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

Gene ID: 57107, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107152562..107459564, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108331503..108638499, complement)
105.20220307 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: 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. PDSS2-Del2, a new variant of PDSS2, promotes tumor cell metastasis and angiogenesis in hepatocellular carcinoma via activating NF-κB. Zeng T, et al. Mol Oncol, 2020 Dec. PMID 33064899, Free PMC Article
  2. PDSS2 Deficiency Induces Hepatocarcinogenesis by Decreasing Mitochondrial Respiration and Reprogramming Glucose Metabolism. Li Y, et al. Cancer Res, 2018 Aug 15. PMID 29967258
  3. Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption. Pirastu N, et al. Sci Rep, 2016 Aug 25. PMID 27561104, Free PMC Article
  4. Decaprenyl diphosphate synthase subunit 2 as a prognosis factor in hepatocellular carcinoma. Huang W, et al. World J Gastroenterol, 2015 Mar 14. PMID 25780306, Free PMC Article
  5. Decreased expression of prenyl diphosphate synthase subunit 2 correlates with reduced survival of patients with gastric cancer. Kanda M, et al. J Exp Clin Cancer Res, 2014 Oct 22. PMID 25330808, Free PMC Article

See all (37) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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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)

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

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
  
part_of transferase 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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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_2023_10

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

  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

  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

  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

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

  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

  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

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

  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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