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PGS1 phosphatidylglycerophosphate synthase 1 [ Homo sapiens (human) ]

Gene ID: 9489, updated on 3-Apr-2024

Summary

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Official Symbol
PGS1provided by HGNC
Official Full Name
phosphatidylglycerophosphate synthase 1provided by HGNC
Primary source
HGNC:HGNC:30029
See related
Ensembl:ENSG00000087157 MIM:614942; AllianceGenome:HGNC:30029
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 9.6), appendix (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PGS1 in Genome Data Viewer
Location:
17q25.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (78378649..78424659)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79272180..79318173)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76374730..76420740)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:76352361-76352860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76352918-76353567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9063 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76355514-76356162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76359520-76360097 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76361253-76361828 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76361829-76362406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76367859-76368426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76368427-76368994 Neighboring gene SOCS3 divergent transcript Neighboring gene suppressor of cytokine signaling 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76374619-76375580 Neighboring gene RNA, 7SL, cytoplasmic 236, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12894 Neighboring gene small nucleolar RNA SNORA30/SNORA37 family Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76396609-76397114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76406789-76407334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76407335-76407878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12895 Neighboring gene Sharpr-MPRA regulatory region 14012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76413655-76414163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76415673-76416357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76418631-76419210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76422004-76422504 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76422505-76423005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76433212-76433840 Neighboring gene dynein axonemal heavy chain 17 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76446189-76446410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76446540-76447118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76461956-76462618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76463282-76463943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9069 Neighboring gene DNAH17 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:76489132-76490331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76493472-76494020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76494021-76494569 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:76502868-76504067 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:76506209-76507408 Neighboring gene RAN binding protein 1 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Purification of phosphatidylglycerophosphate synthase from Chinese hamster ovary cells. Kawasaki K, et al. Biochem J, 2001 Feb 15. PMID 11171073, Free PMC Article
  2. Isolation of a chinese hamster ovary (CHO) cDNA encoding phosphatidylglycerophosphate (PGP) synthase, expression of which corrects the mitochondrial abnormalities of a PGP synthase-defective mutant of CHO-K1 cells. Kawasaki K, et al. J Biol Chem, 1999 Jan 15. PMID 9880566
  3. Sequence identification of 2,375 human brain genes. Adams MD, et al. Nature, 1992 Feb 13. PMID 1538749
  4. Biological, clinical and population relevance of 95 loci for blood lipids. Teslovich TM, et al. Nature, 2010 Aug 5. PMID 20686565, Free PMC Article
  5. Discovery and refinement of loci associated with lipid levels. Willer CJ, et al. Nat Genet, 2013 Nov. PMID 24097068, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC131960, DKFZp762M186

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in cardiolipin biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cardiolipin biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in diacylglycerol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phosphatidylglycerol biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
Names
PGP synthase 1
NP_077733.3
XP_011523789.1
XP_011523790.1
XP_011523791.1
XP_016880846.1
XP_016880847.1
XP_016880848.1
XP_016880849.1
XP_016880850.1
XP_016880853.1
XP_047293057.1
XP_047293058.1
XP_047293059.1
XP_047293060.1
XP_047293061.1
XP_054173832.1
XP_054173833.1
XP_054173834.1
XP_054173835.1
XP_054173836.1
XP_054173837.1
XP_054173838.1
XP_054173839.1
XP_054173840.1
XP_054173841.1
XP_054173842.1
XP_054173843.1
XP_054173844.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_024419.5 → NP_077733.3  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_077733.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein.
    Source sequence(s)
    AK316147, BC108732, BI024108, ES314549
    Consensus CDS
    CCDS42391.1
    UniProtKB/Swiss-Prot
    B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7
    UniProtKB/TrEMBL
    B4DL81
    Related
    ENSP00000262764.5, ENST00000262764.11
    Conserved Domains (3) summary
    cd09135
    Location:96 → 269
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:349 → 508
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:113 → 265
    PLDc_2; PLD-like domain

RNA

  1. NR_110601.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate internal and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC035662, BC108732, BI024108, DC367136, ES314549
    Related
    ENST00000589426.5

  2. NR_110602.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate internal and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK297156, BC108732, BI024108, DC367136, ES314549

  3. NR_111989.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate internal exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK024529, AK225030, BC108732, BI024108, ES314549
    Related
    ENST00000589425.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    78378649..78424659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017025357.2 → XP_016880846.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 598
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  2. XM_017025358.2 → XP_016880847.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 598
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  3. XM_011525487.3 → XP_011523789.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 598
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  4. XM_017025360.2 → XP_016880849.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 558
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  5. XM_011525488.3 → XP_011523790.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 558
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  6. XM_017025359.2 → XP_016880848.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X3

  7. XM_047437101.1 → XP_047293057.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X2

  8. XM_017025361.3 → XP_016880850.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X6

    UniProtKB/Swiss-Prot
    B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7
    UniProtKB/TrEMBL
    B4DL81
    Conserved Domains (3) summary
    cd09135
    Location:96 → 269
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:349 → 508
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:113 → 265
    PLDc_2; PLD-like domain

  9. XM_047437103.1 → XP_047293059.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X9

  10. XM_017025364.3 → XP_016880853.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X8

    UniProtKB/TrEMBL
    B4DL81
    Conserved Domains (3) summary
    cd09135
    Location:96 → 243
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:323 → 482
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    COG1502
    Location:95 → 521
    Cls; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase or related enzyme [Lipid transport and metabolism]

  11. XM_047437104.1 → XP_047293060.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X10

  12. XM_011525489.3 → XP_011523791.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X5

    Conserved Domains (3) summary
    cd09135
    Location:186 → 359
    PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
    cd09137
    Location:439 → 558
    PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
    pfam13091
    Location:203 → 355
    PLDc_2; PLD-like domain

  13. XM_047437105.1 → XP_047293061.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X11

  14. XM_047437102.1 → XP_047293058.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X7

RNA

  1. XR_007065546.1 RNA Sequence

  2. XR_007065547.1 RNA Sequence

  3. XR_001752683.2 RNA Sequence

  4. XR_934604.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    79272180..79318173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317864.1 → XP_054173839.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X6

    UniProtKB/Swiss-Prot
    B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7

  2. XM_054317867.1 → XP_054173842.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X9

  3. XM_054317866.1 → XP_054173841.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X8

  4. XM_054317868.1 → XP_054173843.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X10

  5. XM_054317869.1 → XP_054173844.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X11

  6. XM_054317857.1 → XP_054173832.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

  7. XM_054317858.1 → XP_054173833.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

  8. XM_054317861.1 → XP_054173836.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

  9. XM_054317862.1 → XP_054173837.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

  10. XM_054317860.1 → XP_054173835.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X3

  11. XM_054317859.1 → XP_054173834.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X2

  12. XM_054317863.1 → XP_054173838.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X5

  13. XM_054317865.1 → XP_054173840.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X7

RNA

  1. XR_008484967.1 RNA Sequence

  2. XR_008484969.1 RNA Sequence

  3. XR_008484966.1 RNA Sequence

  4. XR_008484968.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q32NB8.1 GenPept UniProtKB/Swiss-Prot:Q32NB8

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