MGST2

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

Basic information

Region (hg38): 4:139665768-139740745

Links

ENSG00000085871 ∙ NCBI:4258 ∙ OMIM:601733 ∙ HGNC:7063 ∙ Uniprot:Q99735 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 19.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002413.5	NP_002404.1	5	yes	-
ENST00000265498.6	ENSP00000265498.1	5	yes	-
NM_001204366.2	NP_001191295.1	5	-	-
NM_001204367.2	NP_001191296.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MGST2 gene.

• not_specified (20 variants)
• not_provided (3 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. These statistics are base on transcript: NM_002413.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			22		1	23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	1	2

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
		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

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

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