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    AP3D1 adaptor related protein complex 3 subunit delta 1 [ Homo sapiens (human) ]

    Gene ID: 8943, updated on 10-Dec-2024

    Summary

    Official Symbol
    AP3D1provided by HGNC
    Official Full Name
    adaptor related protein complex 3 subunit delta 1provided by HGNC
    Primary source
    HGNC:HGNC:568
    See related
    Ensembl:ENSG00000065000 MIM:607246; AllianceGenome:HGNC:568
    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
    ADTD; HPS10; hBLVR
    Summary
    The protein encoded by this gene is a subunit of the AP3 adaptor-like complex, which is not clathrin-associated, but is associated with the golgi region, as well as more peripheral structures. The AP-3 complex facilitates the budding of vesicles from the golgi membrane, and may be directly involved in trafficking to lysosomes. This subunit is implicated in intracellular biogenesis and trafficking of pigment granules, and possibly platelet dense granules and neurotransmitter vesicles. Defects in this gene are a cause of a new type of Hermansky-Pudlak syndrome. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in testis (RPKM 31.2), kidney (RPKM 22.6) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See AP3D1 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2100988..2164616, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2074043..2137861, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2100987..2151565, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2085331-2086056 Neighboring gene MOB kinase activator 3A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2089069-2090031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096431-2096958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096959-2097484 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2104508-2104680 Neighboring gene IZUMO family member 4 Neighboring gene MPRA-validated peak3230 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2141381-2141538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2144918-2145541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2145542-2146164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13657 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2150717-2150878 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2151574-2152011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9771 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2165242-2165623 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:2168563-2169762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2171045-2171639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2171640-2172234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2173473-2173991 Neighboring gene DOT1 like histone lysine methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2180689-2181272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2195534-2196062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2196063-2196591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2200246-2201219 Neighboring gene uncharacterized LOC124904611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2225862-2226368 Neighboring gene pleckstrin homology domain containing J1 Neighboring gene microRNA 1227

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Envelope surface glycoprotein gp160, precursor env In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    nef HIV-1 Nef co-localizes with the delta subunit of adaptor protein complex 3 (AP-3) in a juxtanuclear region near the cell center of HeLa cells PubMed
    nef The dileucine residues and glutamic acid residue of the EXXXLL motif in HIV-1 Nef (amino acid residues 159-165) are required for Nef binding and stabilization of AP-3 PubMed
    Pr55(Gag) gag The matrix region (residues 1-133) of HIV-1 Gag interacts directly with the delta subunit of the AP-3 complex, and this interaction is required for Gag trafficking to multivesicular bodies PubMed
    gag Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 delta 1 subunit (AP3D1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed
    gag AP3D1 deficiency in HPS2 fibroblasts inhibits HIV-1 Gag assembly and release PubMed
    matrix gag NMR analysis shows that HIV-1 Matrix Protein fails to directly interact with AP-3delta PubMed
    gag The matrix region of HIV-1 Gag interacts directly with the delta subunit of the AP-3 complex, and this interaction is required for Gag trafficking to multivesicular bodies PubMed
    gag In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport  
    involved_in anterograde axonal transport  
    involved_in anterograde synaptic vesicle transport  
    involved_in anterograde synaptic vesicle transport  
    involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib  
    involved_in clathrin-coated vesicle cargo loading, AP-3-mediated PubMed 
    involved_in endosome to melanosome transport PubMed 
    involved_in intracellular protein transport PubMed 
    involved_in intracellular transport PubMed 
    involved_in melanosome assembly PubMed 
    involved_in melanosome organization PubMed 
    involved_in neurotransmitter receptor transport, postsynaptic endosome to lysosome  
    involved_in platelet dense granule organization PubMed 
    involved_in positive regulation of NK T cell differentiation  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in protein localization to membrane PubMed 
    involved_in protein targeting to vacuole  
    involved_in synaptic vesicle budding from endosome  
    involved_in synaptic vesicle coating PubMed 
    involved_in synaptic vesicle membrane organization  
    involved_in synaptic vesicle recycling PubMed 
    involved_in vesicle-mediated transport PubMed 
    involved_in zinc ion import into lysosome PubMed 
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex  
    part_of AP-3 adaptor complex PubMed 
    located_in Golgi apparatus PubMed 
    located_in Golgi membrane  
    located_in axon cytoplasm  
    located_in early endosome PubMed 
    is_active_in endosome membrane  
    located_in endosome membrane PubMed 
    located_in glutamatergic synapse  
    located_in lysosomal membrane PubMed 
    located_in membrane PubMed 
    located_in postsynapse  
    is_active_in presynaptic endosome  
    is_active_in terminal bouton  

    General protein information

    Preferred Names
    AP-3 complex subunit delta-1
    Names
    AP-3 complex delta subunit, partial CDS
    adapter-related protein complex 3 subunit delta-1
    adaptor related protein complex 3 delta 1 subunit
    delta adaptin
    subunit of putative vesicle coat adaptor complex AP-3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_052886.2 RefSeqGene

      Range
      17903..68481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1207

    mRNA and Protein(s)

    1. NM_001261826.3NP_001248755.1  AP-3 complex subunit delta-1 isoform 3

      See identical proteins and their annotated locations for NP_001248755.1

      Status: REVIEWED

      Source sequence(s)
      AB208804, AC005545, BM982261, HY040370
      Consensus CDS
      CCDS58638.1
      UniProtKB/Swiss-Prot
      O14617
      Related
      ENSP00000495274.2, ENST00000643116.3
      Conserved Domains (3) summary
      sd00044
      Location:151172
      HEAT; HEAT repeat [structural motif]
      pfam01602
      Location:32581
      Adaptin_N; Adaptin N terminal region
      pfam06375
      Location:661807
      AP3D1; AP-3 complex subunit delta-1
    2. NM_001374799.1NP_001361728.1  AP-3 complex subunit delta-1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC005257, AC005328, AC005545
      Consensus CDS
      CCDS92482.1
      UniProtKB/TrEMBL
      A0A8V8TQW4
      Related
      ENSP00000514969.1, ENST00000700387.1
      Conserved Domains (3) summary
      sd00044
      Location:151172
      HEAT; HEAT repeat [structural motif]
      pfam01602
      Location:32581
      Adaptin_N; Adaptin N terminal region
      pfam06375
      Location:661807
      AP3D1; AP-3 complex subunit delta-1
    3. NM_003938.8NP_003929.4  AP-3 complex subunit delta-1 isoform 2

      See identical proteins and their annotated locations for NP_003929.4

      Status: REVIEWED

      Source sequence(s)
      AC005545, AF002163, BM982261, HY040370
      Consensus CDS
      CCDS42459.1
      UniProtKB/Swiss-Prot
      O00202, O14617, O75262, Q59HF5, Q96G11, Q9H3C6
      Related
      ENSP00000344055.4, ENST00000345016.9
      Conserved Domains (4) summary
      pfam01602
      Location:32581
      Adaptin_N; Adaptin N terminal region
      pfam06375
      Location:661807
      BLVR; Bovine leukaemia virus receptor (BLVR)
      pfam12717
      Location:155265
      Cnd1; non-SMC mitotic condensation complex subunit 1
      sd00044
      Location:151172
      HEAT; HEAT repeat [structural 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
      2100988..2164616 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439598.1XP_047295554.1  AP-3 complex subunit delta-1 isoform X2

    2. XM_047439597.1XP_047295553.1  AP-3 complex subunit delta-1 isoform X1

    3. XM_047439599.1XP_047295555.1  AP-3 complex subunit delta-1 isoform X4

    4. XM_017027422.2XP_016882911.1  AP-3 complex subunit delta-1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      2074043..2137861 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322491.1XP_054178466.1  AP-3 complex subunit delta-1 isoform X2

    2. XM_054322490.1XP_054178465.1  AP-3 complex subunit delta-1 isoform X1

    3. XM_054322492.1XP_054178467.1  AP-3 complex subunit delta-1 isoform X3

    4. XM_054322493.1XP_054178468.1  AP-3 complex subunit delta-1 isoform X4

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