AP3B1

gene
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Also known as ADTB3AHPS2

Summary

AP3B1 (adaptor related protein complex 3 subunit beta 1, HGNC:566) is a protein-coding gene on chromosome 5q14.1, encoding AP-3 complex subunit beta-1 (O00203). 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.

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.

Source: NCBI Gene 8546 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Hermansky-Pudlak syndrome 2 (Definitive, ClinGen)
  • GWAS associations: 18
  • Clinical variants (ClinVar): 1,000 total — 45 pathogenic, 28 likely-pathogenic
  • Phenotypes (HPO): 47
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_003664

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:566
Approved symbolAP3B1
Nameadaptor related protein complex 3 subunit beta 1
Location5q14.1
Locus typegene with protein product
StatusApproved
AliasesADTB3A, HPS2
Ensembl geneENSG00000132842
Ensembl biotypeprotein_coding
OMIM603401
Entrez8546

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 21 protein_coding, 6 nonsense_mediated_decay, 4 retained_intron, 4 protein_coding_CDS_not_defined

ENST00000255194, ENST00000517561, ENST00000517940, ENST00000519295, ENST00000519888, ENST00000520122, ENST00000522901, ENST00000523204, ENST00000695447, ENST00000695448, ENST00000695449, ENST00000695450, ENST00000695451, ENST00000695452, ENST00000695453, ENST00000695454, ENST00000695455, ENST00000695458, ENST00000695488, ENST00000695505, ENST00000695506, ENST00000695507, ENST00000695510, ENST00000695511, ENST00000695512, ENST00000695513, ENST00000695514, ENST00000695515, ENST00000695540, ENST00000909857, ENST00000909858, ENST00000913629, ENST00000913630, ENST00000913631, ENST00000959993

RefSeq mRNA: 3 — MANE Select: NM_003664 NM_001271769, NM_001410752, NM_003664

CCDS: CCDS4041, CCDS64186, CCDS93737

Canonical transcript exons

ENST00000255194 — 27 exons

ExonStartEnd
ENSE000009716477802069278020789
ENSE000009716487801541078015548
ENSE000010049767814114378141319
ENSE000010049807811612678116234
ENSE000011626217815625878156367
ENSE000011626277816281978162951
ENSE000021178077829445278294698
ENSE000034916487803436178034445
ENSE000035000937812803078128160
ENSE000035246847811375278113923
ENSE000035519497812912178129307
ENSE000036055137808939378089499
ENSE000036144147810095378101025
ENSE000036234257803904378039274
ENSE000036723827811020778110354
ENSE000039641027826752078267595
ENSE000039641037822814478228239
ENSE000039641047821605578216237
ENSE000039641057817578478175838
ENSE000039641067817562678175697
ENSE000039641087824086278240936
ENSE000039641097818150778181662
ENSE000039641117822554278225608
ENSE000039641127816561078165672
ENSE000039641137822737278227532
ENSE000039641147817733978177436
ENSE000039642247800232678003055

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 97.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.6475 / max 482.0866, expressed in 1818 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
6220336.13811817
622012.22251164
622020.7221441
621960.477673
621970.087313

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818897.01gold quality
calcaneal tendonUBERON:000370195.27gold quality
tendonUBERON:000004394.93gold quality
islet of LangerhansUBERON:000000694.03gold quality
adenohypophysisUBERON:000219693.82gold quality
pituitary glandUBERON:000000793.81gold quality
monocyteCL:000057693.78gold quality
mononuclear cellCL:000084293.51gold quality
leukocyteCL:000073893.32gold quality
rectumUBERON:000105292.49gold quality
olfactory bulbUBERON:000226492.25gold quality
stromal cell of endometriumCL:000225591.65gold quality
type B pancreatic cellCL:000016991.59gold quality
mucosa of transverse colonUBERON:000499191.44gold quality
smooth muscle tissueUBERON:000113591.24gold quality
lower esophagus mucosaUBERON:003583491.22gold quality
C1 segment of cervical spinal cordUBERON:000646991.21gold quality
adrenal tissueUBERON:001830391.20gold quality
esophagus mucosaUBERON:000246991.17gold quality
pancreasUBERON:000126490.98gold quality
minor salivary glandUBERON:000183090.88gold quality
left lobe of thyroid glandUBERON:000112090.81gold quality
descending thoracic aortaUBERON:000234590.80gold quality
medial globus pallidusUBERON:000247790.69gold quality
body of pancreasUBERON:000115090.68gold quality
right lobe of thyroid glandUBERON:000111990.52gold quality
corpus epididymisUBERON:000435990.42gold quality
popliteal arteryUBERON:000225090.23gold quality
tibial arteryUBERON:000761090.23gold quality
adult mammalian kidneyUBERON:000008290.19gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.29

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, CEBPB, CREBZF, NFKB, TFAP2A, TP53, ZKSCAN7, ZNF91

miRNA regulators (miRDB)

70 targeting AP3B1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3646100.0073.565283
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4673100.0066.641490
HSA-MIR-548P99.9872.253784
HSA-MIR-1213699.9872.815713
HSA-MIR-433-3P99.9869.371203
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-548N99.9871.944170
HSA-MIR-548AN99.9770.912817
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-338-5P99.9272.342951
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-95-5P99.8972.173973
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-129-5P99.8870.263273
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-313399.8170.923506
HSA-MIR-4645-3P99.7669.33993
HSA-MIR-6794-5P99.7666.381048
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-117999.7168.701040
HSA-MIR-4716-3P99.6966.731022
HSA-MIR-366099.6867.331149
HSA-MIR-452699.6867.071136
HSA-MIR-320299.6667.702737
HSA-MIR-545-5P99.6670.182308
HSA-MIR-6715B-5P99.6469.631420

Literature-anchored findings (GeneRIF, showing 16)

  • Two nonsense mutations in ADTB3A, C1578T (R–>X) and G2028T (E–>X), result in lack of ADTB3A mRNA and beta3A protein production and a severe, G-CSF-responsive neutropenia in addition to oculocutaneous albinism and platelet storage pool deficiency. (PMID:11809908)
  • Description of mutations in HPS genes that cause Hermansky-Pudlak syndrome (review) (PMID:12125811)
  • We defined a homozygous genomic deletion in AP3B1, the gene encoding the beta chain of the adaptor protein-3 (AP-3) complex. The mutation leads to in-frame skipping of exon 15 and thus perturbs proper assembly of the heterotetrameric AP-3 complex. (PMID:16537806)
  • A novel homozygous mutation in AP3B1 was detected in a 2-year-old patient with oculocutaneous albinism and immunodeficiency with Hermansky-Pudlak syndrome type II and eventual acute fatal hemophagocytic lymphohistiocytosis. (PMID:16551969)
  • Mutations in AP3B1 is not associated with familial hemophagocytic lymphohistiocytosis (PMID:18000860)
  • AP-1 and AP-3 are involved in the formation of distinct types of clathrin-coated vesicles, each of which is characterized by the incorporation of specific cargo membrane proteins (PMID:18410487)
  • Experimental investigation of five specific genes, AP3B1, ATP6AP1, BLOC1S1, LAMP2, and RAB11A, has confirmed novel roles for these proteins in the proper initiation of macroautophagy in amino acid-starved fibroblasts. (PMID:19246570)
  • The study provides a description of two unrelated individuals with Hermansky Pudlak syndrome type 2 associated with novel mutations in AP3B1. (PMID:19679886)
  • diphosphoinositol pentakisphosphate-mediated pyrophosphorylation of AP3B1 modulates the interaction with Kif3A and, as a consequence, affects the release of HIV-1 virus-like particles. (PMID:19934039)
  • Data indicate that RUN and FYVE domain protein Rabip4’(RUFY1) interacts specifically and directly with adaptor protein complex AP-3. (PMID:23144738)
  • Using a co-affinity purification strategy, authors have identified the beta subunit of the AP-3 adapter protein complex, AP3B1, as a binding partner for the M proteins of the zoonotic paramyxoviruses Nipah virus and Hendra virus. (PMID:25210190)
  • Synergistic defects of UNC13D and AP3B1 leading to adult hemophagocytic lymphohistiocytosis. (PMID:25980904)
  • point mutation c.2702C>G in exon 23 of the AP3B1 gene caused deletion of 112 bp in the mRNA in two siblings. This mutation activates a cryptic donor splice site that overrules the wild-type donor splice site of this exon. Three other novel mutations in AP3B1 were identified, that is, a nonsense mutation c.716G>A (p.Trp239Ter), a 1-bp and a 4-bp deletion c.177delA and c.1839_1842delTAGA, respectively (PMID:28585318)
  • data show that defects in adaptor protein complex 3-dependent maturation of Weibel-Palade bodies impairs exocytosis by affecting the recruitment of VAMP8. (PMID:30630984)
  • Germline variants in UNC13D and AP3B1 are enriched in COVID-19 patients experiencing severe cytokine storms. (PMID:33867526)
  • HDL cholesterol concentrations and risk of atherosclerotic cardiovascular disease - Insights from randomized clinical trials and human genetics. (PMID:34637926)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioap3b1aENSDARG00000100082
danio_rerioENSDARG00000110056
mus_musculusAp3b1ENSMUSG00000021686
rattus_norvegicusAp3b1ENSRNOG00000010624
drosophila_melanogasterrbFBGN0003210
caenorhabditis_elegansapb-3WBGENE00000163

Paralogs (4): AP2B1 (ENSG00000006125), AP1B1 (ENSG00000100280), AP3B2 (ENSG00000103723), AP4B1 (ENSG00000134262)

Protein

Protein identifiers

AP-3 complex subunit beta-1O00203 (reviewed: O00203)

Alternative names: Adaptor protein complex AP-3 subunit beta-1, Adaptor-related protein complex 3 subunit beta-1, Beta-3A-adaptin, Clathrin assembly protein complex 3 beta-1 large chain

All UniProt accessions (21): A0A0S2Z4Z4, A0A0S2Z5J4, A0A8Q3SHP3, A0A8Q3SHR2, A0A8Q3SHS3, A0A8Q3SHS6, A0A8Q3SHU2, A0A8Q3SHV5, A0A8Q3SHW6, A0A8Q3SHX0, A0A8Q3SI03, A0A8Q3SIM7, A0A8Q3SIS1, O00203, A0A8Q3WKF8, A0A8Q3WKI5, A0A8Q3WKJ9, A0A8Q3WKK0, A0A8Q3WKN2, A0A8Q3WL34, H0YBD0

UniProt curated annotations — full annotation on UniProt →

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 / interactions. 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). AP-3 associates with the BLOC-1 complex. Interacts with KIF3A; interaction is direct; interaction is impaired by pyrophosphorylation of AP3B1.

Subcellular location. Cytoplasmic vesicle. Clathrin-coated vesicle membrane. Golgi apparatus.

Tissue specificity. Ubiquitously expressed.

Post-translational modifications. Phosphorylated on serine residues. Pyrophosphorylation by 5-diphosphoinositol pentakisphosphate (5-IP7) impairs interaction with KIF3A. Serine pyrophosphorylation is achieved by Mg(2+)-dependent, but enzyme independent transfer of a beta-phosphate from a inositol pyrophosphate to a pre-phosphorylated serine residue.

Disease relevance. Hermansky-Pudlak syndrome 2 (HPS2) [MIM:608233] 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. 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the adaptor complexes large subunit family.

Isoforms (2)

UniProt IDNamesCanonical?
O00203-11yes
O00203-32

RefSeq proteins (3): NP_001258698, NP_001397681, NP_003655* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002553Clathrin/coatomer_adapt-like_NDomain
IPR011989ARM-likeHomologous_superfamily
IPR015151B-adaptin_app_sub_CDomain
IPR016024ARM-type_foldHomologous_superfamily
IPR026739AP_betaFamily
IPR026740AP3_betaFamily
IPR029390AP3B_CDomain
IPR029394AP3B1_SerDomain
IPR056314AP3B1/2_CDomain

Pfam: PF01602, PF14796, PF14797, PF24080

UniProt features (24 total): compositionally biased region 9, modified residue 4, region of interest 3, sequence variant 3, sequence conflict 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
9C5CELECTRON MICROSCOPY3.6
9C5AELECTRON MICROSCOPY4.2
9C59ELECTRON MICROSCOPY4.3
9C5BELECTRON MICROSCOPY4.5
9C58ELECTRON MICROSCOPY4.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00203-F175.850.50

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 276, 609, 750, 752

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-432722Golgi Associated Vesicle Biogenesis
R-HSA-6802952Signaling by BRAF and RAF1 fusions
R-HSA-1643685Disease
R-HSA-199991Membrane Trafficking
R-HSA-199992trans-Golgi Network Vesicle Budding
R-HSA-5653656Vesicle-mediated transport
R-HSA-5663202Diseases of signal transduction by growth factor receptors and second messengers
R-HSA-6802957Oncogenic MAPK signaling

MSigDB gene sets: 492 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_SINGLE_FERTILIZATION, GOBP_SYNAPTIC_VESICLE_LOCALIZATION, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_EPITHELIUM_DEVELOPMENT, TAATAAT_MIR126, GOBP_RESPIRATORY_GASEOUS_EXCHANGE_BY_RESPIRATORY_SYSTEM, GOBP_AXO_DENDRITIC_TRANSPORT, GOBP_LYSOSOMAL_TRANSPORT, GOBP_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, GOBP_VACUOLE_ORGANIZATION, GOBP_VESICLE_LOCALIZATION

GO Biological Process (36): cell morphogenesis (GO:0000902), toll-like receptor signaling pathway (GO:0002224), hematopoietic progenitor cell differentiation (GO:0002244), respiratory system process (GO:0003016), protein targeting to lysosome (GO:0006622), intracellular zinc ion homeostasis (GO:0006882), intracellular protein transport (GO:0006886), inflammatory response (GO:0006954), lysosome organization (GO:0007040), spermatogenesis (GO:0007283), single fertilization (GO:0007338), blood coagulation (GO:0007596), anterograde axonal transport (GO:0008089), vesicle-mediated transport (GO:0016192), granulocyte differentiation (GO:0030851), melanosome organization (GO:0032438), protein localization to cell surface (GO:0034394), clathrin-coated vesicle cargo loading, AP-3-mediated (GO:0035654), mRNA transcription by RNA polymerase II (GO:0042789), positive regulation of transcription by RNA polymerase II (GO:0045944), antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007), anterograde synaptic vesicle transport (GO:0048490), homeostasis of number of cells (GO:0048872), positive regulation of NK T cell differentiation (GO:0051138), platelet dense granule organization (GO:0060155), lung morphogenesis (GO:0060425), obsolete establishment of protein localization to mitochondrial membrane involved in mitochondrial fission (GO:0090152), skin epidermis development (GO:0098773), melanosome assembly (GO:1903232), protein targeting (GO:0006605), gene expression (GO:0010467), protein transport (GO:0015031), antigen processing and presentation (GO:0019882), lung development (GO:0030324), pigmentation (GO:0043473), membrane organization (GO:0061024)

GO Molecular Function (4): protein phosphatase binding (GO:0019903), GTP-dependent protein binding (GO:0030742), protein binding (GO:0005515), clathrin binding (GO:0030276)

GO Cellular Component (13): mitochondrion (GO:0005739), lysosomal membrane (GO:0005765), early endosome (GO:0005769), Golgi apparatus (GO:0005794), membrane (GO:0016020), AP-3 adaptor complex (GO:0030123), clathrin adaptor complex (GO:0030131), clathrin-coated vesicle membrane (GO:0030665), axon cytoplasm (GO:1904115), microvesicle (GO:1990742), endomembrane system (GO:0012505), membrane coat (GO:0030117), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
trans-Golgi Network Vesicle Budding1
Oncogenic MAPK signaling1
Vesicle-mediated transport1
Membrane Trafficking1
Disease1
Diseases of signal transduction by growth factor receptors and second messengers1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm4
intracellular protein localization2
transcription by RNA polymerase II2
protein binding2
intracellular membrane-bounded organelle2
cellular anatomical structure2
AP-type membrane coat adaptor complex2
anatomical structure morphogenesis1
pattern recognition receptor signaling pathway1
hemopoiesis1
cell differentiation1
system process1
respiratory gaseous exchange by respiratory system1
protein targeting to vacuole1
lysosomal transport1
protein localization to lysosome1
intracellular monoatomic cation homeostasis1
inorganic ion homeostasis1
protein transport1
intracellular transport1
defense response1
lytic vacuole organization1
developmental process involved in reproduction1
male gamete generation1
fertilization1
hemostasis1
wound healing1
coagulation1
axonal transport1
axon cytoplasm1
transport1
cellular process1
myeloid leukocyte differentiation1
pigment granule organization1
clathrin-coated vesicle cargo loading1
mRNA transcription1
regulation of transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
phosphatase binding1
binding1

Protein interactions and networks

STRING

2054 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AP3B1HPS4Q9NQG7934
AP3B1AP3D1O14617929
AP3B1HPS3Q969F9925
AP3B1AP3S1Q92572895
AP3B1AP3M1Q9Y2T2889
AP3B1HPS6Q86YV9841
AP3B1BLOC1S3Q6QNY0836
AP3B1HPS5Q9UPZ3825
AP3B1LYSTQ99698797
AP3B1BHLHE22Q8NFJ8728
AP3B1BLOC1S6Q9UL45724
AP3B1UNC13DQ70J99720
AP3B1STX11O75558720
AP3B1STXBP2Q15833720
AP3B1DTNBP1Q96EV8719

IntAct

203 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
AP3M1AP3B1psi-mi:“MI:0914”(association)0.640
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
DNALI1AP3B1psi-mi:“MI:0915”(physical association)0.560
BAG6AP3B1psi-mi:“MI:0915”(physical association)0.560
OPTNAP3B1psi-mi:“MI:0915”(physical association)0.560
AP3B1ALS2psi-mi:“MI:0915”(physical association)0.560
AP3B1SNCApsi-mi:“MI:0915”(physical association)0.560
AP3B1HTTpsi-mi:“MI:0915”(physical association)0.560

BioGRID (270): AP3B1 (Co-localization), AP3B1 (Affinity Capture-Western), LRSAM1 (Affinity Capture-Western), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3B1 (Co-fractionation), AP3B1 (Co-fractionation)

ESM2 similar proteins: A0A3Q1LSX9, A1A5G0, A1A5K2, A2A5R2, A2APV2, A2VE70, D3ZYR1, O00203, O04376, O35643, O60308, O75122, P52303, Q05397, Q08AM6, Q08DS7, Q0JRZ9, Q10567, Q13367, Q28FH2, Q32PG1, Q3UQN2, Q4U0G1, Q561M0, Q5R807, Q5ZIW5, Q6NUP7, Q6NXC0, Q6NYW6, Q6ZPF4, Q7TSU1, Q7YRF1, Q7Z460, Q80TV8, Q8BRT1, Q8C0Y0, Q8IVF7, Q8LF36, Q8N7B6, Q8RW96

Diamond homologs: O00203, O13939, O81742, Q13367, Q32PG1, Q54X82, Q556J8, Q7YRF1, Q9JME5, Q9M2T1, Q9SUS3, Q9Z1T1, O35643, O43005, O43079, P27351, P36000, P52303, P62944, P63009, P63010, Q08DS7, Q10567, Q9DBG3, Q9LDK9, Q9WV76, Q9Y6B7

SIGNOR signaling

2 interactions.

AEffectBMechanism
AP3B1“form complex”“AP-3 complex”binding
AP3B1“up-regulates activity”KIF3Abinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 163 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Neurexins and neuroligins814.9×4e-05
Signaling by NOTCH69.9×7e-03
ESR-mediated signaling78.5×6e-03

GO biological processes:

GO termPartnersFoldFDR
integrated stress response signaling526.0×2e-03
positive regulation of miRNA transcription612.9×4e-03
negative regulation of canonical NF-kappaB signal transduction78.9×4e-03
positive regulation of gene expression144.0×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1000 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic45
Likely pathogenic28
Uncertain significance455
Likely benign344
Benign52

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1071422NM_003664.5(AP3B1):c.1619dup (p.Ala541fs)Pathogenic
1072382NM_003664.5(AP3B1):c.2694_2712del (p.Met899fs)Pathogenic
1370969NM_003664.5(AP3B1):c.2738del (p.Lys913fs)Pathogenic
1416408NM_003664.5(AP3B1):c.237_238del (p.Phe80fs)Pathogenic
1451475NM_003664.5(AP3B1):c.2757del (p.Ile919fs)Pathogenic
1455598NM_003664.5(AP3B1):c.2801del (p.Asn934fs)Pathogenic
1456202NM_003664.5(AP3B1):c.1101dup (p.Phe368fs)Pathogenic
1878314NM_003664.5(AP3B1):c.1789dup (p.Ile597fs)Pathogenic
2019152NM_003664.5(AP3B1):c.778del (p.Trp260fs)Pathogenic
2030913NM_003664.5(AP3B1):c.1255C>T (p.Gln419Ter)Pathogenic
224760NM_003664.5(AP3B1):c.2702C>G (p.Ser901Cys)Pathogenic
224761NM_003664.5(AP3B1):c.1754del (p.Val585fs)Pathogenic
224762NM_003664.5(AP3B1):c.716G>A (p.Trp239Ter)Pathogenic
224763NM_003664.5(AP3B1):c.177del (p.Lys59fs)Pathogenic
224764NM_003664.4(AP3B1):c.1839_1842delTAGAPathogenic
2503438NM_003664.5(AP3B1):c.364C>T (p.Arg122Ter)Pathogenic
2676731NM_003664.5(AP3B1):c.1363+1G>APathogenic
2698780NM_003664.5(AP3B1):c.1973_1983dup (p.Pro662fs)Pathogenic
2705668NM_003664.5(AP3B1):c.753T>G (p.Tyr251Ter)Pathogenic
2717774NM_003664.5(AP3B1):c.2675_2679del (p.Pro892fs)Pathogenic
2739632NM_003664.5(AP3B1):c.2734C>T (p.Arg912Ter)Pathogenic
2748816NM_003664.5(AP3B1):c.1408del (p.Gln470fs)Pathogenic
2749771NM_003664.5(AP3B1):c.1930_1937del (p.Pro644fs)Pathogenic
2812558NM_003664.5(AP3B1):c.1907T>G (p.Leu636Ter)Pathogenic
2837529NM_003664.5(AP3B1):c.1286del (p.Gly429fs)Pathogenic
3239621GRCh37/hg19 5q14.1(chr5:77396777-77396849)x1Pathogenic
3246334NC_000005.9:g.(?77590256)(77590403_?)delPathogenic
3653778NM_003664.5(AP3B1):c.624dup (p.Met209fs)Pathogenic
3897901NM_003664.5(AP3B1):c.2514_2515del (p.Pro840fs)Pathogenic
3910635NM_003664.5(AP3B1):c.2249+1delPathogenic

SpliceAI

6053 predictions. Top by Δscore:

VariantEffectΔscore
5:78003057:T:Aacceptor_loss1.0000
5:78015546:CTC:Cacceptor_gain1.0000
5:78015549:C:CCacceptor_gain1.0000
5:78017414:A:ACdonor_gain1.0000
5:78017415:G:Cdonor_gain1.0000
5:78019512:A:Tacceptor_gain1.0000
5:78020788:TA:Tacceptor_gain1.0000
5:78020790:C:CCacceptor_gain1.0000
5:78034359:A:ACdonor_gain1.0000
5:78034360:C:CCdonor_gain1.0000
5:78034360:CCA:Cdonor_gain1.0000
5:78034446:C:CCacceptor_gain1.0000
5:78039270:CTGAC:Cacceptor_gain1.0000
5:78039286:G:Tacceptor_gain1.0000
5:78089391:A:ACdonor_gain1.0000
5:78089392:C:CCdonor_gain1.0000
5:78089392:CA:Cdonor_gain1.0000
5:78089497:TAA:Tacceptor_gain1.0000
5:78089500:C:CCacceptor_gain1.0000
5:78100943:CAATA:Cdonor_gain1.0000
5:78100945:ATACT:Adonor_loss1.0000
5:78100946:TACTT:Tdonor_loss1.0000
5:78100947:A:ACdonor_gain1.0000
5:78100947:ACT:Adonor_loss1.0000
5:78100948:C:CCdonor_gain1.0000
5:78100948:C:Gdonor_loss1.0000
5:78100949:TT:Tdonor_loss1.0000
5:78100950:T:TGdonor_loss1.0000
5:78100951:A:ACdonor_gain1.0000
5:78100951:A:Cdonor_loss1.0000

AlphaMissense

7228 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:78129240:C:GR573P1.000
5:78141177:A:GL539P1.000
5:78175818:A:GL354P1.000
5:78216123:C:GG240R1.000
5:78216123:C:TG240R1.000
5:78216124:C:AW239C1.000
5:78216124:C:GW239C1.000
5:78216126:A:GW239R1.000
5:78216126:A:TW239R1.000
5:78216223:A:CS206R1.000
5:78216223:A:TS206R1.000
5:78216225:T:GS206R1.000
5:78216227:C:TG205D1.000
5:78225558:A:GL196P1.000
5:78225561:A:GL195P1.000
5:78227391:C:GA173P1.000
5:78227396:G:TA171D1.000
5:78227400:C:GA170P1.000
5:78227404:C:AK168N1.000
5:78227404:C:GK168N1.000
5:78227407:C:AR167S1.000
5:78227407:C:GR167S1.000
5:78227408:C:AR167M1.000
5:78227408:C:GR167T1.000
5:78227409:T:AR167W1.000
5:78227411:A:TV166D1.000
5:78227468:A:TI147N1.000
5:78227492:A:GL139P1.000
5:78227504:G:TA135D1.000
5:78227505:C:GA135P1.000

dbSNP variants (sampled 300 via entrez): RS1000005033 (5:78038786 C>A,T), RS1000033267 (5:78135386 A>C), RS1000048293 (5:78274453 G>C), RS1000052093 (5:78035096 G>A,T), RS1000055365 (5:78281052 T>C,G), RS1000079189 (5:78274800 C>T), RS1000105623 (5:78087219 G>C,T), RS1000108289 (5:78185794 C>T), RS1000129255 (5:78257629 C>A), RS1000137027 (5:78117040 A>C,G), RS1000137410 (5:78032020 G>T), RS1000141220 (5:78050030 C>G,T), RS1000153190 (5:78230568 T>G), RS1000158428 (5:78071374 C>T), RS1000177799 (5:78215355 T>G)

Disease associations

OMIM: gene MIM:603401 | disease phenotypes: MIM:608233, MIM:203300

GenCC curated gene-disease

DiseaseClassificationInheritance
Hermansky-Pudlak syndrome 2DefinitiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Hermansky-Pudlak syndrome 2DefinitiveAR

Mondo (7): Hermansky-Pudlak syndrome 2 (MONDO:0011997), autoinflammatory syndrome (MONDO:0019751), prostate cancer (MONDO:0008315), Hermansky-Pudlak syndrome (MONDO:0019312), combined immunodeficiency (MONDO:0015131), thrombocytopenia (MONDO:0002049), intellectual disability (MONDO:0001071)

Orphanet (7): Hermansky-Pudlak syndrome due to AP-3 deficiency (Orphanet:183678), Hermansky-Pudlak syndrome (Orphanet:79430), Autoinflammatory syndrome (Orphanet:93665), Familial prostate cancer (Orphanet:1331), Combined T and B cell immunodeficiency (Orphanet:101972), Hermansky-Pudlak syndrome due to AP3B1 deficiency (Orphanet:664500), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

47 total (30 of 47 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000319Smooth philtrum
HP:0000343Long philtrum
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000403Recurrent otitis media
HP:0000431Wide nasal bridge
HP:0000486Strabismus
HP:0000582Upslanted palpebral fissure
HP:0000613Photophobia
HP:0000639Nystagmus
HP:0000666Horizontal nystagmus
HP:0000670Carious teeth
HP:0000704Periodontitis
HP:0001022Albinism
HP:0001107Ocular albinism
HP:0001256Mild intellectual disability
HP:0001270Motor delay
HP:0001433Hepatosplenomegaly
HP:0001744Splenomegaly
HP:0001873Thrombocytopenia
HP:0001875Decreased total neutrophil count
HP:0002020Gastroesophageal reflux
HP:0002206Pulmonary fibrosis
HP:0002240Hepatomegaly
HP:0002286Fair hair

GWAS associations

18 associations (top):

StudyTraitp-value
GCST001208_9Insulin resistance/response6.000000e-07
GCST003301_5Triglycerides7.000000e-08
GCST006481_8Lung function (FEV1)6.000000e-09
GCST006483_19Lung function (FVC)2.000000e-11
GCST006483_52Lung function (FVC)3.000000e-11
GCST006483_53Lung function (FVC)3.000000e-11
GCST007429_52Lung function (FVC)3.000000e-14
GCST007432_138FEV17.000000e-09
GCST008114_34Type 2 diabetes8.000000e-06
GCST009391_1660Metabolite levels2.000000e-07
GCST010483_4Cardiovascular death, myocardial infarction or stroke in response to clopidogrel treatment8.000000e-06
GCST010988_94Adult body size2.000000e-09
GCST010989_252Body size at age 104.000000e-11
GCST012227_1350Hip circumference adjusted for BMI8.000000e-15
GCST90000025_44Appendicular lean mass1.000000e-18
GCST90002404_210Red cell distribution width2.000000e-09
GCST90011900_104Serum alkaline phosphatase levels3.000000e-08
GCST90013406_139Liver enzyme levels (alkaline phosphatase)3.000000e-13

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004314forced expiratory volume
EFO:0004312vital capacity
EFO:0010470carnosine measurement
EFO:0006919cardiovascular event measurement
EFO:0009819comparative body size at age 10, self-reported
EFO:0008039BMI-adjusted hip circumference
EFO:0004980appendicular lean mass
EFO:0009188Red cell distribution width
EFO:0004533alkaline phosphatase measurement

MeSH disease descriptors (5)

DescriptorNameTree numbers
D022861Hermanski-Pudlak SyndromeC11.270.040.545.400; C15.378.100.100.515; C15.378.100.685.400; C15.378.140.735.400; C15.378.463.735.400; C16.320.099.515; C16.320.290.040.100.400; C16.320.565.100.102.100.400; C16.320.850.080.100.400; C17.800.621.440.102.100.400; C17.800.827.080.100.400; C18.452.648.100.102.100.400
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
D013921ThrombocytopeniaC15.378.140.855; C15.378.243.937
C537709Hermansky Pudlak syndrome 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724792 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

6 potent at pChembl≥5 of 6 total, top 6 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.31Kd49.02nMCHEMBL5653589
7.31ED5049.02nMCHEMBL5653589
7.30Kd50nMMOLIBRESIB
7.10IC5080nMMOLIBRESIB
6.25Kd557.6nMCHEMBL3752910
6.25ED50557.6nMCHEMBL3752910

PubChem BioAssay actives

4 with measured affinity, of 11 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2147868: Binding affinity to human AP3B1 incubated for 45 mins by Kinobead based pull down assaykd0.0490uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2179179: Binding affinity against AP3B1 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysiskd0.0500uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2147868: Binding affinity to human AP3B1 incubated for 45 mins by Kinobead based pull down assaykd0.5576uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression3
sodium arseniteincreases expression, decreases expression, increases abundance2
Benzo(a)pyrenedecreases expression, decreases methylation2
Tobacco Smoke Pollutionaffects expression, increases expression2
aristolochic acid Idecreases expression1
terbufosdecreases methylation1
beta-lapachoneincreases expression1
arsenitedecreases expression, decreases reaction1
di-n-butylphosphoric acidaffects expression1
chloropicrinincreases expression1
bisphenol AFincreases expression1
Fulvestrantdecreases reaction, decreases expression1
Arsenicdecreases expression, increases abundance1
Cadmiumdecreases expression, decreases reaction1
Cannabidiolincreases expression1
Clozapineincreases expression1
Fonofosdecreases methylation1
Estradioldecreases expression, decreases reaction1
Haloperidolincreases expression1
Ivermectindecreases expression1
Parathiondecreases methylation1
Ribonucleotidesaffects binding1
Vanadatesincreases expression1
tert-Butylhydroperoxidedecreases expression1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5650910BindingBinding affinity to human AP3B1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

3 cell lines: 2 induced pluripotent stem cell, 1 finite cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_0R47GM17890Finite cell lineMale
CVCL_A0JYSANi009-AInduced pluripotent stem cellFemale
CVCL_DQ89CHOPHPS2Induced pluripotent stem cellMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer