GSTK1
glutathione S-transferase kappa 1, the group of Soluble glutathione S-transferases
Basic information
Region (hg38): 7:143244093-143270854
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 GSTK1 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 | 13 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 2 | 1 |
Variants in GSTK1
This is a list of pathogenic ClinVar variants found in the GSTK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-143263526-C-T | not specified | Uncertain significance (Oct 13, 2023) | ||
| 7-143263530-G-C | not specified | Uncertain significance (Feb 13, 2023) | ||
| 7-143263533-C-T | not specified | Uncertain significance (May 26, 2022) | ||
| 7-143263571-T-C | not specified | Uncertain significance (Oct 06, 2024) | ||
| 7-143263573-G-T | not specified | Uncertain significance (Apr 07, 2022) | ||
| 7-143264117-T-C | not specified | Uncertain significance (Oct 01, 2024) | ||
| 7-143264574-C-T | not specified | Uncertain significance (Jul 20, 2021) | ||
| 7-143264575-G-T | not specified | Uncertain significance (Oct 21, 2024) | ||
| 7-143264586-T-C | not specified | Uncertain significance (Jul 11, 2023) | ||
| 7-143264596-A-G | not specified | Uncertain significance (Feb 12, 2024) | ||
| 7-143264999-G-T | not specified | Uncertain significance (Nov 25, 2024) | ||
| 7-143265021-G-A | not specified | Uncertain significance (Jan 30, 2024) | ||
| 7-143265057-G-C | not specified | Uncertain significance (May 18, 2023) | ||
| 7-143265058-C-T | not specified | Likely benign (Apr 07, 2022) | ||
| 7-143265090-A-G | Likely benign (Aug 07, 2018) | |||
| 7-143265225-C-G | not specified | Uncertain significance (Mar 06, 2023) | ||
| 7-143267633-G-A | not specified | Uncertain significance (Nov 29, 2023) | ||
| 7-143268111-C-T | Benign (Mar 29, 2018) | |||
| 7-143268160-A-C | not specified | Uncertain significance (Apr 23, 2024) | ||
| 7-143268173-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
| 7-143268784-C-G | Benign (Mar 29, 2018) | |||
| 7-143268820-G-A | not specified | Uncertain significance (May 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GSTK1 | protein_coding | protein_coding | ENST00000479303 | 7 | 26762 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000194 | 0.463 | 125562 | 0 | 185 | 125747 | 0.000736 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.635 | 147 | 170 | 0.863 | 0.00000982 | 1822 |
| Missense in Polyphen | 49 | 57.173 | 0.85705 | 617 | ||
| Synonymous | 0.970 | 61 | 71.4 | 0.854 | 0.00000438 | 573 |
| Loss of Function | 0.662 | 10 | 12.5 | 0.798 | 5.33e-7 | 149 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00250 | 0.00250 |
| Ashkenazi Jewish | 0.00198 | 0.00199 |
| East Asian | 0.0000578 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000582 | 0.000580 |
| Middle Eastern | 0.0000578 | 0.0000544 |
| South Asian | 0.000236 | 0.000229 |
| Other | 0.00261 | 0.00261 |
dbNSFP
Source:
- Function
- FUNCTION: Significant glutathione conjugating activity is found only with the model substrate, 1-chloro-2,4-dinitrobenzene (CDNB).;
- Pathway
- Glutathione metabolism - Homo sapiens (human);Peroxisome - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Metapathway biotransformation Phase I and II;Glutathione conjugation;Phase II - Conjugation of compounds;Metabolism of proteins;glutathione-mediated detoxification;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Biological oxidations;Metabolism;Peroxisomal protein import;Prostaglandin formation from arachidonate;Tryptophan metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Xenobiotics metabolism;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- loftool
- 0.151
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.112
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.442
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.836
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gstk1
- Phenotype
- renal/urinary system phenotype; immune system phenotype; reproductive system 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); hematopoietic system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- gstk1
- Affected structure
- heart
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- protein targeting to peroxisome;glutathione metabolic process;epithelial cell differentiation;oxidation-reduction process;cellular oxidant detoxification;glutathione derivative biosynthetic process
- Cellular component
- mitochondrion;mitochondrial matrix;peroxisome;peroxisomal matrix;cytosol;membrane;extracellular exosome
- Molecular function
- glutathione transferase activity;glutathione peroxidase activity;signaling receptor binding;protein binding;protein disulfide oxidoreductase activity