GPX3

glutathione peroxidase 3, the group of Selenoproteins

Basic information

Region (hg38): 5:151020590-151028988

Links

ENSG00000211445 ∙ NCBI:2878 ∙ OMIM:138321 ∙ HGNC:4555 ∙ Uniprot:P22352 ∙ 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 GPX3 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX3 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in GPX3

This is a list of pathogenic ClinVar variants found in the GPX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151020674-C-A		not specified	Uncertain significance (Sep 16, 2021)
5-151020674-C-G		not specified	Uncertain significance (Jun 30, 2022)
5-151020710-T-A		not specified	Uncertain significance (Dec 06, 2022)
5-151020734-A-T		not specified	Uncertain significance (Jun 30, 2022)
5-151025420-C-A		not specified	Uncertain significance (Sep 14, 2023)
5-151025455-A-G		not specified	Uncertain significance (Dec 27, 2022)
5-151026942-T-A		not specified	Uncertain significance (Apr 28, 2023)
5-151027464-A-G		not specified	Uncertain significance (May 18, 2022)
5-151027476-T-G		not specified	Uncertain significance (Oct 13, 2021)
5-151027952-G-A		not specified	Uncertain significance (Feb 03, 2022)
5-151027987-C-T		not specified	Uncertain significance (May 03, 2023)
5-151028072-A-G		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX3	protein_coding	protein_coding	ENST00000388825	5	8431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0510	0.930	124822	0	41	124863	0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.566	114	132	0.862	0.00000747	1464
Missense in Polyphen		58	62.709	0.9249		686
Synonymous	-0.150	57	55.6	1.03	0.00000332	451
Loss of Function	2.04	4	11.4	0.350	5.72e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000425	0.000425
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.
• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Glutathione metabolism;Selenium Micronutrient Network;Folate Metabolism;Selenium Metabolism and Selenoproteins;Nuclear Receptors Meta-Pathway;NRF2 pathway;One carbon metabolism and related pathways;Oxidative Stress;Metapathway biotransformation Phase I and II;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)

Intolerance Scores

• loftool: 0.640
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.208
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx3
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to lipid hydroperoxide;cellular response to oxidative stress;hydrogen peroxide catabolic process;protein homotetramerization;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular region;extracellular space;extracellular exosome
• Molecular function: peroxidase activity;glutathione peroxidase activity;protein binding;transcription factor binding;selenium binding