GPX8

glutathione peroxidase 8 (putative)

Basic information

Region (hg38): 5:55160166-55167297

Links

ENSG00000164294 ∙ NCBI:493869 ∙ OMIM:617172 ∙ HGNC:33100 ∙ Uniprot:Q8TED1 ∙ 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 GPX8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX8 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			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	1

Variants in GPX8

This is a list of pathogenic ClinVar variants found in the GPX8 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-55160284-C-T		not specified	Likely benign (May 12, 2024)
5-55160289-T-C		not specified	Uncertain significance (Sep 27, 2021)
5-55160359-A-G		not specified	Uncertain significance (Feb 22, 2023)
5-55161011-C-G		not specified	Uncertain significance (Apr 07, 2022)
5-55161058-A-G		not specified	Uncertain significance (Jan 09, 2024)
5-55161140-C-T			Benign (Jan 30, 2018)
5-55161154-T-C		not specified	Uncertain significance (Jun 21, 2023)
5-55161160-C-G		not specified	Uncertain significance (Dec 05, 2022)
5-55161203-C-G		not specified	Uncertain significance (Jul 06, 2021)
5-55164093-T-G		not specified	Uncertain significance (Jun 13, 2023)
5-55164193-T-G		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX8	protein_coding	protein_coding	ENST00000503787	3	6954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0531	0.871	125710	0	32	125742	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.615	84	101	0.828	0.00000432	1350
Missense in Polyphen		28	35.789	0.78237		499
Synonymous	0.252	37	39.0	0.949	0.00000169	410
Loss of Function	1.47	3	7.30	0.411	3.03e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000184	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Detoxification of Reactive Oxygen Species;glutathione redox reactions I;Cellular responses to stress;Cellular responses to external stimuli;reactive oxygen species degradation (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.792
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.303
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpx8
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: cellular response to oxidative stress;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: endoplasmic reticulum lumen;integral component of membrane
• Molecular function: peroxidase activity;glutathione peroxidase activity