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PLD3 phospholipase D family member 3 [ Homo sapiens (human) ]

Gene ID: 23646, updated on 17-Sep-2024

Summary

Official Symbol
PLD3provided by HGNC
Official Full Name
phospholipase D family member 3provided by HGNC
Primary source
HGNC:HGNC:17158
See related
Ensembl:ENSG00000105223 MIM:615698; AllianceGenome:HGNC:17158
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
AD19; HUK4; HU-K4; SCA46
Summary
This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]
Expression
Ubiquitous expression in brain (RPKM 96.3), spleen (RPKM 74.5) and 25 other tissues See more
Orthologs
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Genomic context

See PLD3 in Genome Data Viewer
Location:
19q13.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (40348695..40378485)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43169216..43199111)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (40854602..40884392)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene AKT serine/threonine kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10619 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:40791573-40792404 Neighboring gene microRNA 641 Neighboring gene chromosome 19 open reading frame 47 Neighboring gene RNA, U6 small nuclear 945, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40829016-40829516 Neighboring gene MPRA-validated peak3483 silencer Neighboring gene Sharpr-MPRA regulatory region 7250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14649 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:40873853-40874018 Neighboring gene Sharpr-MPRA regulatory region 12346 Neighboring gene microRNA 6796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40895441-40895990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40895991-40896540 Neighboring gene homeodomain interacting protein kinase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40915393-40915986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40915987-40916578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40920095-40920743 Neighboring gene periaxin

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with PLD3; predicted interaction to occur in the endoplasmic reticulum PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phospholipase D activity TAS
Traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables single-stranded DNA 5'-3' DNA exonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in immune system process IEA
Inferred from Electronic Annotation
more info
 
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in myotube differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of cytokine production involved in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
5'-3' exonuclease PLD3
Names
choline phosphatase 3
hindIII K4L homolog
phosphatidylcholine-hydrolyzing phospholipase D3
NP_001026866.1
NP_001278240.1
NP_036400.2

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_034098.1 RefSeqGene

    Range
    5271..35061
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001031696.4NP_001026866.1  5'-3' exonuclease PLD3

    See identical proteins and their annotated locations for NP_001026866.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC000553, BC096820, BQ640152, DB057420
    Consensus CDS
    CCDS33027.1
    UniProtKB/Swiss-Prot
    Q8IV08, Q92853, Q9BW87
    UniProtKB/TrEMBL
    A0A8V8TPY8
    Related
    ENSP00000348901.5, ENST00000356508.9
    Conserved Domains (1) summary
    cl28150
    Location:77490
    PLDc; Phospholipase D Active site motif
  2. NM_001291311.2NP_001278240.1  5'-3' exonuclease PLD3

    See identical proteins and their annotated locations for NP_001278240.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 2. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC000553, BC096820, BP304863, BQ640152, U60644
    Consensus CDS
    CCDS33027.1
    UniProtKB/Swiss-Prot
    Q8IV08, Q92853, Q9BW87
    UniProtKB/TrEMBL
    A0A8V8TPY8
    Related
    ENSP00000387022.1, ENST00000409281.5
    Conserved Domains (1) summary
    cl28150
    Location:77490
    PLDc; Phospholipase D Active site motif
  3. NM_012268.4NP_036400.2  5'-3' exonuclease PLD3

    See identical proteins and their annotated locations for NP_036400.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longer transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC000553, BP304863, BQ640152, CX785201
    Consensus CDS
    CCDS33027.1
    UniProtKB/Swiss-Prot
    Q8IV08, Q92853, Q9BW87
    UniProtKB/TrEMBL
    A0A8V8TPY8
    Related
    ENSP00000386938.3, ENST00000409735.9
    Conserved Domains (1) summary
    cl28150
    Location:77490
    PLDc; Phospholipase D Active site motif

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    40348695..40378485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    43169216..43199111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)