GSTM2

glutathione S-transferase mu 2, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 1:109668021-109709551

Links

ENSG00000213366 ∙ NCBI:2946 ∙ OMIM:138380 ∙ HGNC:4634 ∙ Uniprot:P28161 ∙ 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 GSTM2 gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTM2 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	2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	6	1	1

Variants in GSTM2

This is a list of pathogenic ClinVar variants found in the GSTM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109668143-A-T		not specified	Uncertain significance (Nov 17, 2022)
1-109668459-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-109668936-G-A		not specified	Uncertain significance (May 09, 2023)
1-109668963-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-109669346-G-C			Benign (Jun 14, 2018)
1-109669374-G-A			Benign (Jul 23, 2018)
1-109669533-C-G		not specified	Uncertain significance (Jan 04, 2024)
1-109671339-A-G		not specified	Uncertain significance (Aug 12, 2022)
1-109671500-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-109674766-C-A		not specified	Uncertain significance (Jul 12, 2022)
1-109674833-G-A			Likely benign (Oct 01, 2022)
1-109687893-A-G		not specified	Uncertain significance (Jun 16, 2023)
1-109688178-C-A			Likely benign (Jun 23, 2018)
1-109689114-C-T		GSTM1-related disorder	Likely benign (Mar 01, 2022)
1-109689252-G-T			Benign (Aug 14, 2018)
1-109689279-T-C			Benign (Aug 14, 2018)
1-109690287-A-C		not specified	Uncertain significance (Nov 18, 2023)
1-109690343-C-T			Benign (Jul 01, 2022)
1-109690472-C-G			Likely benign (Aug 16, 2018)
1-109690515-A-G		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTM2	protein_coding	protein_coding	ENST00000241337	8	41528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.39e-7	0.346	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.836	97	123	0.788	0.00000669	1446
Missense in Polyphen		15	33.072	0.45355		414
Synonymous	-1.29	56	45.0	1.24	0.00000224	378
Loss of Function	0.528	11	13.1	0.842	5.55e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000512	0.000510
Ashkenazi Jewish	0.000994	0.000993
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000371	0.000369
Middle Eastern	0.000381	0.000381
South Asian	0.000392	0.000392
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. {ECO:0000269|PubMed:16549767}.
• 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);Glutathione metabolism;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metapathway biotransformation Phase I and II;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biological oxidations;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.921
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.276
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.652

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gstm7

Gene ontology

• Biological process: glutathione metabolic process;regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum;regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion;regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion;nitrobenzene metabolic process;xenobiotic catabolic process;linoleic acid metabolic process;relaxation of cardiac muscle;negative regulation of ryanodine-sensitive calcium-release channel activity;positive regulation of ryanodine-sensitive calcium-release channel activity;cellular detoxification of nitrogen compound;cellular response to caffeine;cellular oxidant detoxification;glutathione derivative biosynthetic process
• Cellular component: cytoplasm;cytosol;sarcoplasmic reticulum;intercellular bridge;extracellular exosome
• Molecular function: glutathione transferase activity;glutathione peroxidase activity;signaling receptor binding;protein binding;enzyme binding;protein homodimerization activity;glutathione binding