GPX2

glutathione peroxidase 2, the group of Selenoproteins

Basic information

Region (hg38): 14:64939152-64942746

Links

ENSG00000176153 ∙ NCBI:2877 ∙ OMIM:138319 ∙ HGNC:4554 ∙ Uniprot:P18283 ∙ 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 GPX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in GPX2

This is a list of pathogenic ClinVar variants found in the GPX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-64939510-C-A		not specified	Uncertain significance (Sep 22, 2022)
14-64939549-C-T		not specified	Uncertain significance (Jan 30, 2024)
14-64939622-G-A		not specified	Uncertain significance (Jun 29, 2023)
14-64939648-T-C		not specified	Uncertain significance (Apr 04, 2024)
14-64939726-T-A		not specified	Uncertain significance (Nov 21, 2023)
14-64939727-C-T		not specified	Uncertain significance (Sep 20, 2023)
14-64942560-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-64942593-C-T		not specified	Uncertain significance (Jan 17, 2023)
14-64942636-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-64942653-G-A		not specified	Uncertain significance (Jan 19, 2024)
14-64942653-G-T		not specified	Uncertain significance (Dec 12, 2023)
14-64942696-G-A		not specified	Uncertain significance (Feb 06, 2023)
14-64942716-A-G		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX2	protein_coding	protein_coding	ENST00000389614	2	3662

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000150	0.443	124759	0	36	124795	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.212	110	116	0.945	0.00000745	1253
Missense in Polyphen		40	40.288	0.99286		446
Synonymous	-0.261	48	45.8	1.05	0.00000274	381
Loss of Function	0.231	6	6.64	0.903	3.71e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000216
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000168
Middle Eastern	0.000334	0.000334
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could play a major role in protecting mammals from the toxicity of ingested organic hydroperoxides. Tert-butyl hydroperoxide, cumene hydroperoxide and linoleic acid hydroperoxide but not phosphatidycholine hydroperoxide, can act as acceptors.
• 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;Metapathway biotransformation Phase I and II;Detoxification of Reactive Oxygen Species;Gene expression (Transcription);glutathione redox reactions I;Generic Transcription Pathway;Metabolism of lipids;Synthesis of 5-eicosatetraenoic acids;Synthesis of 15-eicosatetraenoic acid derivatives;Synthesis of 12-eicosatetraenoic acid derivatives;Cellular responses to stress;Arachidonic acid metabolism;RNA Polymerase II Transcription;Metabolism;Fatty acid metabolism;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Validated transcriptional targets of TAp63 isoforms;Transcriptional Regulation by TP53;reactive oxygen species degradation;Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Intolerance Scores

• loftool: 0.661
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.231
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism 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); immune system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: electron transport chain;cellular response to oxidative stress;cellular oxidant detoxification
• Cellular component: cytoplasm;cytosol
• Molecular function: peroxidase activity;glutathione peroxidase activity;electron transfer activity