MGST2
microsomal glutathione S-transferase 2, the group of Microsomal glutathione S-transferases
Basic information
Region (hg38): 4:139665768-139740745
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 MGST2 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 | 1 | |||||
| missense | 8 | |||||
| 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 | 2 |
Variants in MGST2
This is a list of pathogenic ClinVar variants found in the MGST2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-139678591-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 4-139695246-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 4-139695246-G-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 4-139695263-C-T | Benign (Jul 17, 2018) | |||
| 4-139703493-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 4-139703502-T-C | Benign (Feb 23, 2018) | |||
| 4-139703505-T-A | not specified | Uncertain significance (Aug 13, 2021) | ||
| 4-139704030-G-A | not specified | Uncertain significance (Jan 27, 2022) | ||
| 4-139704055-G-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 4-139704119-A-G | Uncertain significance (Jun 01, 2024) | |||
| 4-139704137-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 4-139719506-G-C | not specified | Uncertain significance (Jan 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MGST2 | protein_coding | protein_coding | ENST00000265498 | 5 | 74978 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0783 | 0.877 | 125732 | 0 | 15 | 125747 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.373 | 72 | 81.5 | 0.884 | 0.00000443 | 929 |
| Missense in Polyphen | 17 | 25.435 | 0.66838 | 281 | ||
| Synonymous | -1.19 | 40 | 31.5 | 1.27 | 0.00000155 | 300 |
| Loss of Function | 1.71 | 3 | 8.32 | 0.361 | 3.51e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000704 | 0.0000703 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000330 | 0.0000327 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Can catalyze the production of LTC4 from LTA4 and reduced glutathione. Can catalyze the conjugation of 1-chloro-2,4- dinitrobenzene with reduced glutathione.;
- 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);Busulfan Pathway, Pharmacodynamics;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metapathway biotransformation Phase I and II;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Biological oxidations;Metabolism;Prostaglandin formation from arachidonate;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Xenobiotics metabolism;Aflatoxin activation and detoxification;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.151
Intolerance Scores
- loftool
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.57
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- N
- hipred_score
- 0.287
- ghis
- 0.400
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.495
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mgst2
- 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); cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- lipid metabolic process;glutathione biosynthetic process;xenobiotic metabolic process;response to organonitrogen compound;leukotriene biosynthetic process;response to lipopolysaccharide;positive regulation of catalytic activity;membrane lipid catabolic process;positive regulation of inflammatory response;cellular oxidant detoxification;glutathione derivative biosynthetic process
- Cellular component
- nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;organelle membrane;intracellular membrane-bounded organelle
- Molecular function
- glutathione transferase activity;leukotriene-C4 synthase activity;glutathione peroxidase activity;protein binding;enzyme activator activity