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Aliases for PDSS2 Gene

Aliases for PDSS2 Gene

  • Decaprenyl Diphosphate Synthase Subunit 2 2 3 5
  • Prenyl (Decaprenyl) Diphosphate Synthase, Subunit 2 2 3
  • All-Trans-Decaprenyl-Diphosphate Synthase Subunit 2 3 4
  • Decaprenyl Pyrophosphate Synthase Subunit 2 3 4
  • C6orf210 3 4
  • DLP1 3 4
  • Decaprenyl Pyrophosphate Synthetase Subunit 2 3
  • Subunit 2 Of Decaprenyl Diphosphate Synthase 3
  • Decaprenyl-Diphosphate Synthase Subunit 2 3
  • Chromosome 6 Open Reading Frame 210 2
  • Candidate Tumor Suppressor Protein 4
  • EC 2.5.1.91 4
  • BA59I9.3 3
  • COQ10D3 3
  • HDLP1 3

External Ids for PDSS2 Gene

Previous HGNC Symbols for PDSS2 Gene

  • C6orf210

Previous GeneCards Identifiers for PDSS2 Gene

  • GC06M107581
  • GC06M107473
  • GC06M105044

Summaries for PDSS2 Gene

Entrez Gene Summary for PDSS2 Gene

  • 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]

GeneCards Summary for PDSS2 Gene

PDSS2 (Decaprenyl Diphosphate Synthase Subunit 2) is a Protein Coding gene. Diseases associated with PDSS2 include Coenzyme Q10 Deficiency, Primary, 3 and Leigh Syndrome With Nephrotic Syndrome. Among its related pathways are Ubiquinol biosynthesis and Terpenoid backbone biosynthesis. GO annotations related to this gene include protein heterodimerization activity and trans-octaprenyltranstransferase activity. An important paralog of this gene is PDSS1.

UniProtKB/Swiss-Prot for PDSS2 Gene

  • Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.

Gene Wiki entry for PDSS2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDSS2 Gene

Genomics for PDSS2 Gene

Regulatory Elements for PDSS2 Gene

Enhancers for PDSS2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G107488 1.6 Ensembl ENCODE dbSUPER 10.7 -32.7 -32737 7.9 PKNOX1 FOXA2 ARID4B FEZF1 DMAP1 ZNF2 YY1 SLC30A9 FOS ZNF263 PDSS2 SOBP ENSG00000234206
GH06G107220 0.8 ENCODE 8.4 +238.2 238185 1.3 ATF1 PKNOX1 MAX ZBTB40 RAD21 YY1 HNF4G IKZF2 CREM L3MBTL2 PDSS2 GC06M107226 ENSG00000276620
GH06G107151 0.8 ENCODE 6.5 +306.3 306298 3.4 HNRNPUL1 PKNOX1 FEZF1 BMI1 ZNF121 MIXL1 MIER1 CEBPB OVOL3 ZNF843 PDSS2 RNU6-1299P ENSG00000276620
GH06G107437 0.4 ENCODE 12.8 +21.8 21796 1.5 CEBPB CEBPG PDSS2 PIR39325 GC06P107406
GH06G107241 1.1 Ensembl ENCODE 4.6 +217.7 217743 1.8 SOX13 CTCF SAP130 CEBPG ZNF644 RAD21 ZNF335 ZNF121 SCRT2 HOMEZ SOBP PDSS2 GC06P107237 GC06P107246
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDSS2 on UCSC Golden Path with GeneCards custom track

Promoters for PDSS2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000200710 202 2201 PKNOX1 FOXA2 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9

Genomic Location for PDSS2 Gene

Chromosome:
6
Start:
107,152,557 bp from pter
End:
107,459,702 bp from pter
Size:
307,146 bases
Orientation:
Minus strand

Genomic View for PDSS2 Gene

Genes around PDSS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDSS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDSS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDSS2 Gene

Proteins for PDSS2 Gene

  • Protein details for PDSS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86YH6-DLP1_HUMAN
    Recommended name:
    Decaprenyl-diphosphate synthase subunit 2
    Protein Accession:
    Q86YH6
    Secondary Accessions:
    • Q33DR4
    • Q4G158
    • Q5VU38
    • Q5VU39
    • Q9NR58

    Protein attributes for PDSS2 Gene

    Size:
    399 amino acids
    Molecular mass:
    44129 Da
    Quaternary structure:
    • Heterotetramer of 2 DPS1/TPRT and 2 DLP1 subunits.
    SequenceCaution:
    • Sequence=AAH29491.1; Type=Frameshift; Positions=28; Evidence={ECO:0000305}; Sequence=CAH73572.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI22355.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for PDSS2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDSS2 Gene

Post-translational modifications for PDSS2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDSS2 Gene

Domains & Families for PDSS2 Gene

Protein Domains for PDSS2 Gene

Graphical View of Domain Structure for InterPro Entry

Q86YH6

UniProtKB/Swiss-Prot:

DLP1_HUMAN :
  • Belongs to the FPP/GGPP synthase family.
Family:
  • Belongs to the FPP/GGPP synthase family.
genes like me logo Genes that share domains with PDSS2: view

No data available for Gene Families for PDSS2 Gene

Function for PDSS2 Gene

Molecular function for PDSS2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate.
UniProtKB/Swiss-Prot Function:
Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.

Enzyme Numbers (IUBMB) for PDSS2 Gene

Gene Ontology (GO) - Molecular Function for PDSS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000010 contributes_to trans-hexaprenyltranstransferase activity IDA 16262699
GO:0016740 transferase activity IEA --
GO:0046982 protein heterodimerization activity IDA 16262699
GO:0050347 trans-octaprenyltranstransferase activity IEA --
genes like me logo Genes that share ontologies with PDSS2: view
genes like me logo Genes that share phenotypes with PDSS2: view

Human Phenotype Ontology for PDSS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDSS2 Gene

MGI Knock Outs for PDSS2:

Animal Model Products

CRISPR Products

miRNA for PDSS2 Gene

miRTarBase miRNAs that target PDSS2

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for PDSS2 Gene

Localization for PDSS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDSS2 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDSS2 gene
Compartment Confidence
mitochondrion 5
cytosol 5
peroxisome 2

Gene Ontology (GO) - Cellular Components for PDSS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0005829 cytosol IDA --
GO:1990234 transferase complex IDA 16262699
genes like me logo Genes that share ontologies with PDSS2: view

Pathways & Interactions for PDSS2 Gene

genes like me logo Genes that share pathways with PDSS2: view

Pathways by source for PDSS2 Gene

1 BioSystems pathway for PDSS2 Gene
1 KEGG pathway for PDSS2 Gene

UniProtKB/Swiss-Prot Q86YH6-DLP1_HUMAN

  • Pathway: Cofactor biosynthesis; ubiquinone biosynthesis.

Gene Ontology (GO) - Biological Process for PDSS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006744 ubiquinone biosynthetic process TAS --
GO:0008299 isoprenoid biosynthetic process IDA 16262699
GO:0050878 regulation of body fluid levels IEA --
GO:0051290 protein heterotetramerization IEA --
genes like me logo Genes that share ontologies with PDSS2: view

No data available for SIGNOR curated interactions for PDSS2 Gene

Drugs & Compounds for PDSS2 Gene

(2) Drugs for PDSS2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Isopentenyl pyrophosphate Experimental Pharma 0

(3) Additional Compounds for PDSS2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
all-trans-Decaprenyl diphosphate
Farnesyl pyrophosphate
  • (2E,6E)-Farnesyl diphosphate
  • (2E,6E)-Farnesyl pyrophosphate
  • (all-E)-Farnesyl diphosphate
  • (E,E)-Farnesyl diphosphate
  • (E,E)-Farnesyl pyrophosphate
13058-04-3
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with PDSS2: view

Transcripts for PDSS2 Gene

Unigene Clusters for PDSS2 Gene

Prenyl (decaprenyl) diphosphate synthase, subunit 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDSS2 Gene

No ASD Table

Relevant External Links for PDSS2 Gene

GeneLoc Exon Structure for
PDSS2
ECgene alternative splicing isoforms for
PDSS2

Expression for PDSS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDSS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDSS2 Gene

This gene is overexpressed in Bone (52.8) and NK cells (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDSS2 Gene



NURSA nuclear receptor signaling pathways regulating expression of PDSS2 Gene:

PDSS2

SOURCE GeneReport for Unigene cluster for PDSS2 Gene:

Hs.745008

Evidence on tissue expression from TISSUES for PDSS2 Gene

  • Nervous system(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDSS2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • pituitary gland
Thorax:
  • breast
  • heart
  • heart valve
  • lung
Abdomen:
  • kidney
  • liver
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with PDSS2: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PDSS2 Gene

Orthologs for PDSS2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PDSS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDSS2 34 35
  • 99.5 (n)
dog
(Canis familiaris)
Mammalia PDSS2 34 35
  • 92.82 (n)
cow
(Bos Taurus)
Mammalia PDSS2 34 35
  • 92.63 (n)
mouse
(Mus musculus)
Mammalia Pdss2 34 16 35
  • 87.64 (n)
rat
(Rattus norvegicus)
Mammalia Pdss2 34
  • 85.88 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDSS2 35
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDSS2 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDSS2 34 35
  • 75.58 (n)
lizard
(Anolis carolinensis)
Reptilia PDSS2 35
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdss2 34
  • 68.09 (n)
Str.19088 34
zebrafish
(Danio rerio)
Actinopterygii pdss2 34 35
  • 66.2 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3792 34
fruit fly
(Drosophila melanogaster)
Insecta CG10585 34 35
  • 49.72 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006015 34
  • 49.24 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes COQ1 35
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2932 35
  • 31 (a)
OneToOne
Species where no ortholog for PDSS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PDSS2 Gene

ENSEMBL:
Gene Tree for PDSS2 (if available)
TreeFam:
Gene Tree for PDSS2 (if available)

Paralogs for PDSS2 Gene

Paralogs for PDSS2 Gene

Pseudogenes.org Pseudogenes for PDSS2 Gene

genes like me logo Genes that share paralogs with PDSS2: view

Variants for PDSS2 Gene

Sequence variations from dbSNP and Humsavar for PDSS2 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs118203956 Pathogenic, Coenzyme Q10 deficiency, primary, 3 (COQ10D3) [MIM:614652] 107,154,674(-) TCCCT(C/T)GGAGG reference, missense
rs118203955 Pathogenic 107,210,483(-) TACAT(C/G/T)AGGAA intron-variant, reference, missense
rs863224166 Pathogenic 107,210,572(-) CTTGT(A/G)GATAA intron-variant, splice-acceptor-variant
rs143549737 Likely pathogenic 107,459,011(+) GAGGG(G/T)GCTGA intron-variant, reference, missense
rs863224167 Likely pathogenic 107,212,111(-) GTCAT(A/G)AGGTA intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PDSS2 Gene

Variant ID Type Subtype PubMed ID
dgv6135n100 CNV gain 25217958
dgv87n68 CNV loss 17160897
esv1000677 CNV deletion 20482838
esv1575074 CNV insertion 17803354
esv26284 CNV loss 19812545
esv2629723 CNV deletion 19546169
esv2669947 CNV deletion 23128226
esv2676943 CNV deletion 23128226
esv2732546 CNV deletion 23290073
esv2732549 CNV deletion 23290073
esv3610293 CNV loss 21293372
esv3610294 CNV loss 21293372
esv3610295 CNV gain 21293372
esv3610296 CNV loss 21293372
esv3610297 CNV loss 21293372
esv3610298 CNV loss 21293372
esv3610300 CNV loss 21293372
nsv1030534 CNV gain 25217958
nsv1114861 CNV deletion 24896259
nsv1151050 CNV deletion 26484159
nsv516771 CNV loss 19592680
nsv830762 CNV gain 17160897

Variation tolerance for PDSS2 Gene

Residual Variation Intolerance Score: 35.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.75; 57.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDSS2 Gene

Human Gene Mutation Database (HGMD)
PDSS2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDSS2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDSS2 Gene

Disorders for PDSS2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PDSS2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
coenzyme q10 deficiency, primary, 3
  • coq10d3
leigh syndrome with nephrotic syndrome
  • infantile subacute necrotizing encephalopathy with nephrotic syndrome
pdss2-related coenzyme q10 deficiency
  • coenzyme q10 deficiency, primary, 3
glutaric acidemia iic
  • glutaric acidemia iia
leigh syndrome
  • leigh syndrome due to mitochondrial complex i deficiency
- elite association - COSMIC cancer census association via MalaCards
Search PDSS2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

DLP1_HUMAN
  • Coenzyme Q10 deficiency, primary, 3 (COQ10D3) [MIM:614652]: A fatal encephalomyopathic form of coenzyme Q10 deficiency with nephrotic syndrome. Coenzyme Q10 deficiency is an autosomal recessive disorder with variable manifestations consistent with 5 major phenotypes. The phenotypes include an encephalomyopathic form with seizures and ataxia; a multisystem infantile form with encephalopathy, cardiomyopathy and renal failure; a predominantly cerebellar form with ataxia and cerebellar atrophy; Leigh syndrome with growth retardation; and an isolated myopathic form. {ECO:0000269 PubMed:17186472}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PDSS2

Genetic Association Database (GAD)
PDSS2
Human Genome Epidemiology (HuGE) Navigator
PDSS2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDSS2
genes like me logo Genes that share disorders with PDSS2: view

No data available for Genatlas for PDSS2 Gene

Publications for PDSS2 Gene

  1. Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans. (PMID: 16262699) Saiki R. … Kawamukai M. (FEBS J. 2005) 2 3 4 64
  2. Genotype-phenotype correlations in non-Finnish congenital nephrotic syndrome. (PMID: 20507940) Machuca E. … Antignac C. (J. Am. Soc. Nephrol. 2010) 3 46 64
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  5. Anticancer activity of PDSS2, prenyl diphosphate synthase, subunit 2, in gastric cancer tissue and the SGC7901 cell line. (PMID: 19209031) Chen P. … Niu Y.Y. (Anticancer Drugs 2009) 3 22 64

Products for PDSS2 Gene

Sources for PDSS2 Gene

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