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    PLD5 phospholipase D family member 5 [ Homo sapiens (human) ]

    Gene ID: 200150, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PLD5provided by HGNC
    Official Full Name
    phospholipase D family member 5provided by HGNC
    Primary source
    HGNC:HGNC:26879
    See related
    Ensembl:ENSG00000180287 AllianceGenome:HGNC:26879
    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
    Also known as
    PLDC
    Summary
    Predicted to enable catalytic activity. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See PLD5 in Genome Data Viewer
    Location:
    1q43
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (242082986..242530546, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (241495068..241942534, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (242246288..242687999, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1139, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:242220644-242221384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:242223521-242224022 Neighboring gene tubulin beta 8 class VIII pseudogene 6 Neighboring gene tripartite motif containing 39 pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:242373739-242374272 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:242374273-242374807 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:242373205-242373738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2830 Neighboring gene RN7SK pseudogene 12 Neighboring gene uncharacterized LOC105373235 Neighboring gene NANOG hESC enhancer GRCh37_chr1:242433537-242434038 Neighboring gene zinc finger protein 532 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:242541822-242542001 Neighboring gene DEAD-box helicase 55 pseudogene Neighboring gene ribosomal protein L10a pseudogene 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:242611784-242612983 Neighboring gene uncharacterized LOC105373234 Neighboring gene uncharacterized LOC107985466 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:242748387-242749056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:242749057-242749726 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:242756967-242757533 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:242792333-242793532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:242815099-242815628 Neighboring gene ribosomal L24 domain containing 1 pseudogene 4

    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 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. MicroRNA miR-145-5p inhibits Phospholipase D 5 (PLD5) to downregulate cell proliferation and metastasis to mitigate prostate cancer. Liu J, et al. Bioengineered, 2021 Dec. PMID 34238129, Free PMC Article
    2. A genome-wide scan for common alleles affecting risk for autism. Anney R, et al. Hum Mol Genet, 2010 Oct 15. PMID 20663923, Free PMC Article
    3. Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis. McCauley JL, et al. Genes Immun, 2009 Oct. PMID 19626040, Free PMC Article
    4. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Chimusa ER, et al. Hum Mol Genet, 2014 Feb 1. PMID 24057671, Free PMC Article
    5. Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. Li L, et al. BMC Genomics, 2014 Feb 1. PMID 24483146, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MicroRNA miR-145-5p inhibits Phospholipase D 5 (PLD5) to downregulate cell proliferation and metastasis to mitigate prostate cancer.
      Title: MicroRNA miR-145-5p inhibits Phospholipase D 5 (PLD5) to downregulate cell proliferation and metastasis to mitigate prostate cancer.
    2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A genome-wide scan for common alleles affecting risk for autism.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
    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
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40773, MGC120565, MGC120566, MGC120567

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    inactive phospholipase D5
    Names
    inactive PLD 5
    inactive choline phosphatase 5
    inactive phosphatidylcholine-hydrolyzing phospholipase D5

    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_001195811.2 → NP_001182740.1  inactive phospholipase D5 isoform 2

      See identical proteins and their annotated locations for NP_001182740.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AL591686, AY461578
      Consensus CDS
      CCDS55692.1
      UniProtKB/Swiss-Prot
      Q8N7P1
      Related
      ENSP00000401285.1, ENST00000427495.5
      Conserved Domains (3) summary
      cd09146
      Location:49 → 211
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:247 → 440
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      PHA02820
      Location:42 → 465
      PHA02820; phospholipase-D-like protein; Provisional

    2. NM_001195812.2 → NP_001182741.1  inactive phospholipase D5 isoform 3

      See identical proteins and their annotated locations for NP_001182741.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK091691, AL591686, AY461578
      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (3) summary
      cd09149
      Location:101 → 294
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      pfam13091
      Location:125 → 286
      PLDc_2; PLD-like domain
      cl15239
      Location:1 → 65
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    3. NM_001320272.2 → NP_001307201.1  inactive phospholipase D5 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 4, which has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK098092, AL133851, AL445704, AL591686, BU581400
      Conserved Domains (3) summary
      cd09146
      Location:19 → 181
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:217 → 410
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      PHA02820
      Location:20 → 435
      PHA02820; phospholipase-D-like protein; Provisional

    4. NM_001372062.1 → NP_001358991.1  inactive phospholipase D5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL360271, AL445704, AL583845, AL591686
      Consensus CDS
      CCDS1621.2
      UniProtKB/Swiss-Prot
      A1KXV0, B7Z324, Q494U9, Q8N7P1, Q8NB22
      Related
      ENSP00000440896.1, ENST00000536534.7
      Conserved Domains (2) summary
      cd09146
      Location:111 → 273
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:309 → 502
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      242082986..242530546 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544115.3 → XP_011542417.1  inactive phospholipase D5 isoform X2

      See identical proteins and their annotated locations for XP_011542417.1

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (2) summary
      cd09146
      Location:20 → 182
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:218 → 411
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5

    2. XM_011544116.3 → XP_011542418.1  inactive phospholipase D5 isoform X2

      See identical proteins and their annotated locations for XP_011542418.1

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (2) summary
      cd09146
      Location:20 → 182
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:218 → 411
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5

    3. XM_024453867.2 → XP_024309635.1  inactive phospholipase D5 isoform X1

      Conserved Domains (2) summary
      cd09146
      Location:68 → 230
      PLDc_vPLD5_1; Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5
      cd09149
      Location:266 → 459
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5

    4. XM_047448705.1 → XP_047304661.1  inactive phospholipase D5 isoform X4

    5. XM_047448702.1 → XP_047304658.1  inactive phospholipase D5 isoform X4

    6. XM_011544120.3 → XP_011542422.1  inactive phospholipase D5 isoform X5

      See identical proteins and their annotated locations for XP_011542422.1

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (3) summary
      cd09149
      Location:101 → 294
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      pfam13091
      Location:125 → 286
      PLDc_2; PLD-like domain
      cl15239
      Location:1 → 65
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    7. XM_011544119.3 → XP_011542421.2  inactive phospholipase D5 isoform X3

    8. XM_011544121.3 → XP_011542423.1  inactive phospholipase D5 isoform X5

      See identical proteins and their annotated locations for XP_011542423.1

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (3) summary
      cd09149
      Location:101 → 294
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      pfam13091
      Location:125 → 286
      PLDc_2; PLD-like domain
      cl15239
      Location:1 → 65
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    9. XM_017000570.3 → XP_016856059.1  inactive phospholipase D5 isoform X5

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (3) summary
      cd09149
      Location:101 → 294
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      pfam13091
      Location:125 → 286
      PLDc_2; PLD-like domain
      cl15239
      Location:1 → 65
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    10. XM_011544122.4 → XP_011542424.1  inactive phospholipase D5 isoform X5

      See identical proteins and their annotated locations for XP_011542424.1

      UniProtKB/Swiss-Prot
      Q8N7P1
      Conserved Domains (3) summary
      cd09149
      Location:101 → 294
      PLDc_vPLD5_2; Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5
      pfam13091
      Location:125 → 286
      PLDc_2; PLD-like domain
      cl15239
      Location:1 → 65
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      241495068..241942534 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334940.1 → XP_054190915.1  inactive phospholipase D5 isoform X2

    2. XM_054334941.1 → XP_054190916.1  inactive phospholipase D5 isoform X2

    3. XM_054334939.1 → XP_054190914.1  inactive phospholipase D5 isoform X1

    4. XM_054334944.1 → XP_054190919.1  inactive phospholipase D5 isoform X4

    5. XM_054334943.1 → XP_054190918.1  inactive phospholipase D5 isoform X4

    6. XM_054334946.1 → XP_054190921.1  inactive phospholipase D5 isoform X5

    7. XM_054334942.1 → XP_054190917.1  inactive phospholipase D5 isoform X3

    8. XM_054334948.1 → XP_054190923.1  inactive phospholipase D5 isoform X5

    9. XM_054334947.1 → XP_054190922.1  inactive phospholipase D5 isoform X5

    10. XM_054334945.1 → XP_054190920.1  inactive phospholipase D5 isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152666.2: Suppressed sequence

      Description
      NM_152666.2: This RefSeq was removed because currently there is support for the protein but not for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N7P1.2 GenPept UniProtKB/Swiss-Prot:Q8N7P1

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