GPX1

protein-coding

glutathione peroxidase 1, the group of Selenoproteins

Gene summary

The protein encoded by this gene belongs to the glutathione peroxidase family, members of which catalyze the reduction of organic hydroperoxides and hydrogen peroxide (H2O2) by glutathione, and thereby protect cells against oxidative damage. Other studies indicate that H2O2 is also essential for growth-factor mediated signal transduction, mitochondrial function, and maintenance of thiol redox-balance; therefore, by limiting H2O2 accumulation, glutathione peroxidases are also involved in modulating these processes. Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. This isozyme is the most abundant, is ubiquitously expressed and localized in the cytoplasm, and whose preferred substrate is hydrogen peroxide. It is also a selenoprotein, containing the rare amino acid selenocysteine (Sec) at its active site. Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. This gene contains an in-frame GCG trinucleotide repeat in the coding region, and three alleles with 4, 5 or 6 repeats have been found in the human population. The allele with 4 GCG repeats has been significantly associated with breast cancer risk in premenopausal women. Alternatively spliced transcript variants have been found for this gene. Pseudogenes of this locus have been identified on chromosomes X and 21. [provided by RefSeq, Aug 2017]

MANE transcript

NM_000581.4

Inheritance

AR

ClinVar variants

U:56B:4

Top phenotype

Gluthathione peroxidase deficiency

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr3:49,357,174-49,358,605

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~1.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

gluthathione peroxidase deficiencyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0013601

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPX1 variants in ClinVar

4 Conditions Cataloged
Gluthathione peroxidase deficiencyTotal: 29
not specifiedTotal: 29
GPX1-related disorderTotal: 4
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000581.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
52
clinvar
2
clinvar
54
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00561360
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000581.4RefSeqNP_000572.22MANE Select
ENST00000419783.3EnsemblENSP00000407375.12MANE Select
NM_001329455.2RefSeqNP_001316384.12Standard
NM_001329502.2RefSeqNP_001316431.12Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Doxorubicin Pathway (Cancer Cell), Pharmacodynamics
  • Thyroid hormone synthesis - Homo sapiens (human)
  • Glutathione metabolism - Homo sapiens (human)
  • Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human)
  • Huntington,s disease - Homo sapiens (human)

Biological Process

  • temperature homeostasis
  • endothelial cell development
  • negative regulation of inflammatory response to antigenic stimulus
  • purine nucleotide catabolic process
  • triglyceride metabolic process

Molecular Function

  • peroxidase activity
  • glutathione peroxidase activity
  • SH3 domain binding

Cellular Component

  • cytoplasm
  • mitochondrion
  • mitochondrial matrix
  • cytosol
  • Lewy body

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000419783
Coding exons
2
Length
1425
Individuals with no LoFs
124741
Homozygous LoFs
0
Heterozygous LoFs
22
Defined
124763
p
0.0000882
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2981351261.070.000006211289
Missense (PolyPhen)4340.1231.0717473
Synonymous-1.537358.11.260.00000304450
Loss of Function-0.51264.791.252.05e-750

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000260.00026rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.0000560.000056rare
Finnish0.000140.00014rare
European (Non-Finnish)0.0000820.000079rare
South Asian00.0absent
Other0.000520.00050rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Protects the hemoglobin in erythrocytes from oxidative breakdown.;

Intolerance Scores

LoFtool
0.717
RVIS EVS
0.24
RVIS percentile EVS
68.98

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.983

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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