GSTM5

glutathione S-transferase mu 5, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 1:109711779-109775428

Links

ENSG00000134201 ∙ NCBI:2949 ∙ OMIM:138385 ∙ HGNC:4637 ∙ Uniprot:P46439 ∙ 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 GSTM5 gene.

• Inborn genetic diseases (8 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTM5 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
missense			8	1	3	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	4

Variants in GSTM5

This is a list of pathogenic ClinVar variants found in the GSTM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109712621-G-A		not specified	Uncertain significance (May 25, 2022)
1-109713157-T-G		not specified	Uncertain significance (Dec 28, 2022)
1-109713162-G-C		not specified	Uncertain significance (Jan 09, 2024)
1-109713540-C-G			Benign (Apr 26, 2018)
1-109713679-A-G		not specified	Uncertain significance (Nov 03, 2022)
1-109713720-A-G		not specified	Uncertain significance (May 10, 2023)
1-109715016-A-C		not specified	Uncertain significance (Oct 25, 2022)
1-109715019-C-T			Benign (May 25, 2018)
1-109715023-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-109715037-G-A		not specified	Uncertain significance (Feb 17, 2024)
1-109715176-G-A		not specified	Uncertain significance (May 13, 2022)
1-109715192-G-C			Benign (Jan 23, 2018)
1-109715203-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-109715232-C-T			Likely benign (Dec 01, 2022)
1-109717344-A-T		not specified	Uncertain significance (Jan 09, 2024)
1-109717373-C-G		not specified	Uncertain significance (Dec 06, 2021)
1-109717418-A-G			Benign (Aug 26, 2017)
1-109737169-C-G		not specified	Uncertain significance (Mar 31, 2023)
1-109737469-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-109737702-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-109737748-T-G		not specified	Uncertain significance (Jan 31, 2024)
1-109738119-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-109738303-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-109738312-G-A		not specified	Uncertain significance (Jan 25, 2023)
1-109739834-T-A		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTM5	protein_coding	protein_coding	ENST00000256593	8	63187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-7	0.203	125640	0	108	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.944	148	119	1.24	0.00000684	1438
Missense in Polyphen		31	32.226	0.96195		419
Synonymous	0.128	42	43.1	0.975	0.00000221	378
Loss of Function	0.188	11	11.7	0.941	5.09e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000290	0.000290
Middle Eastern	0.000164	0.000163
South Asian	0.00124	0.00124
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. {ECO:0000269|PubMed:10587441}.
• 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;Biological oxidations;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.863
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.44

Haploinsufficiency Scores

• pHI: 0.0439
• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gstm1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: glutathione metabolic process;glutathione derivative biosynthetic process
• Cellular component: cytosol;intercellular bridge
• Molecular function: glutathione transferase activity;protein binding;identical protein binding