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    PDSS2 decaprenyl diphosphate synthase subunit 2 [ Homo sapiens (human) ]

    Gene ID: 57107, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PDSS2provided by HGNC
    Official Full Name
    decaprenyl diphosphate synthase subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:23041
    See related
    Ensembl:ENSG00000164494 MIM:610564; AllianceGenome:HGNC:23041
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DLP1; COQ1B; hDLP1; COQ10D3; C6orf210; bA59I9.3
    Summary
    The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in kidney (RPKM 6.5), adrenal (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDSS2 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107152562..107459564, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108331503..108638499, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (107473766..107780768, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107414410-107414593 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107426683-107427338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107437205-107437968 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:107437969-107438734 Neighboring gene BEN domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24902 Neighboring gene RNA, U6 small nuclear 1299, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107470292-107470792 Neighboring gene ribosomal protein S24 pseudogene 12 Neighboring gene uncharacterized LOC124901366 Neighboring gene MPRA-validated peak6006 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:107780809-107781730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17441 Neighboring gene sine oculis binding protein homolog Neighboring gene NANOG hESC enhancer GRCh37_chr6:107906855-107907747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925473-107925974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925975-107926474 Neighboring gene Sharpr-MPRA regulatory region 6907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107978733-107979310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107979311-107979887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107989710-107990210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107990211-107990711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107994533-107995032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107995930-107996511 Neighboring gene uncharacterized LOC124901367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107996512-107997092

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. PDSS2 Deficiency Induces Hepatocarcinogenesis by Decreasing Mitochondrial Respiration and Reprogramming Glucose Metabolism. Li Y, et al. Cancer Res, 2018 Aug 15. PMID 29967258
    2. Decrease of PDSS2 expression, a novel tumor suppressor, in non-small cell lung cancer. Chen P, et al. Cancer Epidemiol, 2013 Apr. PMID 23312889
    3. Focal segmental glomerulosclerosis is associated with a PDSS2 haplotype and, independently, with a decreased content of coenzyme Q10. Gasser DL, et al. Am J Physiol Renal Physiol, 2013 Oct 15. PMID 23926186, Free PMC Article
    4. The tumor-suppressing activity of the prenyl diphosphate synthase subunit 2 gene in lung cancer cells. Chen P, et al. Anticancer Drugs, 2014 Aug. PMID 24608273
    5. Clinical utility of PDSS2 expression to stratify patients at risk for recurrence of hepatocellular carcinoma. Kanda M, et al. Int J Oncol, 2014 Nov. PMID 25189544

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDSS2 Inhibits the Ferroptosis of Vascular Endothelial Cells in Atherosclerosis by Activating Nrf2.
      Title: PDSS2 Inhibits the Ferroptosis of Vascular Endothelial Cells in Atherosclerosis by Activating Nrf2.
    2. PDSS2-Del2, a new variant of PDSS2, promotes tumor cell metastasis and angiogenesis in hepatocellular carcinoma via activating NF-kappaB.
      Title: PDSS2-Del2, a new variant of PDSS2, promotes tumor cell metastasis and angiogenesis in hepatocellular carcinoma via activating NF-κB.
    3. Study identified the promoter region of the PDSS2 gene for the first time and demonstrated that Sp1 transcription factor could directly regulate the transcription of PDSS2. Also, the expression of Sp1 and PDSS2 are negatively correlated, and higher Sp1 expression with low PDSS2 expression is significantly associated with poor prognosis in lung cancer.
      Title: Sp1 Mediates the Constitutive Expression and Repression of the PDSS2 Gene in Lung Cancer Cells.
    4. Knockdown of PDSS2 induced chromosomal instability in the MIHA immortalized human liver cell line. Furthermore, knockdown of PDSS2 in MIHA induced malignant transformation. Overall, our findings indicate that PDSS2 deficiency might be a novel driving factor in hepatocellular carcinoma (HCC) development
      Title: PDSS2 Deficiency Induces Hepatocarcinogenesis by Decreasing Mitochondrial Respiration and Reprogramming Glucose Metabolism.
    5. Results indicate PDSS2 gene which regulates coffee consumption by regulating the expression of the genes linked to caffeine metabolism.
      Title: Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.
    6. PDSS2 encodes a putative tumor suppressor, and its expression is regulated by hypermethylation of its promoter in gastric cancer cells.
      Title: Decreased expression of prenyl diphosphate synthase subunit 2 correlates with reduced survival of patients with gastric cancer.
    7. Decreased PDSS2 expression is an unfavorable prognostic factor for hepatocellular carcinoma, and PDSS2 has potent anticancer activity in HCC tissues and HepG2 cells.
      Title: Decaprenyl diphosphate synthase subunit 2 as a prognosis factor in hepatocellular carcinoma.
    8. Decreased PDSS2 mRNA levels were detected in HCC tissues of 56 patients, correlated with shorter disease-specific survival, and was identified as an independent prognostic factor
      Title: Clinical utility of PDSS2 expression to stratify patients at risk for recurrence of hepatocellular carcinoma.
    9. PDSS2 has tumor-suppressing activity in human lung cancer cells by enhancing apoptosis and inhibiting tumorigenic capacity.
      Title: The tumor-suppressing activity of the prenyl diphosphate synthase subunit 2 gene in lung cancer cells.
    10. Human PDSS2 polymorphisms are associated with podocyte diseases. A deficiency of coenzyme Q10 is manifested in lymphoblastoid cell lines derived from focal segmental glomerulosclerosis patients.
      Title: Focal segmental glomerulosclerosis is associated with a PDSS2 haplotype and, independently, with a decreased content of coenzyme Q10.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Coenzyme Q10 deficiency, primary, 3
    MedGen: C3553358 OMIM: 614652 GeneReviews: Primary Coenzyme Q10 Deficiency Overview
    		not available

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to all-trans-decaprenyl-diphosphate synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables prenyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cerebellum development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in isoprenoid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in isoprenoid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of body fluid levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquinone biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquinone biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquinone biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of heterotetrameric polyprenyl diphosphate synthase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of polyprenyl diphosphate synthase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    all trans-polyprenyl-diphosphate synthase PDSS2
    Names
    all-trans-decaprenyl-diphosphate synthase subunit 2
    decaprenyl pyrophosphate synthase subunit 2
    decaprenyl pyrophosphate synthetase subunit 2
    prenyl (decaprenyl) diphosphate synthase, subunit 2
    solanesyl-diphosphate synthase subunit 2
    subunit 2 of decaprenyl diphosphate synthase
    NP_065114.3
    XP_011534258.1
    XP_011534259.1
    XP_011534260.1
    XP_011534261.1
    XP_011534262.1
    XP_011534263.1
    XP_011534265.1
    XP_016866571.1
    XP_047275052.1
    XP_047275053.1
    XP_047275054.1
    XP_047275055.1
    XP_047275056.1
    XP_047275057.1
    XP_054211939.1
    XP_054211940.1
    XP_054211941.1
    XP_054211942.1
    XP_054211943.1
    XP_054211944.1
    XP_054211945.1
    XP_054211946.1
    XP_054211947.1
    XP_054211948.1
    XP_054211949.1
    XP_054211950.1
    XP_054211951.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_013033.1 RefSeqGene

      Range
      5012..312014
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020381.4 → NP_065114.3  all trans-polyprenyl-diphosphate synthase PDSS2

      See identical proteins and their annotated locations for NP_065114.3

      Status: REVIEWED

      Source sequence(s)
      AL832290, BC039906, DC341808
      Consensus CDS
      CCDS5059.1
      UniProtKB/Swiss-Prot
      Q33DR4, Q4G158, Q5VU38, Q5VU39, Q86YH6, Q9NR58
      UniProtKB/TrEMBL
      B2RE48
      Related
      ENSP00000358033.4, ENST00000369037.9
      Conserved Domains (1) summary
      cl00210
      Location:68 → 399
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      107152562..107459564 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535960.4 → XP_011534262.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X8

      Conserved Domains (1) summary
      cl00210
      Location:5 → 329
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    2. XM_047419100.1 → XP_047275056.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X12

    3. XM_047419098.1 → XP_047275054.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X9

      UniProtKB/TrEMBL
      B4DWD3

    4. XM_047419101.1 → XP_047275057.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X13

    5. XM_047419099.1 → XP_047275055.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X10

    6. XM_047419097.1 → XP_047275053.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X7

      UniProtKB/TrEMBL
      B2RE48

    7. XM_011535958.4 → XP_011534260.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X3

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:64 → 420
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    8. XM_011535961.4 → XP_011534263.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X11

      See identical proteins and their annotated locations for XP_011534263.1

      UniProtKB/TrEMBL
      B4DKU5
      Conserved Domains (1) summary
      cl00210
      Location:64 → 225
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    9. XM_047419096.1 → XP_047275052.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X4

    10. XM_011535959.4 → XP_011534261.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X6

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:68 → 355
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    11. XM_011535957.4 → XP_011534259.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X2

      Conserved Domains (1) summary
      cl00210
      Location:68 → 421
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    12. XM_011535956.4 → XP_011534258.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X1

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:68 → 465
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    13. XM_017011082.3 → XP_016866571.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X5

      UniProtKB/TrEMBL
      B2RE48

    14. XM_011535963.4 → XP_011534265.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X14

      UniProtKB/Swiss-Prot
      Q86YH6
      Related
      ENSP00000358027.4, ENST00000369031.4
      Conserved Domains (1) summary
      cl00210
      Location:68 → 208
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      108331503..108638499 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355971.1 → XP_054211946.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X8

    2. XM_054355972.1 → XP_054211947.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X9

      UniProtKB/TrEMBL
      B4DWD3

    3. XM_054355975.1 → XP_054211950.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X13

    4. XM_054355973.1 → XP_054211948.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X10

    5. XM_054355970.1 → XP_054211945.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X7

      UniProtKB/TrEMBL
      B2RE48

    6. XM_054355966.1 → XP_054211941.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X3

      UniProtKB/TrEMBL
      B2RE48

    7. XM_054355974.1 → XP_054211949.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X11

      UniProtKB/TrEMBL
      B4DKU5

    8. XM_054355967.1 → XP_054211942.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X4

    9. XM_054355969.1 → XP_054211944.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X6

      UniProtKB/TrEMBL
      B2RE48

    10. XM_054355965.1 → XP_054211940.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X2

    11. XM_054355964.1 → XP_054211939.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X1

      UniProtKB/TrEMBL
      B2RE48

    12. XM_054355968.1 → XP_054211943.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X5

      UniProtKB/TrEMBL
      B2RE48

    13. XM_054355976.1 → XP_054211951.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X14

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86YH6.2 GenPept UniProtKB/Swiss-Prot:Q86YH6

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