PGS1

Chr 17

phosphatidylglycerophosphate synthase 1

NCBI Gene: 9489ENSG00000087157UniProt: Q32NB8

Predicted to enable CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity and calcium ion binding activity. Predicted to be involved in cardiolipin biosynthetic process and diacylglycerol metabolic process. Located in endoplasmic reticulum. Is active in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
0
Pathogenic / LP
0
ClinVar variants
1
Pubs (1 yr)
1.5
Missense Z
1.13
LOEUF
Clinical Summary— PGS1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.13LOEUF
pLI 0.000
Z-score 1.04
OE 0.78 (0.55–1.13)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.50Z-score
OE missense 0.77 (0.69–0.85)
254 obs / 330.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.78 (0.55–1.13)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.77 (0.69–0.85)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.07
0≤1.21.6
LoF obs/exp: 20 / 25.7Missense obs/exp: 254 / 330.7Syn Z: -0.67
DN
0.6454th %ile
GOF
0.6541th %ile
LOF
0.3454th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PGS1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Ethanol extract of Ardisiae Japonicae Herba inhibits hepatoma carcinoma cell proliferation in vitro through regulating lipid metabolism
Gong X et al.·Chin Herb Med
2021
Diagnosis and treatment of pediatric anaplastic lymphoma kinase-positive large B-cell lymphoma: A case report
Zhang M et al.·World J Clin Cases
2021Case report
New insights into the role of mitochondrial metabolic dysregulation and immune infiltration in septic cardiomyopathy by integrated bioinformatics analysis and experimental validation
Li Y et al.·Cell Mol Biol Lett
2024
Analysis of mRNA-lncRNA and mRNA-lncRNA-pathway co-expression networks based on WGCNA in developing pediatric sepsis
Zhang X et al.·Bioengineered
2021
Identification of immune-related mitochondrial metabolic disorder genes in septic shock using bioinformatics and machine learning.
Cui YH et al.·Hereditas
2024
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
A review of disorders of cardiolipin metabolism: Pathophysiology, clinical presentation and future directions.
Carney OS et al.·Mol Genet Metab
2025Review
High-throughput screening identifies suppressors of mitochondrial fragmentation in OPA1 fibroblasts.
Cretin E et al.·EMBO Mol Med
2021
Whole-Exome Sequencing in Papillary Microcarcinoma: Potential Early Biomarkers of Lateral Lymph Node Metastasis.
Kim M et al.·Endocrinol Metab (Seoul)
2021
Diagnostic model based on bioinformatics and machine learning to distinguish Kawasaki disease using multiple datasets.
Zhang M et al.·BMC Pediatr
2022Functional
Comparison of PGS2.0 versus conventional embryo morphology evaluation for patients with recurrent pregnancy loss: a study protocol for a multicentre randomised trial.
Lei C et al.·BMJ Open
2020Clinical trial
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals.
Guo X et al.·Plant Biotechnol J
2022Open Access
Characterisation of PGs1, a subunit of a protein complex co-purifying with tubulin polyglutamylase.
Regnard C et al.·J Cell Sci
2003
Regulation of phosphatidylglycerophosphate synthase by inositol in Saccharomyces cerevisiae is not at the level of PGS1 mRNA abundance.
Zhong Q et al.·J Biol Chem
2003
Phosphatidylglycerolphosphate synthase encoded by the PEL1/PGS1 gene in Saccharomyces cerevisiae is localized in mitochondria and its expression is regulated by phospholipid precursors.
Dzugasová V et al.·Curr Genet
1998
The PEL1 gene (renamed PGS1) encodes the phosphatidylglycero-phosphate synthase of Saccharomyces cerevisiae.
Chang SC et al.·J Biol Chem
1998
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients