PGS1

gene
On this page

Also known as DKFZP762M186

Summary

PGS1 (phosphatidylglycerophosphate synthase 1, HGNC:30029) is a protein-coding gene on chromosome 17q25.3, encoding CDP-diacylglycerol–glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial (Q32NB8). Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin. It is a selective cancer dependency (DepMap: 86.3% of cell lines).

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.

Source: NCBI Gene 9489 — RefSeq curated summary.

At a glance

  • GWAS associations: 49
  • Clinical variants (ClinVar): 107 total
  • Cancer dependency (DepMap): dependent in 86.3% of screened cell lines
  • MANE Select transcript: NM_024419

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30029
Approved symbolPGS1
Namephosphatidylglycerophosphate synthase 1
Location17q25.3
Locus typegene with protein product
StatusApproved
AliasesDKFZP762M186
Ensembl geneENSG00000087157
Ensembl biotypeprotein_coding
OMIM614942
Entrez9489

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 14 protein_coding, 4 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000262764, ENST00000585521, ENST00000586019, ENST00000586325, ENST00000586355, ENST00000586510, ENST00000586880, ENST00000587356, ENST00000588169, ENST00000588281, ENST00000589425, ENST00000589426, ENST00000589689, ENST00000591996, ENST00000592043, ENST00000890418, ENST00000890419, ENST00000890420, ENST00000890421, ENST00000890422, ENST00000920347, ENST00000920348, ENST00000945009

RefSeq mRNA: 1 — MANE Select: NM_024419 NM_024419

CCDS: CCDS42391

Canonical transcript exons

ENST00000262764 — 10 exons

ExonStartEnd
ENSE000034956677841954678419675
ENSE000035362167839934878399537
ENSE000036129527840067778400855
ENSE000036796637841487978415027
ENSE000036797797840356878404089
ENSE000036958127839630878396385
ENSE000036963027839825278398351
ENSE000036975687837864978378808
ENSE000037009237839247678392665
ENSE000038431977842406178424659

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 95.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.7079 / max 359.7862, expressed in 1812 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16307926.56431812
1631050.143666

Top tissues by expression

273 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017895.19gold quality
right lungUBERON:000216794.04gold quality
upper lobe of left lungUBERON:000895294.01gold quality
spleenUBERON:000210693.04gold quality
upper lobe of lungUBERON:000894893.04gold quality
monocyteCL:000057692.08gold quality
sural nerveUBERON:001548891.75gold quality
mononuclear cellCL:000084291.74gold quality
leukocyteCL:000073891.41gold quality
lymph nodeUBERON:000002991.24gold quality
right lobe of thyroid glandUBERON:000111991.17gold quality
stromal cell of endometriumCL:000225591.09gold quality
granulocyteCL:000009491.01gold quality
left lobe of thyroid glandUBERON:000112090.92gold quality
left uterine tubeUBERON:000130390.89gold quality
omental fat padUBERON:001041490.89gold quality
peritoneumUBERON:000235890.87gold quality
metanephros cortexUBERON:001053390.68gold quality
endocervixUBERON:000045890.65gold quality
body of uterusUBERON:000985390.61gold quality
vermiform appendixUBERON:000115490.45gold quality
thyroid glandUBERON:000204690.33gold quality
lower esophagus muscularis layerUBERON:003583390.30gold quality
lower esophagusUBERON:001347390.27gold quality
adipose tissue of abdominal regionUBERON:000780890.19gold quality
right ovaryUBERON:000211890.03gold quality
caecumUBERON:000115389.95gold quality
gall bladderUBERON:000211089.94gold quality
tibial nerveUBERON:000132389.84gold quality
small intestine Peyer’s patchUBERON:000345489.84gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes15.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting PGS1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4283100.0066.422097
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-806899.9873.852376
HSA-MIR-548AN99.9770.912817
HSA-MIR-205-3P99.9269.923165
HSA-MIR-394199.8670.542735
HSA-MIR-323A-3P99.7970.301739
HSA-MIR-46699.6770.852863
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-467299.5071.582893
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-317199.4969.06776
HSA-MIR-464399.4967.631791
HSA-MIR-132499.4666.571302
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-4722-3P99.3565.221099
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-21-3P99.2168.951312
HSA-MIR-146A-3P99.1368.991881
HSA-MIR-447899.0765.162320
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-181A-2-3P98.9167.601168
HSA-MIR-4716-5P98.8268.571168
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-76098.8166.651392
HSA-MIR-3922-5P98.7766.531059
HSA-MIR-6811-3P98.6266.54944
HSA-MIR-427498.5966.10630
HSA-MIR-425298.4566.37987

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 86.3% of screened cell lines.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopgs1ENSDARG00000075857
mus_musculusPgs1ENSMUSG00000017715
rattus_norvegicusPgs1ENSRNOG00000002949
drosophila_melanogasterPGS1FBGN0038649
caenorhabditis_eleganspgs-1WBGENE00021677

Protein

Protein identifiers

CDP-diacylglycerol–glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrialQ32NB8 (reviewed: Q32NB8)

Alternative names: Phosphatidylglycerophosphate synthase 1

All UniProt accessions (8): Q32NB8, K7EJP6, K7EL44, K7ELT9, K7EPX0, K7EQ89, K7EQF5, U3KQD9

UniProt curated annotations — full annotation on UniProt →

Function. Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin.

Subcellular location. Mitochondrion.

Activity regulation. Activated by calcium and magnesium and inhibited by other bivalent cations.

Pathway. Phospholipid metabolism; phosphatidylglycerol biosynthesis; phosphatidylglycerol from CDP-diacylglycerol: step 1/2.

Similarity. Belongs to the CDP-alcohol phosphatidyltransferase class-II family.

Isoforms (4)

UniProt IDNamesCanonical?
Q32NB8-11yes
Q32NB8-22
Q32NB8-33
Q32NB8-44

RefSeq proteins (1): NP_077733* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001736PLipase_D/transphosphatidylaseDomain
IPR016270PGS1Family

Enzyme classification (BRENDA):

  • EC 2.7.8.5 — CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase (BRENDA: 19 organisms, 23 substrates, 20 inhibitors, 26 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

8 substrates with measured Km, best-characterized 8. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
CDP-DIACYLGLYCEROL0.012–0.2889
GLYCEROL 3-PHOSPHATE0.02–0.176
SN-GLYCEROL 3-PHOSPHATE0.1–0.324
DCDP-DIACYLGLYCEROL0.0342
(D)CDP-DIACYLGLYCEROL0.041
CMP0.191
DL-2-HEXADECOXY-3-OCTADECOXYPROPYLPHOSPHONYL-O-(0.081
DL-3,4-DIOCTADECOXYBUTYLPHOSPHONYL-O-(CYTIDINE 50.061

Catalyzed reactions (Rhea), 1 shown:

  • a CDP-1,2-diacyl-sn-glycerol + sn-glycerol 3-phosphate = a 1,2-diacyl-sn-glycero-3-phospho-(1’-sn-glycero-3’-phosphate) + CMP + H(+) (RHEA:12593)

UniProt features (16 total): splice variant 7, active site 3, domain 2, transit peptide 1, chain 1, binding site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q32NB8-F185.690.73

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 220; 222; 227

Ligand- & substrate-binding residues (1): 124–131

Post-translational modifications (1): 49

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1483148Synthesis of PG

MSigDB gene sets: 186 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLGLYCEROL_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GGAANCGGAANY_UNKNOWN, WCTCNATGGY_UNKNOWN, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_NEUTRAL_LIPID_METABOLIC_PROCESS

GO Biological Process (5): phosphatidylglycerol biosynthetic process (GO:0006655), cardiolipin biosynthetic process (GO:0032049), diacylglycerol metabolic process (GO:0046339), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (6): calcium ion binding (GO:0005509), ATP binding (GO:0005524), CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), transferase activity (GO:0016740)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), endoplasmic reticulum (GO:0005783), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glycerophospholipid biosynthesis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
intracellular membrane-bounded organelle2
phosphatidylglycerol metabolic process1
glycerophospholipid biosynthetic process1
phosphatidylglycerol biosynthetic process1
cardiolipin metabolic process1
acylglycerol metabolic process1
primary metabolic process1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
metal ion binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
CDP-alcohol phosphatidyltransferase activity1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
catalytic activity1
organelle inner membrane1
mitochondrial membrane1
mitochondrion1
intracellular organelle lumen1
endomembrane system1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1446 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PGS1CRLS1Q9UJA2744
PGS1CDS1Q92903713
PGS1TAMM41Q96BW9710
PGS1CDIPTO14735680
PGS1PTPMT1Q8WUK0657
PGS1CDS2O95674642
PGS1CHPT1Q8WUD6613
PGS1TAFAZZINQ16635559
PGS1PEMTQ9UBM1556
PGS1SELENOIQ9C0D9549
PGS1PISDQ9UG56515
PGS1LCLAT1Q6UWP7452
PGS1CEPT1Q9Y6K0446
PGS1PRELID1Q9Y255422
PGS1DHRS7BQ6IAN0389

IntAct

9 interactions, top by confidence:

ABTypeScore
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
IMPDH1BCAT2psi-mi:“MI:0914”(association)0.530
Myh10LMO7psi-mi:“MI:0914”(association)0.350
PFDN5GTPBP10psi-mi:“MI:0914”(association)0.350
H2APGNPATpsi-mi:“MI:0914”(association)0.350
SLC25A25HAX1psi-mi:“MI:0914”(association)0.350
GABARAPPGS1psi-mi:“MI:0915”(physical association)0.000
PGS1PDLIM1psi-mi:“MI:0915”(physical association)0.000

BioGRID (21): PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-RNA), PGS1 (Proximity Label-MS), PGS1 (Proximity Label-MS), PGS1 (Proximity Label-MS), PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-MS), PGS1 (Negative Genetic), PGS1 (Negative Genetic), PGS1 (Negative Genetic), PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-MS), PGS1 (Affinity Capture-MS)

ESM2 similar proteins: A3KGK3, A6H603, A9ULG4, B1H1N7, B5DFG1, B6CZ46, D6MZJ6, E9QAM5, F1QG30, O35049, O60906, O70572, O75064, O95382, O95398, P10937, P70261, Q149M9, Q1LXZ7, Q2KHV9, Q2KJ28, Q32NB8, Q3U1Y4, Q5R8K7, Q5XIL6, Q5ZHN9, Q68DD2, Q6NVG1, Q6ZNJ1, Q6ZPS2, Q6ZQA0, Q76MJ5, Q7TMC8, Q80YU0, Q8BHF7, Q8N0W3, Q91X21, Q95KI5, Q99MQ3, Q9BXM7

Diamond homologs: P25578, P79001, Q2KJ28, Q32NB8, Q5R8K7, Q5ZHN9, Q7KWX2, Q8BHF7, Q9HDW1, Q9Z2Z7

SIGNOR signaling

2 interactions.

AEffectBMechanism
PGS1up-regulates“1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate(3-)”“chemical modification”
CDP-diacylglycerol(2-)“up-regulates activity”PGS1“chemical activation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

107 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance82
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3585 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:78404087:A:TK467I1.000
17:78399502:G:CK222N0.999
17:78399502:G:TK222N0.999
17:78399533:A:CS233R0.999
17:78399535:C:AS233R0.999
17:78399535:C:GS233R0.999
17:78400683:C:AN236K0.999
17:78400683:C:GN236K0.999
17:78400715:A:CD247A0.999
17:78403939:T:CF418L0.999
17:78403941:C:AF418L0.999
17:78403941:C:GF418L0.999
17:78404080:C:GH465D0.999
17:78404089:G:CG468R0.999
17:78414940:T:AN488K0.999
17:78414940:T:GN488K0.999
17:78414951:G:TR492M0.999
17:78399494:C:GH220D0.998
17:78399500:A:GK222E0.998
17:78400708:C:AR245S0.998
17:78400709:G:CR245P0.998
17:78400714:G:CD247H0.998
17:78400715:A:TD247V0.998
17:78403849:T:CY388H0.998
17:78403970:T:AI428N0.998
17:78404088:A:CK467N0.998
17:78404088:A:TK467N0.998
17:78414929:G:CG485R0.998
17:78414930:G:AG485D0.998
17:78414951:G:CR492T0.998

dbSNP variants (sampled 300 via entrez): RS1000164166 (17:78423199 G>C), RS1000191163 (17:78378826 G>A), RS1000261582 (17:78401801 T>C), RS1000276694 (17:78391332 G>A), RS1000346124 (17:78419998 A>G), RS1000365048 (17:78420149 C>T), RS1000467241 (17:78424003 A>T), RS1000559601 (17:78392889 C>T), RS1000577747 (17:78386765 C>T), RS1000588398 (17:78382372 G>A), RS1000601232 (17:78398181 C>A,T), RS1000684369 (17:78388018 A>G), RS1000714657 (17:78415651 A>G,T), RS1000754187 (17:78387806 C>T), RS1000797316 (17:78423869 C>G,T)

Disease associations

OMIM: gene MIM:614942 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

49 associations (top):

StudyTraitp-value
GCST000755_25HDL cholesterol5.000000e-09
GCST002223_1HDL cholesterol2.000000e-11
GCST002899_6HDL cholesterol4.000000e-08
GCST004232_54HDL cholesterol levels1.000000e-13
GCST004612_84High light scatter reticulocyte percentage of red cells6.000000e-09
GCST004628_25Immature fraction of reticulocytes1.000000e-13
GCST006611_4HDL cholesterol8.000000e-35
GCST006612_36LDL cholesterol2.000000e-11
GCST006613_96Triglycerides7.000000e-17
GCST006614_104Total cholesterol levels5.000000e-13
GCST006979_255Heel bone mineral density2.000000e-16
GCST008070_21HDL cholesterol levels3.000000e-11
GCST008070_89HDL cholesterol levels7.000000e-09
GCST008074_15Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)6.000000e-06
GCST008074_154Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)4.000000e-10
GCST008075_165HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)6.000000e-28
GCST008075_28HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)3.000000e-21
GCST008079_133LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)2.000000e-06
GCST008079_91LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)3.000000e-07
GCST008083_125Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)1.000000e-09
GCST008084_130HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)2.000000e-06
GCST008084_215HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)4.000000e-31
GCST008084_42HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)5.000000e-22
GCST008085_139HDL cholesterol levels in current drinkers2.000000e-14
GCST008085_65HDL cholesterol levels in current drinkers2.000000e-17
GCST008087_36Triglyceride levels in current drinkers2.000000e-06
GCST009368_67HDL cholesterol levels x long total sleep time interaction (2df test)6.000000e-09
GCST009602_24Metabolic syndrome5.000000e-10
GCST010173_111Triglyceride levels5.000000e-12
GCST010204_203Low density lipoprotein cholesterol levels5.000000e-15

EFO canonical traits (17, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007986reticulocyte count
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0004574total cholesterol measurement
EFO:0009270heel bone mineral density
EFO:0004329alcohol drinking
EFO:0000195metabolic syndrome
EFO:0004614apolipoprotein A 1 measurement
EFO:0004615apolipoprotein B measurement
EFO:0006925lipoprotein A measurement
EFO:0004509hemoglobin measurement
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0010701mean reticulocyte volume
EFO:0007985platelet crit
EFO:0009188Red cell distribution width
EFO:0004736aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
urushioldecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
abrineincreases expression1
Resveratrolincreases expression, affects cotreatment1
Norethindrone Acetateaffects cotreatment, increases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, increases expression1
Plant Extractsaffects cotreatment, increases expression1
Quercetinincreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.