MGST1
microsomal glutathione S-transferase 1, the group of Microsomal glutathione S-transferases
Basic information
Region (hg38): 12:16347142-16609259
Previous symbols: [ "GST12" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGST1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020300.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 20 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 20 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MGST1 | protein_coding | protein_coding | ENST00000396209 | 3 | 262118 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00266 | 0.578 | 125472 | 3 | 266 | 125741 | 0.00107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.495 | 98 | 85.1 | 1.15 | 0.00000438 | 1007 |
| Missense in Polyphen | 26 | 24.354 | 1.0676 | 313 | ||
| Synonymous | 0.528 | 27 | 30.7 | 0.879 | 0.00000147 | 312 |
| Loss of Function | 0.338 | 4 | 4.80 | 0.834 | 2.65e-7 | 63 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00316 | 0.00316 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000326 | 0.000326 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.000326 | 0.000326 |
| South Asian | 0.00513 | 0.00508 |
| Other | 0.000333 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Has a wide substrate specificity.;
- 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);Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Oxidative Stress;Metapathway biotransformation Phase I and II;Neutrophil degranulation;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Biological oxidations;Innate Immune System;Immune System;Metabolism;Prostaglandin formation from arachidonate;Tryptophan metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Xenobiotics metabolism;Aflatoxin activation and detoxification;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.229
Intolerance Scores
- loftool
- 0.910
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.124
- hipred
- N
- hipred_score
- 0.302
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.735
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mgst1
- Phenotype
Zebrafish Information Network
- Gene name
- mgst1.1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- prostaglandin biosynthetic process;glutathione metabolic process;xenobiotic metabolic process;response to organonitrogen compound;response to lipopolysaccharide;Leydig cell differentiation;response to drug;neutrophil degranulation;oxidation-reduction process;protein homotrimerization;cellular response to lipid hydroperoxide;cellular oxidant detoxification;glutathione derivative biosynthetic process
- Cellular component
- nucleus;mitochondrion;mitochondrial outer membrane;peroxisomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;azurophil granule membrane;apical part of cell
- Molecular function
- glutathione transferase activity;glutathione peroxidase activity;protein binding;protein homodimerization activity;glutathione binding;prostaglandin-E synthase activity