MGST3

microsomal glutathione S-transferase 3, the group of Microsomal glutathione S-transferases

Basic information

Region (hg38): 1:165631212-165661796

Links

ENSG00000143198 ∙ NCBI:4259 ∙ OMIM:604564 ∙ HGNC:7064 ∙ Uniprot:O14880 ∙ 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 MGST3 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGST3 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						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in MGST3

This is a list of pathogenic ClinVar variants found in the MGST3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-165632229-G-A		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
1-165646920-C-T		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
1-165649842-C-T		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
1-165649930-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-165649957-A-G		not specified	Uncertain significance (Jun 27, 2023)
1-165651072-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-165651555-G-A		Pulmonary disease, chronic obstructive, susceptibility to	association (Jul 05, 2022)
1-165652002-A-C		not specified	Uncertain significance (May 23, 2023)
1-165652030-C-T		not specified	Uncertain significance (Sep 14, 2021)
1-165654279-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-165654282-A-G		not specified	Likely benign (Feb 27, 2023)
1-165654316-G-C		not specified	Uncertain significance (May 03, 2023)
1-165655562-G-T		Pulmonary disease, chronic obstructive, susceptibility to	association (May 13, 2022)
1-165655786-G-T		Pulmonary disease, chronic obstructive, susceptibility to	protective (May 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGST3	protein_coding	protein_coding	ENST00000367889	5	30936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000203	0.743	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.952	64	89.3	0.717	0.00000510	971
Missense in Polyphen		17	29.693	0.57253		302
Synonymous	0.983	24	31.0	0.775	0.00000160	311
Loss of Function	0.997	7	10.5	0.668	7.95e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000615	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Also functions as a glutathione peroxidase.
• 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);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: 0.162

Intolerance Scores

• loftool: 0.652
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.0762
• hipred: N
• hipred_score: 0.407
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.586

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgst3
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: lipid metabolic process;xenobiotic metabolic process;response to organonitrogen compound;leukotriene biosynthetic process;cellular oxidant detoxification;glutathione derivative biosynthetic process
• Cellular component: nuclear envelope;endoplasmic reticulum;endoplasmic reticulum 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