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

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A homozygous AP3D1 missense variant in patients with sensorineural hearing loss as the leading manifestation.
Title: A homozygous AP3D1 missense variant in patients with sensorineural hearing loss as the leading manifestation.
Connecting COPD GWAS Genes: FAM13A Controls TGFbeta2 Secretion by Modulating AP-3 Transport.
Title: Connecting COPD GWAS Genes: FAM13A Controls TGFβ2 Secretion by Modulating AP-3 Transport.
A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers.
Title: A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers.
We further demonstrated an abnormal storage pathway in the platelets. The current study represents a second confirmation report and implicates AP3D1 mutations as a cause of Hermansky-Pudlak Syndrome type 10.
Title: Biallelic mutations in AP3D1 cause Hermansky-Pudlak syndrome type 10 associated with immunodeficiency and seizure disorder.
A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese
Title: A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.
Unexpectedly, no evidence of binding between the N-terminal matrix (MA) domain of HIV-1 Gag and the cellular Adaptor Protein AP-3 (AP-3delta) was observed in these in vitro experiments.
Title: The HIV-1 matrix protein does not interact directly with the protein interactive domain of AP-3δ.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
The studies demonstrate a role for AP-3 in HIV replication in a tetraspanin-rich compartment in dendritic cells (DC) and contribute to the elucidation of the trafficking pathways required for DC-T cell transfer of HIV-1 infection.
Title: HIV-1 replication in dendritic cells occurs through a tetraspanin-containing compartment enriched in AP-3.
The matrix region of HIV-1 Gag interacts directly with the delta subunit of the AP-3 complex, and that this interaction plays an important functional role in particle assembly
Title: AP-3 directs the intracellular trafficking of HIV-1 Gag and plays a key role in particle assembly.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Associated conditions

Description	Tests
Hermansky-Pudlak syndrome 10 MedGen: C4310746 OMIM: 617050 GeneReviews: Hermansky-Pudlak Syndrome	not available

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH93528 (e-PCR)
- UniSTS:88616

G19943 (e-PCR)
- UniSTS:70735

A002D02 (e-PCR)
- UniSTS:70736

G67894 (e-PCR)
- UniSTS:225630

WI-19632 (e-PCR)
- UniSTS:34916

SHGC-23975 (e-PCR)
- UniSTS:84393

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterograde axonal transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterograde synaptic vesicle transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterograde synaptic vesicle transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IEA Inferred from Electronic Annotation more info
involved_in clathrin-coated vesicle cargo loading, AP-3-mediated	NAS Non-traceable Author Statement more info	PubMed
involved_in endosome to melanosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	TAS Traceable Author Statement more info	PubMed
involved_in intracellular transport	NAS Non-traceable Author Statement more info	PubMed
involved_in melanosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in melanosome organization	IC Inferred by Curator more info	PubMed
involved_in neurotransmitter receptor transport, postsynaptic endosome to lysosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in platelet dense granule organization	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of NK T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in protein localization to membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle budding from endosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle coating	NAS Non-traceable Author Statement more info	PubMed
involved_in synaptic vesicle membrane organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle recycling	NAS Non-traceable Author Statement more info	PubMed
involved_in vesicle-mediated transport	NAS Non-traceable Author Statement more info	PubMed
involved_in zinc ion import into lysosome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of AP-3 adaptor complex	NAS Non-traceable Author Statement more info	PubMed
located_in Golgi apparatus	TAS Traceable Author Statement more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in early endosome	NAS Non-traceable Author Statement more info	PubMed
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in postsynapse	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic endosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in terminal bouton	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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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)

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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

NG_052886.2 RefSeqGene

Range

17903..68481

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_1207

mRNA and Protein(s)

NM_001261826.3 → NP_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:151 → 172

HEAT; HEAT repeat [structural motif]

pfam01602
Location:32 → 581

Adaptin_N; Adaptin N terminal region

pfam06375
Location:661 → 807

AP3D1; AP-3 complex subunit delta-1
NM_001374799.1 → NP_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:151 → 172

HEAT; HEAT repeat [structural motif]

pfam01602
Location:32 → 581

Adaptin_N; Adaptin N terminal region

pfam06375
Location:661 → 807

AP3D1; AP-3 complex subunit delta-1
NM_003938.8 → NP_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:32 → 581

Adaptin_N; Adaptin N terminal region

pfam06375
Location:661 → 807

BLVR; Bovine leukaemia virus receptor (BLVR)

pfam12717
Location:155 → 265

Cnd1; non-SMC mitotic condensation complex subunit 1

sd00044
Location:151 → 172

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

2100988..2164616 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439598.1 → XP_047295554.1 AP-3 complex subunit delta-1 isoform X2
XM_047439597.1 → XP_047295553.1 AP-3 complex subunit delta-1 isoform X1
XM_047439599.1 → XP_047295555.1 AP-3 complex subunit delta-1 isoform X4
XM_017027422.2 → XP_016882911.1 AP-3 complex subunit delta-1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

2074043..2137861 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322491.1 → XP_054178466.1 AP-3 complex subunit delta-1 isoform X2
XM_054322490.1 → XP_054178465.1 AP-3 complex subunit delta-1 isoform X1
XM_054322492.1 → XP_054178467.1 AP-3 complex subunit delta-1 isoform X3
XM_054322493.1 → XP_054178468.1 AP-3 complex subunit delta-1 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001077523.1: Suppressed sequence

Description

NM_001077523.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.