GPX5

glutathione peroxidase 5

Basic information

Region (hg38): 6:28525880-28534955

Links

ENSG00000224586 ∙ NCBI:2880 ∙ OMIM:603435 ∙ HGNC:4557 ∙ Uniprot:O75715 ∙ 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 GPX5 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX5 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			8			8
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	0	0

Variants in GPX5

This is a list of pathogenic ClinVar variants found in the GPX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28526031-G-C		not specified	Uncertain significance (Jul 21, 2021)
6-28526041-C-T			Uncertain significance (-)
6-28529457-T-G		not specified	Uncertain significance (Jul 27, 2022)
6-28529571-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-28529580-T-C		not specified	Uncertain significance (Feb 23, 2023)
6-28529583-G-T		not specified	Uncertain significance (Oct 14, 2023)
6-28529599-A-C		not specified	Uncertain significance (Sep 13, 2023)
6-28531810-T-G		not specified	Uncertain significance (Mar 07, 2024)
6-28531811-A-G		not specified	Uncertain significance (Jan 30, 2024)
6-28531880-T-A		not specified	Uncertain significance (Jun 11, 2021)
6-28532328-C-T		not specified	Uncertain significance (Feb 02, 2022)
6-28532406-T-C		not specified	Uncertain significance (Dec 07, 2023)
6-28533967-T-C		not specified	Uncertain significance (Jan 19, 2024)
6-28533982-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-28534102-C-T		not specified	Uncertain significance (Apr 14, 2022)
6-28534139-C-A		not specified	Likely benign (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX5	protein_coding	protein_coding	ENST00000412168	5	9028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000552	0.720	125682	0	55	125737	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.245	109	116	0.936	0.00000603	1454
Missense in Polyphen		36	38.03	0.94663		503
Synonymous	-0.214	48	46.1	1.04	0.00000261	411
Loss of Function	0.882	6	8.83	0.680	3.70e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00191	0.00190
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00191	0.00190
South Asian	0.000185	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protects cells and enzymes from oxidative damage, by catalyzing the reduction of hydrogen peroxide, lipid peroxides and organic hydroperoxide, by glutathione. May constitute a glutathione peroxidase-like protective system against peroxide damage in sperm membrane lipids.
• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);One carbon metabolism and related pathways;Detoxification of Reactive Oxygen Species;glutathione redox reactions I;Cellular responses to stress;Linoleate metabolism;Cellular responses to external stimuli;reactive oxygen species degradation;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.745
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.66

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.296
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx5
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: lipid metabolic process;cellular response to oxidative stress;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular region
• Molecular function: peroxidase activity;glutathione peroxidase activity