GSTA1

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

Basic information

Region (hg38): 6:52791370-52803860

Links

ENSG00000243955 ∙ NCBI:2938 ∙ OMIM:138359 ∙ HGNC:4626 ∙ Uniprot:P08263 ∙ 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 GSTA1 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTA1 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			7			7
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	7	1	1

Variants in GSTA1

This is a list of pathogenic ClinVar variants found in the GSTA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-52791940-T-C		not specified	Uncertain significance (Oct 05, 2023)
6-52792957-C-T		not specified	Uncertain significance (Jul 06, 2021)
6-52794144-T-C		not specified	Uncertain significance (Jan 17, 2024)
6-52794148-G-A		not specified	Uncertain significance (May 18, 2023)
6-52794233-C-A		not specified	Uncertain significance (Oct 12, 2022)
6-52794234-A-G		not specified	Uncertain significance (Dec 27, 2023)
6-52794240-G-T		not specified	Uncertain significance (Jan 04, 2024)
6-52794256-A-G		not specified	Uncertain significance (Jun 29, 2023)
6-52796178-G-A			Benign (Jul 17, 2018)
6-52796249-T-C		not specified	Uncertain significance (Nov 30, 2021)
6-52796280-A-C			Likely benign (Apr 06, 2018)
6-52799213-T-C		not specified	Uncertain significance (May 23, 2023)
6-52799231-G-A		not specified	Uncertain significance (Dec 28, 2022)
6-52799253-G-A			Benign (Jul 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTA1	protein_coding	protein_coding	ENST00000334575	6	12247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000173	0.257	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.60	167	118	1.41	0.00000591	1466
Missense in Polyphen		52	36.03	1.4433		511
Synonymous	-2.39	61	41.4	1.47	0.00000205	402
Loss of Function	0.119	9	9.39	0.958	3.92e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000197	0.000196
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. {ECO:0000269|PubMed:20606271}.
• 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;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Glutathione metabolism;Nuclear Receptors Meta-Pathway;NRF2 pathway;Estrogen metabolism;Glutathione conjugation;Phase II - Conjugation of compounds;glutathione-mediated detoxification;Biological oxidations;Metabolism;4-hydroxy-2-nonenal detoxification (Consensus)

Intolerance Scores

• loftool: 0.890
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.0566
• hipred: N
• hipred_score: 0.112
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Gene ontology

• Biological process: glutathione metabolic process;epithelial cell differentiation;linoleic acid metabolic process;cellular oxidant detoxification;glutathione derivative biosynthetic process
• Cellular component: cytosol;extracellular exosome
• Molecular function: glutathione transferase activity;glutathione peroxidase activity