GPX4

Chr 19AR

glutathione peroxidase 4

Also known as: GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx, snPHGPx

The protein encoded by this gene belongs to the glutathione peroxidase family, members of which catalyze the reduction of hydrogen peroxide, organic hydroperoxides and lipid hydroperoxides, and thereby protect cells against oxidative damage. Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. This isozyme has a high preference for lipid hydroperoxides and protects cells against membrane lipid peroxidation and cell death. It is also required for normal sperm development; thus, it has been identified as a 'moonlighting' protein because of its ability to serve dual functions as a peroxidase, as well as a structural protein in mature spermatozoa. Mutations in this gene are associated with Sedaghatian type of spondylometaphyseal dysplasia (SMDS). This isozyme 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. Transcript variants resulting from alternative splicing or use of alternate promoters have been described to encode isoforms with different subcellular localization. [provided by RefSeq, Dec 2018]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Spondylometaphyseal dysplasia, Sedaghatian typeMIM #250220
AR

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
4
Active trials
5022
Pubs (1 yr)
P/LP submissions
P/LP missense
1.28
LOEUF
LOF
Mechanism· G2P

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
1.28LOEUF
pLI 0.000
Z-score 0.91
OE 0.71 (0.411.28)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-1.08Z-score
OE missense 1.27 (1.121.45)
159 obs / 125.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.71 (0.411.28)
00.351.4
Missense OE?1.27 (1.121.45)
00.61.4
Synonymous OE?1.59
01.21.6
LoF obs/exp: 8 / 11.3Missense obs/exp: 159 / 125.2Syn Z: -3.47

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

GPX4 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.