GPX6

glutathione peroxidase 6, the group of Selenoproteins

Basic information

Region (hg38): 6:28503295-28528215

Previous symbols: [ "GPXP3" ]

Links

ENSG00000198704 ∙ NCBI:257202 ∙ OMIM:607913 ∙ HGNC:4558 ∙ Uniprot:P59796 ∙ 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 GPX6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX6 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			9		2	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	9	0	2

Variants in GPX6

This is a list of pathogenic ClinVar variants found in the GPX6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28504375-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-28504387-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-28504476-T-C			Benign (Dec 31, 2019)
6-28504483-T-A		not specified	Uncertain significance (Jan 24, 2024)
6-28505767-A-G		not specified	Uncertain significance (Jun 16, 2024)
6-28510759-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-28510780-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-28510835-A-G			Benign (Jun 27, 2018)
6-28510853-T-C		not specified	Uncertain significance (Nov 30, 2022)
6-28510858-G-T		not specified	Uncertain significance (Aug 30, 2021)
6-28515697-A-G		not specified	Uncertain significance (Mar 28, 2023)
6-28515727-T-A		not specified	Uncertain significance (Nov 18, 2023)
6-28526031-G-C		not specified	Uncertain significance (Jul 21, 2021)
6-28526041-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX6	protein_coding	protein_coding	ENST00000361902	5	24920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000258	0.315	125020	0	17	125037	0.0000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.474	100	114	0.875	0.00000549	1452
Missense in Polyphen		22	33.05	0.66566		461
Synonymous	2.10	29	47.4	0.612	0.00000257	412
Loss of Function	0.271	9	9.92	0.907	4.18e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000165
Finnish	0.0000928	0.0000926
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000167	0.000165
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Selenium Micronutrient Network;Folate Metabolism;Selenium Metabolism and Selenoproteins;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)

Intolerance Scores

• loftool: 0.728
• rvis_EVS: 1.77
• rvis_percentile_EVS: 96.79

Haploinsufficiency Scores

• pHI: 0.0563
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx6

Gene ontology

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