MGST1

microsomal glutathione S-transferase 1, the group of Microsomal glutathione S-transferases

Basic information

Region (hg38): 12:16347142-16609259

Previous symbols: [ "GST12" ]

Links

ENSG00000008394 ∙ NCBI:4257 ∙ OMIM:138330 ∙ HGNC:7061 ∙ Uniprot:P10620 ∙ 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 MGST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGST1 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		1
missense			10	1		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	10	2	0

Variants in MGST1

This is a list of pathogenic ClinVar variants found in the MGST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-16352362-G-A		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
12-16354357-A-C			Likely benign (May 18, 2018)
12-16357656-A-G		not specified	Uncertain significance (Jan 07, 2022)
12-16357665-C-G		not specified	Uncertain significance (Dec 19, 2023)
12-16357681-G-A		not specified	Uncertain significance (Feb 02, 2022)
12-16357695-C-T		not specified	Uncertain significance (Mar 20, 2023)
12-16357696-G-A		not specified	Uncertain significance (Sep 22, 2023)
12-16360227-G-C		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
12-16363836-G-A		not specified	Uncertain significance (Jun 16, 2024)
12-16363905-T-C		not specified	Uncertain significance (Aug 16, 2021)
12-16363943-C-T		not specified	Uncertain significance (Oct 22, 2021)
12-16363979-G-A		not specified	Likely benign (Mar 11, 2024)
12-16363982-G-A		not specified	Uncertain significance (May 02, 2024)
12-16363986-A-G		not specified	Uncertain significance (Oct 28, 2023)
12-16364003-A-G		not specified	Uncertain significance (Apr 25, 2022)
12-16364098-T-G		Pulmonary disease, chronic obstructive, susceptibility to	protective (Jul 05, 2022)
12-16366334-G-T		Pulmonary disease, chronic obstructive, susceptibility to	protective (Jul 05, 2022)
12-16551238-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-16594154-T-C			Likely benign (Jun 05, 2018)
12-16600827-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-16600832-G-A		not specified	Uncertain significance (Jun 22, 2024)
12-16600847-T-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGST1	protein_coding	protein_coding	ENST00000396209	3	262118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00266	0.578	125472	3	266	125741	0.00107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	98	85.1	1.15	0.00000438	1007
Missense in Polyphen		26	24.354	1.0676		313
Synonymous	0.528	27	30.7	0.879	0.00000147	312
Loss of Function	0.338	4	4.80	0.834	2.65e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00316	0.00316
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000326	0.000326
South Asian	0.00513	0.00508
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Has a wide substrate specificity.
• 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);Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Oxidative Stress;Metapathway biotransformation Phase I and II;Neutrophil degranulation;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Biological oxidations;Innate Immune System;Immune System;Metabolism;Prostaglandin formation from arachidonate;Tryptophan metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Xenobiotics metabolism;Aflatoxin activation and detoxification;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.910
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.302
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.735

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgst1

Zebrafish Information Network

• Gene name: mgst1.1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: prostaglandin biosynthetic process;glutathione metabolic process;xenobiotic metabolic process;response to organonitrogen compound;response to lipopolysaccharide;Leydig cell differentiation;response to drug;neutrophil degranulation;oxidation-reduction process;protein homotrimerization;cellular response to lipid hydroperoxide;cellular oxidant detoxification;glutathione derivative biosynthetic process
• Cellular component: nucleus;mitochondrion;mitochondrial outer membrane;peroxisomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;azurophil granule membrane;apical part of cell
• Molecular function: glutathione transferase activity;glutathione peroxidase activity;protein binding;protein homodimerization activity;glutathione binding;prostaglandin-E synthase activity