GSTK1
protein-codingglutathione S-transferase kappa 1, the group of Soluble glutathione S-transferases
Gene summary
This gene encodes a member of the kappa class of the glutathione transferase superfamily of enzymes that function in cellular detoxification. The encoded protein is localized to the peroxisome and catalyzes the conjugation of glutathione to a wide range of hydrophobic substates facilitating the removal of these compounds from cells. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GSTK1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015917.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 34 | 4 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 39 | 4 | 1 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057001.1 | 8 | MANE Select | |
| Ensembl | ENSP00000351181.5 | 8 | MANE Select | |
| RefSeq | NP_001137151.1 | 7 | Standard | |
| RefSeq | NP_001137152.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gstk1 | Danio rerio | Structure: heart Quality: decreased functionality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- protein targeting to peroxisome
- glutathione metabolic process
- epithelial cell differentiation
- oxidation-reduction process
- cellular oxidant detoxification
Molecular Function
- glutathione transferase activity
- glutathione peroxidase activity
- signaling receptor binding
- protein binding
- protein disulfide oxidoreductase activity
Cellular Component
- mitochondrion
- mitochondrial matrix
- peroxisome
- peroxisomal matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000479303
- Coding exons
- 7
- Length
- 26762
- Individuals with no LoFs
- 125562
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 185
- Defined
- 125747
- p
- 0.000736
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.635 | 147 | 170 | 0.863 | 0.00000982 | 1822 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.0019 | 0.0019 | notable |
| Ashkenazi Jewish | 0.0020 | 0.0020 | notable |
| East Asian | 0.000058 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00058 | 0.00058 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.0026 | 0.0026 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Significant glutathione conjugating activity is found only with the model substrate, 1-chloro-2,4-dinitrobenzene (CDNB).;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.151
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.836
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |