GSTA2
Basic information
Region (hg38): 6:52750087-52763475
Previous symbols: [ "GST2" ]
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 GSTA2 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 | 10 | 14 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 10 | 4 | 0 |
Variants in GSTA2
This is a list of pathogenic ClinVar variants found in the GSTA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-52751592-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
6-52751620-T-G | not specified | Uncertain significance (Sep 09, 2024) | ||
6-52751624-C-T | not specified | Uncertain significance (Apr 27, 2024) | ||
6-52751674-C-A | not specified | Uncertain significance (Dec 22, 2023) | ||
6-52751678-C-A | not specified | Uncertain significance (Jun 05, 2023) | ||
6-52751708-C-A | not specified | Uncertain significance (Oct 25, 2023) | ||
6-52752867-G-A | not specified | Uncertain significance (Sep 03, 2024) | ||
6-52752869-G-C | not specified | Likely benign (Jul 25, 2023) | ||
6-52752880-T-C | not specified | Uncertain significance (May 07, 2024) | ||
6-52752885-G-A | not specified | Uncertain significance (Aug 08, 2022) | ||
6-52752895-G-T | not specified | Likely benign (Nov 27, 2023) | ||
6-52752907-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
6-52752969-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
6-52752981-A-G | not specified | Likely benign (Nov 07, 2023) | ||
6-52752988-T-A | not specified | Uncertain significance (Nov 18, 2022) | ||
6-52754970-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
6-52755046-T-C | not specified | Uncertain significance (Mar 06, 2023) | ||
6-52757892-A-G | not specified | Likely benign (May 30, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GSTA2 | protein_coding | protein_coding | ENST00000493422 | 6 | 13471 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.56e-7 | 0.168 | 125641 | 1 | 105 | 125747 | 0.000422 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.50 | 162 | 116 | 1.39 | 0.00000574 | 1466 |
Missense in Polyphen | 29 | 19.759 | 1.4677 | 258 | ||
Synonymous | -2.77 | 61 | 39.0 | 1.56 | 0.00000178 | 395 |
Loss of Function | -0.0505 | 10 | 9.83 | 1.02 | 4.11e-7 | 132 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000521 | 0.000521 |
Ashkenazi Jewish | 0.00558 | 0.00477 |
East Asian | 0.000435 | 0.000435 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000241 | 0.000237 |
Middle Eastern | 0.000435 | 0.000435 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000864 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles.;
- Pathway
- Glutathione metabolism - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Aryl Hydrocarbon Receptor Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcriptional activation by NRF2;Liver steatosis AOP;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;oxidative stress induced gene expression via nrf2;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biological oxidations;Metabolism
(Consensus)
Intolerance Scores
- loftool
- 0.846
- rvis_EVS
- 0.95
- rvis_percentile_EVS
- 90.06
Haploinsufficiency Scores
- pHI
- 0.0583
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.246
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- glutathione metabolic process;epithelial cell differentiation;interleukin-12-mediated signaling pathway;glutathione derivative biosynthetic process
- Cellular component
- cytosol;extracellular exosome
- Molecular function
- glutathione transferase activity;protein binding