GPX7
Basic information
Region (hg38): 1:52602371-52609051
Links
Phenotypes
GenCC
Source:
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 GPX7 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in GPX7
This is a list of pathogenic ClinVar variants found in the GPX7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-52602440-C-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| 1-52602471-A-G | not specified | Likely benign (Jul 02, 2024) | ||
| 1-52602498-C-A | not specified | Uncertain significance (Sep 30, 2021) | ||
| 1-52606705-G-T | not specified | Uncertain significance (Nov 10, 2024) | ||
| 1-52606717-G-A | not specified | Uncertain significance (Mar 15, 2024) | ||
| 1-52606786-G-T | not specified | Uncertain significance (Apr 24, 2023) | ||
| 1-52606810-T-G | not specified | Uncertain significance (Jun 28, 2024) | ||
| 1-52606873-G-A | not specified | Uncertain significance (Dec 08, 2023) | ||
| 1-52606909-G-A | not specified | Uncertain significance (Nov 26, 2024) | ||
| 1-52608300-T-C | not specified | Uncertain significance (Jun 24, 2022) | ||
| 1-52608346-C-T | not specified | Uncertain significance (Mar 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GPX7 | protein_coding | protein_coding | ENST00000361314 | 3 | 6680 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000585 | 0.461 | 125605 | 1 | 142 | 125748 | 0.000569 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.184 | 96 | 101 | 0.949 | 0.00000555 | 1195 |
| Missense in Polyphen | 35 | 39.383 | 0.88871 | 470 | ||
| Synonymous | 0.840 | 37 | 44.1 | 0.839 | 0.00000252 | 373 |
| Loss of Function | 0.580 | 9 | 11.1 | 0.812 | 8.32e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000387 | 0.000325 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000217 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000150 | 0.000149 |
| Middle Eastern | 0.000217 | 0.000217 |
| South Asian | 0.00363 | 0.00360 |
| Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: It protects esophageal epithelia from hydrogen peroxide- induced oxidative stress. It suppresses acidic bile acid-induced reactive oxigen species (ROS) and protects against oxidative DNA damage and double-strand breaks. {ECO:0000269|PubMed:22157330}.;
- Pathway
- Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);One carbon metabolism and related pathways;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)
Recessive Scores
- pRec
- 0.191
Intolerance Scores
- loftool
- 0.781
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- N
- hipred_score
- 0.197
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.949
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpx7
- Phenotype
- cellular 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); neoplasm; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; liver/biliary system 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- cellular response to oxidative stress;oxidation-reduction process;cellular oxidant detoxification
- Cellular component
- extracellular region;endoplasmic reticulum;endoplasmic reticulum lumen
- Molecular function
- catalase activity;peroxidase activity;glutathione peroxidase activity;protein binding