GSTM4
glutathione S-transferase mu 4, the group of Soluble glutathione S-transferases
Basic information
Region (hg38): 1:109656099-109665496
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 GSTM4 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 | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in GSTM4
This is a list of pathogenic ClinVar variants found in the GSTM4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-109656399-A-G | not specified | Uncertain significance (Dec 21, 2022) | ||
| 1-109656770-A-T | not specified | Uncertain significance (Jul 15, 2024) | ||
| 1-109656776-C-T | not specified | Uncertain significance (Nov 15, 2024) | ||
| 1-109656778-A-C | not specified | Uncertain significance (Sep 30, 2024) | ||
| 1-109657657-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 1-109657794-G-T | not specified | Uncertain significance (Mar 27, 2023) | ||
| 1-109657828-G-T | not specified | Uncertain significance (Aug 05, 2024) | ||
| 1-109657850-G-C | not specified | Uncertain significance (Jan 24, 2023) | ||
| 1-109657855-T-G | not specified | Uncertain significance (Apr 27, 2022) | ||
| 1-109657861-A-C | not specified | Uncertain significance (May 11, 2022) | ||
| 1-109658821-T-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 1-109658853-A-G | not specified | Uncertain significance (Jul 17, 2023) | ||
| 1-109658902-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 1-109659046-G-A | not specified | Uncertain significance (May 03, 2024) | ||
| 1-109659072-G-T | not specified | Uncertain significance (Aug 28, 2023) | ||
| 1-109659102-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 1-109661172-A-G | not specified | Uncertain significance (May 29, 2024) | ||
| 1-109661254-A-G | Likely benign (Jun 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GSTM4 | protein_coding | protein_coding | ENST00000369836 | 8 | 9416 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.38e-8 | 0.115 | 125194 | 2 | 552 | 125748 | 0.00221 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.133 | 117 | 121 | 0.966 | 0.00000705 | 1446 |
| Missense in Polyphen | 30 | 30.128 | 0.99575 | 378 | ||
| Synonymous | -1.65 | 59 | 44.9 | 1.31 | 0.00000268 | 381 |
| Loss of Function | -0.0355 | 12 | 11.9 | 1.01 | 5.15e-7 | 152 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00413 | 0.00414 |
| Ashkenazi Jewish | 0.00278 | 0.00278 |
| East Asian | 0.00147 | 0.00147 |
| Finnish | 0.00115 | 0.00116 |
| European (Non-Finnish) | 0.00310 | 0.00309 |
| Middle Eastern | 0.00147 | 0.00147 |
| South Asian | 0.000915 | 0.000915 |
| Other | 0.00212 | 0.00212 |
dbNSFP
Source:
- Function
- FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Active on 1- chloro-2,4-dinitrobenzene.;
- 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);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metapathway biotransformation Phase I and II;Glutathione conjugation;Metabolism of lipids;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biosynthesis of DHA-derived sulfido conjugates;Biological oxidations;Metabolism;Biosynthesis of maresin conjugates in tissue regeneration (MCTR);Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.0957
Intolerance Scores
- loftool
- 0.971
- rvis_EVS
- 1.28
- rvis_percentile_EVS
- 93.71
Haploinsufficiency Scores
- pHI
- 0.137
- hipred
- N
- hipred_score
- 0.206
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.859
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gstm4
- Phenotype
- immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- glutathione metabolic process;nitrobenzene metabolic process;xenobiotic catabolic process;long-chain fatty acid biosynthetic process;glutathione derivative biosynthetic process
- Cellular component
- cytoplasm;cytosol;intercellular bridge
- Molecular function
- glutathione transferase activity;protein binding;enzyme binding;protein homodimerization activity;glutathione binding