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Aliases for AP3D1 Gene

Aliases for AP3D1 Gene

  • Adaptor Related Protein Complex 3 Delta 1 Subunit 2 3 5
  • Adaptor-Related Protein Complex 3 Subunit Delta-1 3 4
  • Subunit Of Putative Vesicle Coat Adaptor Complex AP-3 3
  • Adaptor-Related Protein Complex 3, Delta 1 Subunit 2
  • Adapter-Related Protein Complex 3 Subunit Delta-1 3
  • AP-3 Complex Delta Subunit, Partial CDS 3
  • AP-3 Complex Subunit Delta-1 3
  • AP-3 Complex Subunit Delta 4
  • Delta Adaptin 3
  • Delta-Adaptin 4
  • HPS10 3
  • HBLVR 3
  • ADTD 3

External Ids for AP3D1 Gene

Previous GeneCards Identifiers for AP3D1 Gene

  • GC19M002163
  • GC19M002040
  • GC19M002051
  • GC19M001873

Summaries for AP3D1 Gene

Entrez Gene Summary for AP3D1 Gene

  • 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]

GeneCards Summary for AP3D1 Gene

AP3D1 (Adaptor Related Protein Complex 3 Delta 1 Subunit) is a Protein Coding gene. Diseases associated with AP3D1 include Anogenital Venereal Wart and Hermansky-Pudlak Syndrome. Among its related pathways are Lysosome. GO annotations related to this gene include binding and protein transporter activity.

UniProtKB/Swiss-Prot for AP3D1 Gene

  • Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. Involved in process of CD8+ T-cell and NK cell degranulation (PubMed:26744459). In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals (By similarity).

Gene Wiki entry for AP3D1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AP3D1 Gene

Genomics for AP3D1 Gene

Regulatory Elements for AP3D1 Gene

Enhancers for AP3D1 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
GH19G002160 1.8 FANTOM5 ENCODE dbSUPER 9.2 -3.3 -3276 13.7 CREB3L1 MLX ZFP64 DMAP1 YBX1 FEZF1 YY1 SLC30A9 ZNF143 SP3 ZNF77 SF3A2 LOC100288123 CIRBP GADD45B ENSG00000267139 DOT1L ENSG00000267317 ZNF554 ADAT3
GH19G002149 1.3 ENCODE dbSUPER 12.6 +13.7 13726 3.7 HDGF PKNOX1 MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF766 AP3D1 AMH SF3A2 PLEKHJ1 IZUMO4 DOT1L GC19P002134
GH19G002184 1.5 FANTOM5 Ensembl ENCODE dbSUPER 6.2 -22.7 -22738 5.0 HDGF FEZF1 HIC1 POLR2A EED FOS RELB IKZF2 MAFK NFE2L2 AMH MIR1227 SF3A2 PLEKHJ1 IZUMO4 AP3D1 GC19M002178 LOC105372239
GH19G002123 0.6 ENCODE 14.7 +40.6 40609 0.2 ZNF263 CTCF MIER1 SIN3A MIER2 REST HIC1 HDAC2 POLR2A ZBTB26 AP3D1 BTBD2 SF3A2 MIR1227 GC19P002129 PIR47033
GH19G002211 0.9 ENCODE 9.2 -48.8 -48830 3.6 ELF3 ATF1 MLX ZFP64 ARID4B DMAP1 DNMT3B ZSCAN9 RARA ZNF121 LOC105372239 MIR1227 SF3A2 PLEKHJ1 AP3D1 GC19M002178
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around AP3D1 on UCSC Golden Path with GeneCards custom track

Promoters for AP3D1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000105811 -235 2601 HDGF MLX CREB3L1 ARNT ZFP64 ARID4B SIN3A DMAP1 FEZF1 ZNF2

Genomic Location for AP3D1 Gene

Chromosome:
19
Start:
2,100,988 bp from pter
End:
2,164,465 bp from pter
Size:
63,478 bases
Orientation:
Minus strand

Genomic View for AP3D1 Gene

Genes around AP3D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AP3D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AP3D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AP3D1 Gene

Proteins for AP3D1 Gene

  • Protein details for AP3D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14617-AP3D1_HUMAN
    Recommended name:
    AP-3 complex subunit delta-1
    Protein Accession:
    O14617
    Secondary Accessions:
    • O00202
    • O75262
    • Q59HF5
    • Q96G11
    • Q9H3C6

    Protein attributes for AP3D1 Gene

    Size:
    1153 amino acids
    Molecular mass:
    130158 Da
    Quaternary structure:
    • AP-3 associates with the BLOC-1 complex (By similarity). Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large adaptins (delta-type subunit AP3D1 and beta-type subunit AP3B1 or AP3B2), a medium adaptin (mu-type subunit AP3M1 or AP3M2) and a small adaptin (sigma-type subunit APS1 or AP3S2) (By similarity). Interacts with SLC30A2 (PubMed:25808614).
    SequenceCaution:
    • Sequence=AAG35473.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Presence of an unrelated sequence found on chromosome 7.; Evidence={ECO:0000305}; Sequence=AAH10065.1; Type=Miscellaneous discrepancy; Note=Lack of 8 exons and truncation of 2 other exons in the C- terminus. Alternative splicing seems doubtful, since exon-intron junctions are not the consensus ones.; Evidence={ECO:0000305}; Sequence=BAD92041.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for AP3D1 Gene

    Alternative splice isoforms for AP3D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AP3D1 Gene

Post-translational modifications for AP3D1 Gene

  • Ubiquitination at posLast=1616 and Lys176
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for AP3D1 Gene

Domains & Families for AP3D1 Gene

Suggested Antigen Peptide Sequences for AP3D1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O14617

UniProtKB/Swiss-Prot:

AP3D1_HUMAN :
  • Belongs to the adaptor complexes large subunit family.
Family:
  • Belongs to the adaptor complexes large subunit family.
genes like me logo Genes that share domains with AP3D1: view

No data available for Gene Families for AP3D1 Gene

Function for AP3D1 Gene

Molecular function for AP3D1 Gene

UniProtKB/Swiss-Prot Function:
Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. Involved in process of CD8+ T-cell and NK cell degranulation (PubMed:26744459). In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals (By similarity).

Gene Ontology (GO) - Molecular Function for AP3D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity TAS 9303295
genes like me logo Genes that share ontologies with AP3D1: view
genes like me logo Genes that share phenotypes with AP3D1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for AP3D1 Gene

Localization for AP3D1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AP3D1 Gene

Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side.

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 AP3D1 gene
Compartment Confidence
lysosome 5
endosome 5
nucleus 4
golgi apparatus 4
plasma membrane 3
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for AP3D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IEA --
GO:0005765 lysosomal membrane IDA 17897319
GO:0005794 Golgi apparatus TAS,IEA 9151686
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with AP3D1: view

Pathways & Interactions for AP3D1 Gene

SuperPathways for AP3D1 Gene

SuperPathway Contained pathways
1 Lysosome
genes like me logo Genes that share pathways with AP3D1: view

Pathways by source for AP3D1 Gene

1 KEGG pathway for AP3D1 Gene

Gene Ontology (GO) - Biological Process for AP3D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006726 eye pigment biosynthetic process TAS 9303295
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA,TAS 9151686
GO:0008089 anterograde axonal transport ISS --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with AP3D1: view

No data available for SIGNOR curated interactions for AP3D1 Gene

Drugs & Compounds for AP3D1 Gene

No Compound Related Data Available

Transcripts for AP3D1 Gene

Unigene Clusters for AP3D1 Gene

Adaptor-related protein complex 3, delta 1 subunit:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for AP3D1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19 ^ 20a · 20b ^ 21a · 21b ^
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: - - - - - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

ExUns: 22a · 22b · 22c ^ 23a · 23b · 23c · 23d · 23e · 23f ^ 24a · 24b ^ 25a · 25b · 25c · 25d ^ 26 ^ 27a · 27b ^ 28a · 28b · 28c ^ 29a · 29b ^ 30a · 30b · 30c ·
SP1:
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: - -
SP6: -
SP7: - - - - - - - -
SP8:
SP9: -
SP10: - -
SP11:
SP12: -
SP13:

Relevant External Links for AP3D1 Gene

GeneLoc Exon Structure for
AP3D1
ECgene alternative splicing isoforms for
AP3D1

Expression for AP3D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AP3D1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for AP3D1 Gene

This gene is overexpressed in Frontal cortex (10.9), Peripheral blood mononuclear cells (7.8), and Brain (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for AP3D1 Gene



Protein tissue co-expression partners for AP3D1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of AP3D1 Gene:

AP3D1

SOURCE GeneReport for Unigene cluster for AP3D1 Gene:

Hs.512815

mRNA Expression by UniProt/SwissProt for AP3D1 Gene:

O14617-AP3D1_HUMAN
Tissue specificity: Present in all adult tissues examined with the highest levels in skeletal muscle, heart, pancreas and testis.

Evidence on tissue expression from TISSUES for AP3D1 Gene

  • Nervous system(4.8)
  • Heart(4.4)
  • Liver(4.4)
  • Muscle(4.4)
  • Blood(4.3)
  • Skin(3.4)
  • Lung(3.3)
  • Eye(2.7)
  • Intestine(2.7)
  • Kidney(2)
genes like me logo Genes that share expression patterns with AP3D1: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for AP3D1 Gene

Orthologs for AP3D1 Gene

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

Orthologs for AP3D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia AP3D1 34 35
  • 99.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia AP3D1 35
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia AP3D1 35
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia AP3D1 34 35
  • 86.31 (n)
cow
(Bos Taurus)
Mammalia AP3D1 34 35
  • 85.04 (n)
mouse
(Mus musculus)
Mammalia Ap3d1 34 16 35
  • 83.82 (n)
rat
(Rattus norvegicus)
Mammalia Ap3d1 34
  • 83.56 (n)
chicken
(Gallus gallus)
Aves AP3D1 34 35
  • 77.7 (n)
lizard
(Anolis carolinensis)
Reptilia AP3D1 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.217 34
zebrafish
(Danio rerio)
Actinopterygii ap3d1 35
  • 75 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta g 36 35
  • 49 (a)
worm
(Caenorhabditis elegans)
Secernentea apd-3 35
  • 46 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL076W 34
  • 50.41 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E19405g 34
  • 45 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes APL5 34 35
  • 44.46 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 82 (a)
OneToMany
CSA.9291 35
  • 50 (a)
OneToMany
-- 35
  • 41 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU04652 34
  • 50 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes apl5 34
  • 47.85 (n)
Species where no ortholog for AP3D1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for AP3D1 Gene

ENSEMBL:
Gene Tree for AP3D1 (if available)
TreeFam:
Gene Tree for AP3D1 (if available)

Paralogs for AP3D1 Gene

Pseudogenes.org Pseudogenes for AP3D1 Gene

genes like me logo Genes that share paralogs with AP3D1: view

No data available for Paralogs for AP3D1 Gene

Variants for AP3D1 Gene

Sequence variations from dbSNP and Humsavar for AP3D1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs879255646 Pathogenic 2,102,255(-) ACTCT(-/GT)CTCAG reference, frameshift-variant
rs1000028430 -- 2,120,389(+) CTGTG(A/C)CTCCA intron-variant
rs1000057504 -- 2,148,456(+) GGTCT(C/T)TTCTA intron-variant
rs1000062358 -- 2,108,126(+) ACAGA(A/G)AGGAC intron-variant
rs1000144622 -- 2,136,281(+) TCCCT(C/T)GGCGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for AP3D1 Gene

Variant ID Type Subtype PubMed ID
esv1514310 CNV deletion 17803354
esv1666079 CNV deletion 17803354
esv23222 CNV gain+loss 19812545
esv2659904 CNV deletion 23128226
esv2674090 CNV deletion 23128226
esv2674634 CNV deletion 23128226
esv2717875 CNV deletion 23290073
esv2717876 CNV deletion 23290073
esv2717877 CNV deletion 23290073
esv2717878 CNV deletion 23290073
esv3396388 CNV duplication 20981092
esv3583205 CNV loss 25503493
esv3893156 CNV loss 25118596
esv996177 CNV deletion 20482838
nsv1071492 CNV deletion 25765185
nsv1077334 CNV duplication 25765185
nsv523590 CNV loss 19592680
nsv578381 CNV loss 21841781
nsv828392 CNV loss 20364138
nsv833706 CNV loss 17160897

Variation tolerance for AP3D1 Gene

Residual Variation Intolerance Score: 4.61% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.13; 61.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for AP3D1 Gene

Human Gene Mutation Database (HGMD)
AP3D1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AP3D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AP3D1 Gene

Disorders for AP3D1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for AP3D1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
anogenital venereal wart
  • anogenital human papilloma virus infectious disease
hermansky-pudlak syndrome
  • hps
- elite association - COSMIC cancer census association via MalaCards
Search AP3D1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

AP3D1_HUMAN
  • Hermansky-Pudlak syndrome 10 (HPS10) [MIM:617050]: A form of Hermansky-Pudlak syndrome, a genetically heterogeneous autosomal recessive disorder characterized by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS. HPS10 patients manifest albinism, neutropenia, immunodeficiency, neurodevelopmental delay, generalized seizures, and impaired hearing. {ECO:0000269 PubMed:26744459}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for AP3D1

Genetic Association Database (GAD)
AP3D1
Human Genome Epidemiology (HuGE) Navigator
AP3D1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
AP3D1
genes like me logo Genes that share disorders with AP3D1: view

No data available for Genatlas for AP3D1 Gene

Publications for AP3D1 Gene

  1. Altered expression of a novel adaptin leads to defective pigment granule biogenesis in the Drosophila eye color mutant garnet. (PMID: 9303295) Ooi C.E. … Bonifacino J.S. (EMBO J. 1997) 2 3 4 22 64
  2. Characterization of the adaptor-related protein complex, AP-3. (PMID: 9151686) Simpson F. … Robinson M.S. (J. Cell Biol. 1997) 2 3 4 64
  3. Mutations in AP3D1 associated with immunodeficiency and seizures define a new type of Hermansky-Pudlak syndrome. (PMID: 26744459) Ammann S. … Ehl S. (Blood 2016) 3 4 64
  4. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 46 64
  5. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2010) 3 46 64

Products for AP3D1 Gene

Sources for AP3D1 Gene

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