Seroatlas · Human Serome Atlas

AP3D1

AP-3 complex subunit delta-1

Also known as: ADTD, AP3D1_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O14617
Gene: AP3D1
Ensembl: ENSG00000065000
Chromosome: 19
Canonical length: 1153 aa
Protein class: Disease related genes, Human disease related genes, Plasma proteins, Predicted intracellular proteins
Subcellular location: Cytosol

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

1153 residues, UniProt reviewed canonical sequence.

>O14617|AP3D1
     1  MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC
    61  KLTYLQMLGY DISWAAFNII EVMSASKFTF KRIGYLAASQ SFHEGTDVIM LTTNQIRKDL
   121  SSPSQYDTGV ALTGLSCFVT PDLARDLAND IMTLMSHTKP YIRKKAVLIM YKVFLKYPES
   181  LRPAFPRLKE KLEDPDPGVQ SAAVNVICEL ARRNPKNYLS LAPLFFKLMT SSTNNWVLIK
   241  IIKLFGALTP LEPRLGKKLI EPLTNLIHST SAMSLLYECV NTVIAVLISL SSGMPNHSAS
   301  IQLCVQKLRI LIEDSDQNLK YLGLLAMSKI LKTHPKSVQS HKDLILQCLD DKDESIRLRA
   361  LDLLYGMVSK KNLMEIVKKL MTHVDKAEGT TYRDELLTKI IDICSQSNYQ YITNFEWYIS
   421  ILVELTRLEG TRHGHLIAAQ MLDVAIRVKA IRKFAVSQMS ALLDSAHLLA SSTQRNGICE
   481  VLYAAAWICG EFSEHLQEPH HTLEAMLRPR VTTLPGHIQA VYVQNVVKLY ASILQQKEQA
   541  GEAEGAQAVT QLMVDRLPQF VQSADLEVQE RASCILQLVK HIQKLQAKDV PVAEEVSALF
   601  AGELNPVAPK AQKKVPVPEG LDLDAWINEP LSDSESEDER PRAVFHEEEQ RRPKHRPSEA
   661  DEEELARRRE ARKQEQANNP FYIKSSPSPQ KRYQDTPGVE HIPVVQIDLS VPLKVPGLPM
   721  SDQYVKLEEE RRHRQKLEKD KRRKKRKEKE KKGKRRHSSL PTESDEDIAP AQQVDIVTEE
   781  MPENALPSDE DDKDPNDPYR ALDIDLDKPL ADSEKLPIQK HRNTETSKSP EKDVPMVEKK
   841  SKKPKKKEKK HKEKERDKEK KKEKEKKKSP KPKKKKHRKE KEERTKGKKK SKKQPPGSEE
   901  AAGEPVQNGA PEEEQLPPES SYSLLAENSY VKMTCDIRGS LQEDSQVTVA IVLENRSSSI
   961  LKGMELSVLD SLNARMARPQ GSSVHDGVPV PFQLPPGVSN EAQYVFTIQS IVMAQKLKGT
  1021  LSFIAKNDEG ATHEKLDFRL HFSCSSYLIT TPCYSDAFAK LLESGDLSMS SIKVDGIRMS
  1081  FQNLLAKICF HHHFSVVERV DSCASMYSRS IQGHHVCLLV KKGENSVSVD GKCSDSTLLS
  1141  NLLEEMKATL AKC

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against AP3D1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Other membrane
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.35
Highest tissue expression: 67 nTPM

Expression across tissuesHPA

Tissue

pancreas: 67 nTPM
pituitary gland: 58 nTPM
liver: 54 nTPM
skeletal muscle: 48 nTPM
heart muscle: 43 nTPM
adrenal gland: 43 nTPM

Single-cell type

differentiating spermatogonia: 149 nCPM
early primary spermatocytes: 149 nCPM
esophageal apical cells: 136 nCPM
epididymal principal cells: 120 nCPM
syncytiotrophoblasts: 119 nCPM
somatotrophs: 115 nCPM

Immune cell

plasmacytoid DC: 7.3 nTPM
MAIT T-cell: 5.4 nTPM
NK-cell: 5.3 nTPM
memory CD8 T-cell: 4 nTPM
myeloid DC: 3.7 nTPM
memory CD4 T-cell: 3.4 nTPM

Brain region

pons: 109 nTPM
midbrain: 100 nTPM
hippocampal formation: 98 nTPM
cerebral cortex: 92 nTPM
hypothalamus: 92 nTPM
thalamus: 91 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about AP3D1.

Disease | AllUniProt

Conditions AP3D1 is implicated in, by any mechanism.

Hermansky-Pudlak syndrome 10 (HPS10) MIM:617050

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 1,522 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Hermansky-Pudlak syndrome 10

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.3
gnomAD pLI: 0.99
gnomAD missense Z: 1.94
DepMap mean gene effect: -0.1
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Cellular components

Protein domainsUniProt · Pfam · InterPro

Clathrin/coatomer adaptor, adaptin-like, N-terminal
Armadillo-like helical
Armadillo-type fold
Adaptin N terminal region
AP-3 complex subunit delta domain, metazoa
Adaptor protein complex AP-3, delta subunit
AP-3 complex subunit delta, Mu C-terminal domain
AP-3 complex subunit delta-1
AP3 Mu C-terminal domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of AP3D1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads AP3D1 as an antibody target. Whether an autoantibody or antibody against AP3D1 could matter depends on whether native AP3D1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

AP3D1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label AP3D1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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