GPX1

glutathione peroxidase 1, the group of Selenoproteins

Basic information

Region (hg38): 3:49357173-49358605

Links

ENSG00000233276 ∙ NCBI:2876 ∙ OMIM:138320 ∙ HGNC:4553 ∙ Uniprot:P07203 ∙ 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 GPX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX1 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			28		3	31
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1		2	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	30	0	7

Variants in GPX1

This is a list of pathogenic ClinVar variants found in the GPX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49357401-G-A		GLUTATHIONE PEROXIDASE POLYMORPHISM • Gluthathione peroxidase deficiency	Benign (Aug 16, 2021)
3-49357408-G-A		Gluthathione peroxidase deficiency	Uncertain significance (Oct 17, 2023)
3-49357420-C-T		GPX1-related disorder	Benign (Nov 25, 2019)
3-49357428-T-A		not specified	Uncertain significance (Jul 12, 2023)
3-49357432-G-A		Gluthathione peroxidase deficiency • not specified	Uncertain significance (Jun 03, 2022)
3-49357436-G-C		Gluthathione peroxidase deficiency	Uncertain significance (Mar 10, 2022)
3-49357489-G-A		Gluthathione peroxidase deficiency	Uncertain significance (Jul 31, 2023)
3-49357561-G-A		Gluthathione peroxidase deficiency	Uncertain significance (Jun 27, 2023)
3-49357582-C-A		not specified	Uncertain significance (Aug 26, 2022)
3-49357588-C-T		Gluthathione peroxidase deficiency	Uncertain significance (May 24, 2023)
3-49357605-G-A		Gluthathione peroxidase deficiency • not specified	Uncertain significance (Nov 13, 2023)
3-49357627-G-A		not specified	Uncertain significance (May 07, 2024)
3-49357638-C-G		Gluthathione peroxidase deficiency	Uncertain significance (Sep 08, 2021)
3-49357663-C-G		not specified	Uncertain significance (Mar 20, 2024)
3-49357669-G-A		not specified	Uncertain significance (Dec 30, 2023)
3-49357698-G-C		Gluthathione peroxidase deficiency	Uncertain significance (Aug 08, 2022)
3-49357714-G-A		not specified	Uncertain significance (Jan 07, 2022)
3-49357738-T-G		not specified	Uncertain significance (Dec 05, 2022)
3-49357741-C-G		not specified	Uncertain significance (Apr 08, 2022)
3-49358048-C-A			Benign (May 31, 2018)
3-49358051-G-T		Gluthathione peroxidase deficiency	Uncertain significance (Mar 10, 2022)
3-49358056-C-A		Gluthathione peroxidase deficiency	Uncertain significance (May 30, 2023)
3-49358115-T-C		Gluthathione peroxidase deficiency	Uncertain significance (Oct 31, 2022)
3-49358139-G-A		not specified	Uncertain significance (Jun 10, 2022)
3-49358154-A-G		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX1	protein_coding	protein_coding	ENST00000419783	2	1425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000385	0.227	124741	0	22	124763	0.0000882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.298	135	126	1.07	0.00000621	1289
Missense in Polyphen		43	40.123	1.0717		473
Synonymous	-1.53	73	58.1	1.26	0.00000304	450
Loss of Function	-0.512	6	4.79	1.25	2.05e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000321	0.000316
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.000143	0.000139
European (Non-Finnish)	0.0000824	0.0000795
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.000516	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protects the hemoglobin in erythrocytes from oxidative breakdown.
• Pathway: Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Doxorubicin Pathway, Pharmacokinetics;Oxidative Stress Pathway (Erythrocyte);Pathway_PA165980337;Oxidative Stress Pathway (Erythrocyte);Oxidative Stress Regulatory Pathway (Erythrocyte);Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Gamma-glutamyl-transpeptidase deficiency;5-oxoprolinase deficiency;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Gamma-Glutamyltransferase Deficiency;Glutathione Metabolism;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Glutathione Synthetase Deficiency;5-Oxoprolinuria;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;Glutathione metabolism;Selenium Micronutrient Network;Folate Metabolism;Amyotrophic lateral sclerosis (ALS);Selenium Metabolism and Selenoproteins;Association Between Physico-Chemical Features and Toxicity Associated Pathways;One carbon metabolism and related pathways;TYROBP Causal Network;Oxidative Stress;Detoxification of Reactive Oxygen Species;cardiac protection against ros;glutathione redox reactions I;Metabolism of lipids;Nucleobase catabolism;Metabolism of nucleotides;Synthesis of 5-eicosatetraenoic acids;Synthesis of 15-eicosatetraenoic acid derivatives;Synthesis of 12-eicosatetraenoic acid derivatives;Cellular responses to stress;Arachidonic acid metabolism;Metabolism;Fatty acid metabolism;Linoleate metabolism;Cellular responses to external stimuli;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Direct p53 effectors;Purine catabolism;reactive oxygen species degradation;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.717
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.336
• hipred: N
• hipred_score: 0.272
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; vision/eye phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; 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); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: temperature homeostasis;endothelial cell development;negative regulation of inflammatory response to antigenic stimulus;purine nucleotide catabolic process;triglyceride metabolic process;glutathione metabolic process;sensory perception of sound;intrinsic apoptotic signaling pathway in response to oxidative stress;response to xenobiotic stimulus;response to symbiotic bacterium;UV protection;response to selenium ion;response to gamma radiation;protein oxidation;lipoxygenase pathway;response to hydroperoxide;regulation of mammary gland epithelial cell proliferation;cellular response to oxidative stress;regulation of gene expression, epigenetic;vasodilation;response to hydrogen peroxide;hydrogen peroxide catabolic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;skeletal muscle tissue regeneration;regulation of neuron apoptotic process;blood vessel endothelial cell migration;fat cell differentiation;cell redox homeostasis;skeletal muscle fiber development;myoblast proliferation;interaction with symbiont;positive regulation of protein kinase B signaling;heart contraction;angiogenesis involved in wound healing;regulation of proteasomal protein catabolic process;negative regulation of release of cytochrome c from mitochondria;cellular oxidant detoxification;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway;positive regulation of supramolecular fiber organization
• Cellular component: cytoplasm;mitochondrion;mitochondrial matrix;cytosol;Lewy body
• Molecular function: peroxidase activity;glutathione peroxidase activity;SH3 domain binding