MGST2

microsomal glutathione S-transferase 2, the group of Microsomal glutathione S-transferases

Basic information

Region (hg38): 4:139665767-139740745

Links

ENSG00000085871 ∙ NCBI:4258 ∙ OMIM:601733 ∙ HGNC:7063 ∙ Uniprot:Q99735 ∙ 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 MGST2 gene.

• Inborn genetic diseases (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGST2 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			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in MGST2

This is a list of pathogenic ClinVar variants found in the MGST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-139678591-C-T		not specified	Uncertain significance (Dec 27, 2023)
4-139695246-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-139695246-G-T		not specified	Uncertain significance (Feb 22, 2023)
4-139695263-C-T			Benign (Jul 17, 2018)
4-139703502-T-C			Benign (Feb 23, 2018)
4-139703505-T-A		not specified	Uncertain significance (Aug 13, 2021)
4-139704030-G-A		not specified	Uncertain significance (Jan 27, 2022)
4-139704055-G-T		not specified	Uncertain significance (Feb 01, 2023)
4-139704137-C-T		not specified	Uncertain significance (Feb 15, 2023)
4-139719506-G-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGST2	protein_coding	protein_coding	ENST00000265498	5	74978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0783	0.877	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.373	72	81.5	0.884	0.00000443	929
Missense in Polyphen		17	25.435	0.66838		281
Synonymous	-1.19	40	31.5	1.27	0.00000155	300
Loss of Function	1.71	3	8.32	0.361	3.51e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000330	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can catalyze the production of LTC4 from LTA4 and reduced glutathione. Can catalyze the conjugation of 1-chloro-2,4- dinitrobenzene with reduced glutathione.
• 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);Busulfan Pathway, Pharmacodynamics;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metapathway biotransformation Phase I and II;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Androgen and estrogen biosynthesis and metabolism;Leukotriene metabolism;Biological oxidations;Metabolism;Prostaglandin formation from arachidonate;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Xenobiotics metabolism;Aflatoxin activation and detoxification;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.287
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.495

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgst2
• 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid metabolic process;glutathione biosynthetic process;xenobiotic metabolic process;response to organonitrogen compound;leukotriene biosynthetic process;response to lipopolysaccharide;positive regulation of catalytic activity;membrane lipid catabolic process;positive regulation of inflammatory response;cellular oxidant detoxification;glutathione derivative biosynthetic process
• Cellular component: nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: glutathione transferase activity;leukotriene-C4 synthase activity;glutathione peroxidase activity;protein binding;enzyme activator activity