GSTK1

glutathione S-transferase kappa 1, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 7:143244093-143270854

Links

ENSG00000197448

∙ NCBI:373156 ∙ OMIM:602321 ∙ HGNC:16906 ∙ Uniprot:Q9Y2Q3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GSTK1 gene.

not_specified (37 variants)
not_provided (4 variants)

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. These statistics are base on transcript: NM_000015917.3. 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 clinvar	1
missense			30 clinvar	3 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	3	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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