GSTM4

glutathione S-transferase mu 4, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 1:109656098-109665496

Links

ENSG00000168765 ∙ NCBI:2948 ∙ OMIM:138333 ∙ HGNC:4636 ∙ Uniprot:Q03013 ∙ 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 GSTM4 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTM4 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			9			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	9	0	0

Variants in GSTM4

This is a list of pathogenic ClinVar variants found in the GSTM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109656399-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-109657657-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-109657794-G-T		not specified	Uncertain significance (Mar 27, 2023)
1-109657850-G-C		not specified	Uncertain significance (Jan 24, 2023)
1-109657855-T-G		not specified	Uncertain significance (Apr 27, 2022)
1-109657861-A-C		not specified	Uncertain significance (May 11, 2022)
1-109658821-T-G		not specified	Uncertain significance (Jun 11, 2021)
1-109658853-A-G		not specified	Uncertain significance (Jul 17, 2023)
1-109658902-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-109659072-G-T		not specified	Uncertain significance (Aug 28, 2023)
1-109659102-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-109661254-A-G			Likely benign (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTM4	protein_coding	protein_coding	ENST00000369836	8	9416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-8	0.115	125194	2	552	125748	0.00221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.133	117	121	0.966	0.00000705	1446
Missense in Polyphen		30	30.128	0.99575		378
Synonymous	-1.65	59	44.9	1.31	0.00000268	381
Loss of Function	-0.0355	12	11.9	1.01	5.15e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00413	0.00414
Ashkenazi Jewish	0.00278	0.00278
East Asian	0.00147	0.00147
Finnish	0.00115	0.00116
European (Non-Finnish)	0.00310	0.00309
Middle Eastern	0.00147	0.00147
South Asian	0.000915	0.000915
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Active on 1- chloro-2,4-dinitrobenzene.
• 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);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metapathway biotransformation Phase I and II;Glutathione conjugation;Metabolism of lipids;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biosynthesis of DHA-derived sulfido conjugates;Biological oxidations;Metabolism;Biosynthesis of maresin conjugates in tissue regeneration (MCTR);Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0957

Intolerance Scores

• loftool: 0.971
• rvis_EVS: 1.28
• rvis_percentile_EVS: 93.71

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.206

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gstm4
• Phenotype: immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: glutathione metabolic process;nitrobenzene metabolic process;xenobiotic catabolic process;long-chain fatty acid biosynthetic process;glutathione derivative biosynthetic process
• Cellular component: cytoplasm;cytosol;intercellular bridge
• Molecular function: glutathione transferase activity;protein binding;enzyme binding;protein homodimerization activity;glutathione binding