Aliases for PLD6 Gene

Aliases for PLD6 Gene

  • Phospholipase D Family Member 6 2 3 5
  • Phosphatidylcholine-Hydrolyzing Phospholipase D6 3 4
  • Mitochondrial Cardiolipin Hydrolase 3 4
  • Mitochondrial Phospholipase 3 4
  • Protein Zucchini Homolog 3 4
  • Choline Phosphatase 6 3 4
  • Phospholipase D6 3 4
  • MitoPLD 3 4
  • PLD 6 3 4
  • Phospholipase D Family, Member 6 2
  • EC 3.1.-.- 4
  • ZUC 3

External Ids for PLD6 Gene

Previous GeneCards Identifiers for PLD6 Gene

  • GC17M017048
  • GC17M016857
  • GC17M017104

Summaries for PLD6 Gene

GeneCards Summary for PLD6 Gene

PLD6 (Phospholipase D Family Member 6) is a Protein Coding gene. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and cardiolipin hydrolase activity.

UniProtKB/Swiss-Prot Summary for PLD6 Gene

  • Endonuclease that plays a critical role in PIWI-interacting RNA (piRNA) biogenesis during spermatogenesis. piRNAs provide essential protection against the activity of mobile genetic elements (By similarity). piRNA-mediated transposon silencing is thus critical for maintaining genome stability, in particular in germline cells when transposons are mobilized as a consequence of wide-spread genomic demethylation (By similarity). Has been proposed to act as a cardiolipin hydrolase to generate phosphatidic acid at mitochondrial surface (By similarity). Although it cannot be excluded that it can act as a phospholipase in some circumstances, it should be noted that cardiolipin hydrolase activity is either undetectable in vitro, or very low (PubMed:21397848). In addition, cardiolipin is almost exclusively found on the inner mitochondrial membrane, while PLD6 localizes to the outer mitochondrial membrane, facing the cytosol (PubMed:21397848). Has been shown to be a backbone-non-specific, single strand-specific nuclease, cleaving either RNA or DNA substrates with similar affinity. Produces 5' phosphate and 3' hydroxyl termini, suggesting it could directly participate in the processing of primary piRNA transcripts (By similarity). Also acts as a regulator of mitochondrial shape through facilitating mitochondrial fusion (PubMed:17028579, PubMed:26711011).

Additional gene information for PLD6 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLD6 Gene

Genomics for PLD6 Gene

GeneHancer (GH) Regulatory Elements for PLD6 Gene

Promoters and enhancers for PLD6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J017203 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 761.5 +0.9 925 4.1 ZNF785 SIN3A ZBTB40 SP1 SREBF1 MLX POLR2A USF2 NR2F1 NR2F6 PLD6 FLCN UPF3AP1 LOC100419436 RAI1 SMCR5 DRG2 NT5M NCOR1 DRC3
GH17J017208 Enhancer 0.2 ENCODE 750.6 -1.9 -1869 0.2 PLD6 lnc-PLD6-2 ENSG00000264187 FLCN MPRIP
GH17J017040 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 34 +162.5 162469 6.1 SIN3A SP1 ZBTB6 RBPJ POLR2A TCF7L2 FOS MYC NFYC L3MBTL2 MPRIP ENSG00000287910 piR-32428-001 lnc-TNFRSF13B-3 piR-52781 piR-47121-001 FLCN MPRIP-AS1 PLD6 PIGL
GH17J017086 Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas dbSUPER 17.4 +112.5 112549 13.6 SMARCE1 HLF RAD21 TEAD4 ZNF652 ELF3 SP1 CBFA2T2 CEBPG PRDM1 FLCN PLD6 MPRIP NT5M KRT16P6 piR-47265 MPRIP-AS1
GH17J017149 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 18.7 +53.6 53630 9.8 RAD21 NFIB SP1 MAFK CREM CREB1 ZIC2 POLR2A RXRA PRDM10 FLCN PLD6 MPRIP MPRIP-AS1 NT5M COPS3 PEMT ZNF624 piR-30305-001 piR-35618-001
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLD6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLD6 gene promoter:
  • AhR
  • Arnt
  • CUTL1
  • GR
  • GR-alpha
  • GR-beta
  • NRSF form 1
  • NRSF form 2
  • p300
  • POU3F2

Genomic Locations for PLD6 Gene

Genomic Locations for PLD6 Gene
chr17:17,200,995-17,206,333
(GRCh38/hg38)
Size:
5,339 bases
Orientation:
Minus strand
chr17:17,104,309-17,109,646
(GRCh37/hg19)
Size:
5,338 bases
Orientation:
Minus strand

Genomic View for PLD6 Gene

Genes around PLD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLD6 Gene

Proteins for PLD6 Gene

  • Protein details for PLD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N2A8-PLD6_HUMAN
    Recommended name:
    Mitochondrial cardiolipin hydrolase
    Protein Accession:
    Q8N2A8
    Secondary Accessions:
    • Q8N5Y1

    Protein attributes for PLD6 Gene

    Size:
    252 amino acids
    Molecular mass:
    28273 Da
    Quaternary structure:
    • Homodimer (PubMed:17028579). Interacts with MOV10L1 (By similarity). Interacts with MIGA1 and MIGA2; possibly facilitating homodimer formation (PubMed:26711011).

neXtProt entry for PLD6 Gene

Post-translational modifications for PLD6 Gene

  • Ubiquitination at Lys158
  • Modification sites at PhosphoSitePlus

Other Protein References for PLD6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PLD6 Gene

Domains & Families for PLD6 Gene

Gene Families for PLD6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PLD6 Gene

Suggested Antigen Peptide Sequences for PLD6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55057 (B4DHV4_HUMAN)
  • Protein zucchini homolog (PLD6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N2A8

UniProtKB/Swiss-Prot:

PLD6_HUMAN :
  • In contrast to other members of the phospholipase D family, contains only one PLD phosphodiesterase domain, suggesting that it has a single half-catalytic and requires homodimerization to form a complete active site.
  • Belongs to the phospholipase D family. MitoPLD/Zucchini subfamily.
Domain:
  • In contrast to other members of the phospholipase D family, contains only one PLD phosphodiesterase domain, suggesting that it has a single half-catalytic and requires homodimerization to form a complete active site.
Family:
  • Belongs to the phospholipase D family. MitoPLD/Zucchini subfamily.
genes like me logo Genes that share domains with PLD6: view

Function for PLD6 Gene

Molecular function for PLD6 Gene

UniProtKB/Swiss-Prot Function:
Endonuclease that plays a critical role in PIWI-interacting RNA (piRNA) biogenesis during spermatogenesis. piRNAs provide essential protection against the activity of mobile genetic elements (By similarity). piRNA-mediated transposon silencing is thus critical for maintaining genome stability, in particular in germline cells when transposons are mobilized as a consequence of wide-spread genomic demethylation (By similarity). Has been proposed to act as a cardiolipin hydrolase to generate phosphatidic acid at mitochondrial surface (By similarity). Although it cannot be excluded that it can act as a phospholipase in some circumstances, it should be noted that cardiolipin hydrolase activity is either undetectable in vitro, or very low (PubMed:21397848). In addition, cardiolipin is almost exclusively found on the inner mitochondrial membrane, while PLD6 localizes to the outer mitochondrial membrane, facing the cytosol (PubMed:21397848). Has been shown to be a backbone-non-specific, single strand-specific nuclease, cleaving either RNA or DNA substrates with similar affinity. Produces 5' phosphate and 3' hydroxyl termini, suggesting it could directly participate in the processing of primary piRNA transcripts (By similarity). Also acts as a regulator of mitochondrial shape through facilitating mitochondrial fusion (PubMed:17028579, PubMed:26711011).
UniProtKB/Swiss-Prot EnzymeRegulation:
SsDNA hydrolase activity does not depend upon, but it stimulated by, the presence of Ca(2+) and Mn(2+).

Enzyme Numbers (IUBMB) for PLD6 Gene

Phenotypes From GWAS Catalog for PLD6 Gene

Gene Ontology (GO) - Molecular Function for PLD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0005515 protein binding IPI 26711011
GO:0016787 hydrolase activity IEA --
GO:0035755 cardiolipin hydrolase activity IDA 17028579
genes like me logo Genes that share ontologies with PLD6: view
genes like me logo Genes that share phenotypes with PLD6: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PLD6 Gene

Localization for PLD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLD6 Gene

Mitochondrion outer membrane; Single-pass membrane protein.

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 PLD6 gene
Compartment Confidence
mitochondrion 5
extracellular 2
cytosol 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for PLD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005741 mitochondrial outer membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PLD6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLD6 Gene

Pathways & Interactions for PLD6 Gene

genes like me logo Genes that share pathways with PLD6: view

Pathways by source for PLD6 Gene

Gene Ontology (GO) - Biological Process for PLD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006654 phosphatidic acid biosynthetic process TAS --
GO:0007283 spermatogenesis IEA --
GO:0007286 spermatid development ISS,IEA --
GO:0008053 mitochondrial fusion IMP 17028579
genes like me logo Genes that share ontologies with PLD6: view

No data available for SIGNOR curated interactions for PLD6 Gene

Drugs & Compounds for PLD6 Gene

(1) Drugs for PLD6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra 218

(3) Additional Compounds for PLD6 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
PC(18:1(9Z)e/2:0)
  • (2-Acetyloxy-3-octadec-9-enoxypropyl) 2-trimethylazaniumylethyl phosphate
  • 2-Acetyl-1-(9Z-octadecenyl)-sn-glycero-3-phosphocholine
  • PC(O-18:1(9Z)/2:0)
Phosphatidylcholines Group A
  • (Z,Z)-(1)-(7-Oleoyl-4-oxido-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-enyl)trimethylammonium 4-oxide
  • (Z,Z)-4-Hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide hydroxide inner salt
  • 1,2-Dioleoyl-rac-glycero-3-phosphocholine
  • 1,2-Dioleoylglycerol-3-phosphorylcholine
  • 1,2-Dioleoylglyceryl-3-phosphorylcholine
68737-67-7
Phosphatidylcholines Group B
  • 1-Hexadecyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine
  • 2-(9Z,12Z-Octadecadienoyl)-1-hexadecyl-sn-glycero-3-phosphocholine
  • PC Ae C34:2
  • PC(16:0E/18:2(9Z,12Z))
  • PC(O-34:2)
88542-95-4
genes like me logo Genes that share compounds with PLD6: view

Transcripts for PLD6 Gene

mRNA/cDNA for PLD6 Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(62) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLD6 Gene

No ASD Table

Relevant External Links for PLD6 Gene

GeneLoc Exon Structure for
PLD6
ECgene alternative splicing isoforms for
PLD6

Expression for PLD6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLD6 Gene

mRNA differential expression in normal tissues according to GTEx for PLD6 Gene

This gene is overexpressed in Testis (x5.8).

Protein differential expression in normal tissues from HIPED for PLD6 Gene

This gene is overexpressed in Plasma (43.1), Ovary (19.4), and Testis (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PLD6 Gene



Protein tissue co-expression partners for PLD6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLD6 Gene:

PLD6

SOURCE GeneReport for Unigene cluster for PLD6 Gene:

Hs.729079

mRNA Expression by UniProt/SwissProt for PLD6 Gene:

Q8N2A8-PLD6_HUMAN
Tissue specificity: Widely expressed. Expression is not limited to testis and ovary.

Evidence on tissue expression from TISSUES for PLD6 Gene

  • Nervous system(4.2)
  • Liver(2)
genes like me logo Genes that share expression patterns with PLD6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLD6 Gene

Orthologs for PLD6 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLD6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLD6 33 32
  • 99.34 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PLD6 33 32
  • 86.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLD6 33 32
  • 83.87 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pld6 33
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pld6 32
  • 81.31 (n)
oppossum
(Monodelphis domestica)
Mammalia PLD6 33
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pld6 32
  • 65.52 (n)
Str.16063 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.16857 32
zebrafish
(Danio rerio)
Actinopterygii pld6 33 32
  • 60.16 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta zuc 33
  • 25 (a)
OneToOne
Species where no ortholog for PLD6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PLD6 Gene

ENSEMBL:
Gene Tree for PLD6 (if available)
TreeFam:
Gene Tree for PLD6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLD6: view image

Paralogs for PLD6 Gene

No data available for Paralogs for PLD6 Gene

Variants for PLD6 Gene

Sequence variations from dbSNP and Humsavar for PLD6 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000032971 -- 17,202,051(-) T/C 3_prime_UTR_variant
rs1000122328 -- 17,203,205(-) A/G intron_variant
rs1000136455 -- 17,207,069(-) C/T upstream_transcript_variant
rs1000540053 -- 17,204,595(-) C/A intron_variant
rs1001226432 -- 17,201,757(-) A/G 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PLD6 Gene

Variant ID Type Subtype PubMed ID
dgv893e212 CNV loss 25503493
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv833380 CNV loss 17160897

Variation tolerance for PLD6 Gene

Gene Damage Index Score: 0.36; 7.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLD6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLD6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLD6 Gene

Disorders for PLD6 Gene

Additional Disease Information for PLD6

No disorders were found for PLD6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PLD6 Gene

Publications for PLD6 Gene

  1. Measuring Phospholipase D Enzymatic Activity Through Biochemical and Imaging Methods. (PMID: 28063496) Philip F … Frohman MA (Methods in enzymology 2017) 2 3 56
  2. Mitoguardin Regulates Mitochondrial Fusion through MitoPLD and Is Required for Neuronal Homeostasis. (PMID: 26711011) Zhang Y … Tong C (Molecular cell 2016) 3 4 56
  3. piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. (PMID: 21397848) Huang H … Frohman MA (Developmental cell 2011) 3 4 56
  4. A common lipid links Mfn-mediated mitochondrial fusion and SNARE-regulated exocytosis. (PMID: 17028579) Choi SY … Frohman MA (Nature cell biology 2006) 3 4 56
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56

Products for PLD6 Gene

Sources for PLD6 Gene