GSTM1

glutathione S-transferase mu 1, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 1:109687814-109709039

Previous symbols: [ "GST1" ]

Links

ENSG00000134184 ∙ NCBI:2944 ∙ OMIM:138350 ∙ HGNC:4632 ∙ Uniprot:P09488 ∙ 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 GSTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTM1 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			3	3	3	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	3	3

Variants in GSTM1

This is a list of pathogenic ClinVar variants found in the GSTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109687893-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
GSTM1	protein_coding	protein_coding	ENST00000309851	8	21226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00206	0.921	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	72	118	0.608	0.00000630	1435
Missense in Polyphen		12	32.499	0.36925		402
Synonymous	2.37	22	41.4	0.532	0.00000207	363
Loss of Function	1.54	6	11.7	0.513	4.91e-7	158

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. {ECO:0000269|PubMed:16548513}.
• 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;Platinum Pathway, Pharmacokinetics/Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Cyclophosphamide Action Pathway;Cyclophosphamide Metabolism Pathway;Glutathione metabolism;Nuclear Receptors Meta-Pathway;NRF2 pathway;Benzene metabolism;Estrogen metabolism;Aflatoxin B1 metabolism;Metapathway biotransformation Phase I and II;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biological oxidations;Metabolism;C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.489

Intolerance Scores

• loftool: 0.686
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.84

Haploinsufficiency Scores

• pHI: 0.0308
• hipred: N
• hipred_score: 0.373

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gstm2

Gene ontology

• Biological process: glutathione metabolic process;nitrobenzene metabolic process;xenobiotic catabolic process;cellular detoxification of nitrogen compound;glutathione derivative biosynthetic process
• Cellular component: cytoplasm;cytosol;intercellular bridge
• Molecular function: glutathione transferase activity;enzyme binding;protein homodimerization activity;glutathione binding