 | 0.00000747 | 1464 |
| Missense in Polyphen | 58 | 62.709 | 0.9249 | 686 | ||
| Synonymous | -0.150 | 57 | 55.6 | 1.03 | 0.00000332 | 451 |
| Loss of Function | 2.04 | 4 | 11.4 | 0.350 | 5.72e-7 | 125 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000351 | 0.000351 |
| Ashkenazi Jewish | 0.0000995 | 0.0000993 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000425 | 0.000425 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protects cells and enzymes from oxidative damage, by catalyzing the reduction of hydrogen peroxide, lipid peroxides and organic hydroperoxide, by glutathione.;
- Pathway
- Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Glutathione metabolism;Selenium Micronutrient Network;Folate Metabolism;Selenium Metabolism and Selenoproteins;Nuclear Receptors Meta-Pathway;NRF2 pathway;One carbon metabolism and related pathways;Oxidative Stress;Metapathway biotransformation Phase I and II;Detoxification of Reactive Oxygen Species;glutathione redox reactions I;Cellular responses to stress;Linoleate metabolism;Cellular responses to external stimuli;reactive oxygen species degradation;Arachidonic acid metabolism
(Consensus)
Intolerance Scores
- loftool
- 0.640
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.380
- hipred
- N
- hipred_score
- 0.208
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.233
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpx3
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- response to lipid hydroperoxide;cellular response to oxidative stress;hydrogen peroxide catabolic process;protein homotetramerization;oxidation-reduction process;cellular oxidant detoxification
- Cellular component
- extracellular region;extracellular space;extracellular exosome
- Molecular function
- peroxidase activity;glutathione peroxidase activity;protein binding;transcription factor binding;selenium binding