GPX7

glutathione peroxidase 7

Basic information

Region (hg38): 1:52602371-52609051

Links

ENSG00000116157

∙ NCBI:2882 ∙ OMIM:615784 ∙ HGNC:4559 ∙ Uniprot:Q96SL4 ∙ 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 GPX7 gene.

not_specified (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPX7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015696.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			17 clinvar	1 clinvar		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPX7	protein_coding	protein_coding	ENST00000361314	3	6680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000585	0.461	125605	1	142	125748	0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.184	96	101	0.949	0.00000555	1195
Missense in Polyphen		35	39.383	0.88871		470
Synonymous	0.840	37	44.1	0.839	0.00000252	373
Loss of Function	0.580	9	11.1	0.812	8.32e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000325
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000217	0.000217
South Asian	0.00363	0.00360
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: It protects esophageal epithelia from hydrogen peroxide- induced oxidative stress. It suppresses acidic bile acid-induced reactive oxigen species (ROS) and protects against oxidative DNA damage and double-strand breaks. {ECO:0000269|PubMed:22157330}.;
Pathway: Thyroid hormone synthesis - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);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)

Recessive Scores

pRec: 0.191

Intolerance Scores

loftool: 0.781
rvis_EVS: -0.05
rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

pHI: 0.133
hipred: N
hipred_score: 0.197
ghis: 0.543

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.949

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gpx7
Phenotype: cellular 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); neoplasm; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; liver/biliary system phenotype; 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;

Gene ontology

Biological process: cellular response to oxidative stress;oxidation-reduction process;cellular oxidant detoxification
Cellular component: extracellular region;endoplasmic reticulum;endoplasmic reticulum lumen
Molecular function: catalase activity;peroxidase activity;glutathione peroxidase activity;protein binding