GSTP1

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

Basic information

Region (hg38): 11:67583741-67586656

Previous symbols: [ "FAEES3", "GST3" ]

Links

ENSG00000084207 ∙ NCBI:2950 ∙ OMIM:134660 ∙ HGNC:4638 ∙ Uniprot:P09211 ∙ 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 GSTP1 gene.

• not provided (13 variants)
• Inborn genetic diseases (3 variants)
• Pulmonary disease, chronic obstructive, susceptibility to (1 variants)
• Abnormality of immune system physiology (1 variants)
• Neoplasm of the large intestine (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTP1 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	2	3
missense			3		2	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					8	8
Total	0	0	3	1	12

Variants in GSTP1

This is a list of pathogenic ClinVar variants found in the GSTP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-67583826-G-A			Benign (Jun 09, 2021)
11-67584060-G-A			Benign (Jun 19, 2021)
11-67584069-A-G			Benign (Nov 12, 2018)
11-67584114-C-G			Benign (Nov 12, 2018)
11-67584303-C-T			Benign (Jun 19, 2021)
11-67584481-C-G		not specified	Uncertain significance (Jan 29, 2024)
11-67584690-C-T			Benign (Jun 09, 2021)
11-67584737-C-A		not specified	Uncertain significance (May 16, 2023)
11-67584785-C-A			Benign (Jun 19, 2021)
11-67585218-A-G		Neoplasm of the large intestine • Abnormality of immune system physiology	Benign (Jun 09, 2021)
11-67585218-A-A		-	no classification for the single variant (-)
11-67585320-TC-CA		Kala-azar susceptibility 2	Likely pathogenic (Sep 14, 2017)
11-67585782-G-A			Benign (Jun 19, 2021)
11-67586108-C-T		Pulmonary disease, chronic obstructive, susceptibility to	Benign (Jun 09, 2021)
11-67586108-C-C		-	no classification for the single variant (-)
11-67586373-C-T			Benign (Jun 19, 2021)
11-67586398-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-67586428-A-C		not specified	Uncertain significance (Feb 27, 2024)
11-67586463-G-A			Likely benign (Mar 30, 2018)
11-67586464-T-A		not specified	Uncertain significance (Sep 13, 2023)
11-67586499-T-C			Benign (Jun 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTP1	protein_coding	protein_coding	ENST00000398606	7	3066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0142	0.959	124783	0	16	124799	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.334	129	119	1.09	0.00000661	1323
Missense in Polyphen		26	28.673	0.90677		407
Synonymous	1.00	46	55.5	0.829	0.00000321	433
Loss of Function	1.93	5	12.3	0.406	5.34e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000187
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000530
Middle Eastern	0.0000557	0.0000556
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Regulates negatively CDK5 activity via p25/p35 translocation to prevent neurodegeneration. {ECO:0000269|PubMed:21668448}.
• Pathway: Glutathione metabolism - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Prostate cancer - 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);Busulfan Pathway, Pharmacodynamics;Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;Ifosfamide Pathway, Pharmacodynamics;Acetaminophen Metabolism Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Exercise-induced Circadian Regulation;Arachidonate Epoxygenase - Epoxide Hydrolase;Metapathway biotransformation Phase I and II;Neutrophil degranulation;Detoxification of Reactive Oxygen Species;multi-drug resistance factors;Glutathione conjugation;Phase II - Conjugation of compounds;Cellular responses to stress;glutathione-mediated detoxification;Biological oxidations;Innate Immune System;Immune System;Metabolism;4-hydroxy-2-nonenal detoxification;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.753

Intolerance Scores

• loftool: 0.722
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.202
• hipred: Y
• hipred_score: 0.588
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gstp3

Gene ontology

• Biological process: response to reactive oxygen species;negative regulation of acute inflammatory response;negative regulation of protein kinase activity;glutathione metabolic process;xenobiotic metabolic process;central nervous system development;negative regulation of biosynthetic process;negative regulation of tumor necrosis factor-mediated signaling pathway;oligodendrocyte development;animal organ regeneration;response to estradiol;negative regulation of interleukin-1 beta production;negative regulation of tumor necrosis factor production;cellular response to insulin stimulus;regulation of stress-activated MAPK cascade;negative regulation of stress-activated MAPK cascade;positive regulation of superoxide anion generation;response to L-ascorbic acid;common myeloid progenitor cell proliferation;nitric oxide storage;negative regulation of apoptotic process;negative regulation of I-kappaB kinase/NF-kappaB signaling;response to amino acid;neutrophil degranulation;negative regulation of MAP kinase activity;negative regulation of MAPK cascade;negative regulation of JUN kinase activity;linoleic acid metabolic process;response to ethanol;negative regulation of fibroblast proliferation;negative regulation of nitric-oxide synthase biosynthetic process;regulation of ERK1 and ERK2 cascade;negative regulation of ERK1 and ERK2 cascade;negative regulation of leukocyte proliferation;cellular response to lipopolysaccharide;cellular response to epidermal growth factor stimulus;cellular response to glucocorticoid stimulus;cellular response to cell-matrix adhesion;negative regulation of monocyte chemotactic protein-1 production;negative regulation of smooth muscle cell chemotaxis;cellular oxidant detoxification;glutathione derivative biosynthetic process;negative regulation of vascular smooth muscle cell proliferation;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;mitochondrion;cytosol;plasma membrane;vesicle;secretory granule lumen;extracellular exosome;TRAF2-GSTP1 complex;ficolin-1-rich granule lumen
• Molecular function: glutathione transferase activity;glutathione peroxidase activity;protein binding;drug binding;JUN kinase binding;kinase regulator activity;S-nitrosoglutathione binding;dinitrosyl-iron complex binding;glutathione binding;nitric oxide binding