Human Gene AP3B1 (uc003kfj.4)
  Description: Homo sapiens adaptor-related protein complex 3, beta 1 subunit (AP3B1), transcript variant 1, mRNA.
RefSeq Summary (NM_003664): This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is part of the heterotetrameric AP-3 protein complex which interacts with the scaffolding protein clathrin. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr5:77,298,150-77,590,579 Size: 292,430 Total Exon Count: 27 Strand: -
Coding Region
   Position: hg19 chr5:77,298,726-77,590,403 Size: 291,678 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:77,298,150-77,590,579)mRNA (may differ from genome)Protein (1094 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer
GeneCardsGeneNetworkH-INVHGNCHPRDLynx
MGIneXtProtOMIMPubMedReactomeUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: AP3B1_HUMAN
DESCRIPTION: RecName: Full=AP-3 complex subunit beta-1; AltName: Full=Adapter-related protein complex 3 subunit beta-1; AltName: Full=Adaptor protein complex AP-3 subunit beta-1; AltName: Full=Beta-3A-adaptin; AltName: Full=Clathrin assembly protein complex 3 beta-1 large chain;
FUNCTION: Subunit of non-clathrin- and clathrin-associated adaptor protein complex 3 (AP-3) that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. AP-3 appears to be involved in the sorting of a subset of transmembrane proteins targeted to lysosomes and lysosome-related organelles. 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.
SUBUNIT: AP-3 associates with the BLOC-1 complex (By similarity). Adaptor protein complex 3 (AP-3) is an 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).
SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasmic vesicle, clathrin-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Golgi apparatus (By similarity). Note=Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi complex (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Phosphorylated on serine residues.
DISEASE: Defects in AP3B1 are the cause of Hermansky-Pudlak syndrome type 2 (HPS2) [MIM:608233]. Hermansky-Pudlak syndrome (HPS) is a genetically heterogeneous, rare, 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. HPS2 differs from the other forms of HPS in that it includes immunodeficiency in its phenotype and patients with HPS2 have an increased susceptibility to infections.
SIMILARITY: Belongs to the adaptor complexes large subunit family.
WEB RESOURCE: Name=AP3B1base; Note=AP3B1 mutation db; URL="http://bioinf.uta.fi/AP3B1base/";
WEB RESOURCE: Name=Mutations of the ADTB3A gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/adtb3mut.htm";
WEB RESOURCE: Name=Albinism database (ADB); Note=AP3B1 mutations; URL="http://albinismdb.med.umn.edu/hps2mut.htm";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/AP3B1";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): AP3B1
CDC HuGE Published Literature: AP3B1
Positive Disease Associations: Carotid Artery Diseases
Related Studies:
  1. Carotid Artery Diseases
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.

-  MalaCards Disease Associations
  MalaCards Gene Search: AP3B1
Diseases sorted by gene-association score: hermansky-pudlak syndrome 2* (1687), hermansky-pudlak syndrome (30), oculocutaneous albinism (21), storage pool platelet disease (12), hermansky-pudlak syndrome 1 (12), hemophagocytic lymphohistiocytosis (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.25 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 327.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.00176-0.438 Picture PostScript Text
3' UTR -127.56576-0.221 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR026740 - AP3_beta
IPR026739 - AP_beta
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR002553 - Clathrin/coatomer_adapt-like_N

Pfam Domains:
PF01602 - Adaptin N terminal region
PF12717 - non-SMC mitotic condensation complex subunit 1
PF14796 - Clathrin-adaptor complex-3 beta-1 subunit C-terminal
PF14797 - Serine-rich region of AP3B1, clathrin-adaptor complex

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain

ModBase Predicted Comparative 3D Structure on O00203
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
     SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019903 protein phosphatase binding
GO:0030742 GTP-dependent protein binding

Biological Process:
GO:0006622 protein targeting to lysosome
GO:0006886 intracellular protein transport
GO:0007596 blood coagulation
GO:0008089 anterograde axonal transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0019882 antigen processing and presentation
GO:0032438 melanosome organization
GO:0048007 antigen processing and presentation, exogenous lipid antigen via MHC class Ib
GO:0048490 anterograde synaptic vesicle transport
GO:0051138 positive regulation of NK T cell differentiation

Cellular Component:
GO:0005765 lysosomal membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0030117 membrane coat
GO:0030123 AP-3 adaptor complex
GO:0030131 clathrin adaptor complex
GO:0030665 clathrin-coated vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:1904115 axon cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC038444 - Homo sapiens adaptor-related protein complex 3, beta 1 subunit, mRNA (cDNA clone MGC:40360 IMAGE:3914400), complete cds.
BX538041 - Homo sapiens mRNA; cDNA DKFZp686F10145 (from clone DKFZp686F10145).
U81504 - Homo sapiens beta-3A-adaptin subunit of the AP-3 complex mRNA, complete cds.
AK291201 - Homo sapiens cDNA FLJ76822 complete cds, highly similar to Homo sapiens adaptor-related protein complex 3, beta 1 subunit (AP3B1), mRNA.
U91931 - Homo sapiens AP-3 complex beta3A subunit mRNA, complete cds.
AK225908 - Homo sapiens mRNA for Adapter-related protein complex 3 beta 1 subunit variant, clone: FCC119E04.
EU176289 - Synthetic construct Homo sapiens clone IMAGE:100006405; FLH179552.01X; RZPDo839G01251D adaptor-related protein complex 3, beta 1 subunit (AP3B1) gene, encodes complete protein.
DQ894915 - Synthetic construct Homo sapiens clone IMAGE:100009375; FLH179545.01L; RZPDo839H09129D adaptor-related protein complex 3, beta 1 subunit (AP3B1) gene, encodes complete protein.
KU178426 - Homo sapiens adaptor-related protein complex 3 beta 1 subunit isoform 1 (AP3B1) mRNA, partial cds.
KU178427 - Homo sapiens adaptor-related protein complex 3 beta 1 subunit isoform 2 (AP3B1) mRNA, complete cds, alternatively spliced.
KU178428 - Homo sapiens adaptor-related protein complex 3 beta 1 subunit isoform 3 (AP3B1) mRNA, complete cds, alternatively spliced.
AY623424 - Homo sapiens adaptor-related protein complex 3 beta 1 subunit mRNA, partial cds.
BC020230 - Homo sapiens cDNA clone IMAGE:4623212, containing frame-shift errors.
AK303300 - Homo sapiens cDNA FLJ51426 complete cds, highly similar to Adapter-related protein complex 3 beta-1 subunit.
JD069039 - Sequence 50063 from Patent EP1572962.
JD410020 - Sequence 391044 from Patent EP1572962.
JD557058 - Sequence 538082 from Patent EP1572962.
JD082868 - Sequence 63892 from Patent EP1572962.
JD315990 - Sequence 297014 from Patent EP1572962.
CU691576 - Synthetic construct Homo sapiens gateway clone IMAGE:100020516 5' read AP3B1 mRNA.
BC113045 - Homo sapiens cDNA clone IMAGE:40022061.
JD056270 - Sequence 37294 from Patent EP1572962.
JD540268 - Sequence 521292 from Patent EP1572962.
JD157816 - Sequence 138840 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein O00203 (Reactome details) participates in the following event(s):

R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-199991 Membrane Trafficking
R-HSA-5663202 Diseases of signal transduction
R-HSA-5653656 Vesicle-mediated transport
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ADTB3A, AP3B1_HUMAN, NM_003664, NP_001258698, O00203, O00580, Q7Z393, Q9HD66, uc003kfj.3
UCSC ID: uc003kfj.4
RefSeq Accession: NM_003664
Protein: O00203 (aka AP3B1_HUMAN or A3B1_HUMAN)
CCDS: CCDS4041.1, CCDS64186.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene AP3B1:
hps (Hermansky-Pudlak Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003664.4
exon count: 27CDS single in 3' UTR: no RNA size: 4060
ORF size: 3285CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6434.50frame shift in genome: no % Coverage: 99.43
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.