GSTA4

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

Basic information

Region (hg38): 6:52977948-52995304

Links

ENSG00000170899 ∙ NCBI:2941 ∙ OMIM:605450 ∙ HGNC:4629 ∙ Uniprot:O15217 ∙ 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 GSTA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTA4 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in GSTA4

This is a list of pathogenic ClinVar variants found in the GSTA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-52978512-A-C		not specified	Uncertain significance (May 08, 2024)
6-52978550-A-C		not specified	Uncertain significance (Dec 08, 2023)
6-52978570-T-C		not specified	Uncertain significance (Feb 16, 2023)
6-52982678-G-C		not specified	Uncertain significance (Mar 30, 2024)
6-52982687-G-T		not specified	Uncertain significance (Dec 19, 2023)
6-52984479-A-C		not specified	Uncertain significance (Apr 01, 2024)
6-52984497-C-A		not specified	Uncertain significance (Dec 17, 2023)
6-52984544-A-G			Benign (Dec 03, 2018)
6-52984555-A-G		not specified	Uncertain significance (Feb 07, 2023)
6-52984592-C-T		not specified	Uncertain significance (May 13, 2022)
6-52985542-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-52985543-A-C		not specified	Uncertain significance (Jan 09, 2024)
6-52987360-C-T		not specified	Uncertain significance (Oct 26, 2022)
6-52987378-G-C		not specified	Uncertain significance (Nov 21, 2023)
6-52994200-C-T		not specified	Uncertain significance (Mar 18, 2024)
6-52994220-G-C		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTA4	protein_coding	protein_coding	ENST00000370963	6	17426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0110	0.952	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	110	118	0.931	0.00000561	1466
Missense in Polyphen		38	43.475	0.87406		569
Synonymous	-1.15	55	45.2	1.22	0.00000240	411
Loss of Function	1.81	5	11.7	0.429	5.80e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000245
Ashkenazi Jewish	0.00263	0.00258
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000242	0.000229
Other	0.000340	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. This isozyme has a high catalytic efficiency with 4-hydroxyalkenals such as 4- hydroxynonenal (4-HNE). {ECO:0000269|PubMed:10329152, ECO:0000269|PubMed:20085333}.
• 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;4-hydroxy-2-nonenal detoxification (Consensus)

Recessive Scores

• pRec: 0.209

Intolerance Scores

• loftool: 0.736
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.218
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

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;xenobiotic metabolic process;glutathione derivative biosynthetic process
• Cellular component: cytosol
• Molecular function: glutathione transferase activity;protein binding;identical protein binding;protein homodimerization activity