AP3M2

gene
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Also known as CLA20AP47B

Summary

AP3M2 (adaptor related protein complex 3 subunit mu 2, HGNC:570) is a protein-coding gene on chromosome 8p11.21, encoding AP-3 complex subunit mu-2 (P53677). Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated.

This gene encodes a subunit of the heterotetrameric adaptor-related protein comlex 3 (AP-3), which belongs to the adaptor complexes medium subunits family. The AP-3 complex plays a role in protein trafficking to lysosomes and specialized organelles. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 10947 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 62 total — 1 pathogenic
  • MANE Select transcript: NM_006803

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:570
Approved symbolAP3M2
Nameadaptor related protein complex 3 subunit mu 2
Location8p11.21
Locus typegene with protein product
StatusApproved
AliasesCLA20, AP47B
Ensembl geneENSG00000070718
Ensembl biotypeprotein_coding
OMIM610469
Entrez10947

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 12 protein_coding, 3 nonsense_mediated_decay, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000396926, ENST00000517499, ENST00000517865, ENST00000517922, ENST00000517969, ENST00000518421, ENST00000520685, ENST00000520689, ENST00000521235, ENST00000521280, ENST00000521899, ENST00000522288, ENST00000522320, ENST00000522606, ENST00000523249, ENST00000530375, ENST00000858465, ENST00000913686, ENST00000913687, ENST00000943124

RefSeq mRNA: 2 — MANE Select: NM_006803 NM_001134296, NM_006803

CCDS: CCDS6125

Canonical transcript exons

ENST00000396926 — 9 exons

ExonStartEnd
ENSE000011926554216716442167371
ENSE000011926744215461642154960
ENSE000015267764216896142171183
ENSE000020987924215306342153105
ENSE000034738134216542742165560
ENSE000034828894216507142165156
ENSE000035135954216228142162418
ENSE000035155764216766642167810
ENSE000035905794215794142158112

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 97.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.7001 / max 132.9119, expressed in 1753 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
8867113.65811752
886720.042014

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011597.60gold quality
middle temporal gyrusUBERON:000277197.16gold quality
Brodmann (1909) area 23UBERON:001355495.97gold quality
secondary oocyteCL:000065594.47gold quality
Brodmann (1909) area 10UBERON:001354194.21gold quality
frontal poleUBERON:000279593.67gold quality
prefrontal cortexUBERON:000045192.93gold quality
Brodmann (1909) area 46UBERON:000648392.75gold quality
cranial nerve IIUBERON:000094192.65gold quality
oocyteCL:000002392.19gold quality
primary visual cortexUBERON:000243692.01gold quality
orbitofrontal cortexUBERON:000416792.01gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.86gold quality
dorsolateral prefrontal cortexUBERON:000983491.77gold quality
frontal cortexUBERON:000187091.60gold quality
frontal lobeUBERON:001652591.60gold quality
neocortexUBERON:000195091.33gold quality
Brodmann (1909) area 9UBERON:001354091.23gold quality
superior frontal gyrusUBERON:000266191.16gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.79gold quality
cerebral cortexUBERON:000095690.74gold quality
cingulate cortexUBERON:000302790.57gold quality
right frontal lobeUBERON:000281090.56gold quality
anterior cingulate cortexUBERON:000983590.54gold quality
ponsUBERON:000098890.53gold quality
cortical plateUBERON:000534390.25gold quality
hypothalamusUBERON:000189890.19gold quality
entorhinal cortexUBERON:000272890.16gold quality
middle frontal gyrusUBERON:000270289.94gold quality
telencephalonUBERON:000189389.62gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting AP3M2, 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-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-118499.9968.191458
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-56899.9869.862084
HSA-MIR-548P99.9872.253784
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-651-3P99.9473.485177
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-568099.9169.833421
HSA-MIR-368699.9070.532432
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-629-3P99.8567.991875
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-205-5P99.8170.051557
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-62399.7668.161170
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-3059-5P99.7069.932491

Literature-anchored findings (GeneRIF, showing 1)

  • some AP3M2 mutations still remain candidates for unmapped disorders including epilepsy, febrile seizure, and other neuronal developmental disorders associated with functional abnormalities of GABAergic transmission (PMID:17293072)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioap3m2ENSDARG00000016128
mus_musculusAp3m2ENSMUSG00000031539
rattus_norvegicusAp3m2ENSRNOG00000018650
drosophila_melanogastercmFBGN0000330

Paralogs (7): AP1M1 (ENSG00000072958), AP1M2 (ENSG00000129354), STON2 (ENSG00000140022), AP2M1 (ENSG00000161203), AP3M1 (ENSG00000185009), AP4M1 (ENSG00000221838), STON1 (ENSG00000243244)

Protein

Protein identifiers

AP-3 complex subunit mu-2P53677 (reviewed: P53677)

Alternative names: Adaptor-related protein complex 3 subunit mu-2, Clathrin assembly protein assembly protein complex 3 mu-2 medium chain, Clathrin coat assembly protein AP47 homolog 2, Clathrin coat-associated protein AP47 homolog 2, Golgi adaptor AP-1 47 kDa protein homolog 2, HA1 47 kDa subunit homolog 2, Mu3B-adaptin, P47B

All UniProt accessions (10): P53677, A0A1D5RMS9, A0A384NYL6, E5RGF3, E5RI83, E5RJ52, E7ER80, H0YAY4, H0YBA0, H0YBM0

UniProt curated annotations — full annotation on UniProt →

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. 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. AP-3 associates with the BLOC-1 complex. 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).

Subcellular location. Golgi apparatus. Cytoplasmic vesicle membrane.

Similarity. Belongs to the adaptor complexes medium subunit family.

Isoforms (2)

UniProt IDNamesCanonical?
P53677-11yes
P53677-22

RefSeq proteins (2): NP_001127768, NP_006794* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001392Clathrin_muFamily
IPR011012Longin-like_dom_sfHomologous_superfamily
IPR018240Clathrin_mu_CSConserved_site
IPR022775AP_mu_sigma_suDomain
IPR028565MHDDomain
IPR036168AP2_Mu_C_sfHomologous_superfamily
IPR050431Adaptor_comp_med_subunitFamily

Pfam: PF00928, PF01217

UniProt features (4 total): splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P53677-F193.070.82

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 303 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_SYNAPTIC_VESICLE_LOCALIZATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_AXO_DENDRITIC_TRANSPORT, GOBP_VESICLE_LOCALIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, FISCHER_G1_S_CELL_CYCLE, GOBP_VESICLE_ORGANIZATION, GOBP_SYNAPTIC_VESICLE_CYTOSKELETAL_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOBP_VACUOLAR_TRANSPORT, KEGG_LYSOSOME, GOBP_VESICLE_MEDIATED_TRANSPORT

GO Biological Process (10): intracellular protein transport (GO:0006886), endocytosis (GO:0006897), anterograde axonal transport (GO:0008089), synaptic vesicle coating (GO:0016183), clathrin-coated vesicle cargo loading, AP-3-mediated (GO:0035654), synaptic vesicle recycling (GO:0036465), anterograde synaptic vesicle transport (GO:0048490), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), synaptic vesicle endocytosis (GO:0048488)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (14): early endosome (GO:0005769), Golgi apparatus (GO:0005794), synaptic vesicle (GO:0008021), AP-type membrane coat adaptor complex (GO:0030119), AP-3 adaptor complex (GO:0030123), clathrin adaptor complex (GO:0030131), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), axon cytoplasm (GO:1904115), cytoplasm (GO:0005737), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport3
cellular anatomical structure3
intracellular protein localization2
cytoplasm2
AP-type membrane coat adaptor complex2
synapse2
protein transport1
intracellular transport1
vesicle budding from membrane1
membrane invagination1
vesicle-mediated transport1
import into cell1
axonal transport1
axon cytoplasm1
vesicle coat assembly1
synaptic vesicle budding from presynaptic endocytic zone membrane1
clathrin-coated vesicle cargo loading1
establishment of localization in cell1
synaptic vesicle cycle1
anterograde axonal transport1
synaptic vesicle transport along microtubule1
establishment of protein localization1
cellular process1
synaptic vesicle recycling1
presynaptic endocytosis1
binding1
endosome1
endomembrane system1
intracellular membrane-bounded organelle1
exocytic vesicle1
presynapse1
membrane coat1
membrane protein complex1
clathrin coat1
vesicle membrane1
cytoplasmic vesicle1
intracellular vesicle1
axon1
neuron projection cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

860 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AP3M2AP3D1O14617839
AP3M2GSTM1P09488711
AP3M2AP3S1Q92572657
AP3M2AP3B1O00203562
AP3M2AP3B2Q13367529
AP3M2AP1S1P61966485
AP3M2ZNF398Q8TD17445
AP3M2RABGGTAQ92696397
AP3M2AP3S2P59780387
AP3M2BLOC1S6Q9UL45384
AP3M2SMIM12Q96EX1382
AP3M2UBE2CO00762381
AP3M2LRRC40Q9H9A6366
AP3M2DUSP13BQ9UII6358
AP3M2BEND7Q8N7W2353

IntAct

27 interactions, top by confidence:

ABTypeScore
AP3M1AP3B1psi-mi:“MI:0914”(association)0.640
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
TUBA4ATXNDC9psi-mi:“MI:0914”(association)0.640
AP3M2AP3B1psi-mi:“MI:0914”(association)0.530
AP3S1AP3B1psi-mi:“MI:0914”(association)0.530
EDAAP3B1psi-mi:“MI:0914”(association)0.530
EPB41L3AP3B1psi-mi:“MI:0914”(association)0.530
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
LYPD4DPYSL4psi-mi:“MI:0914”(association)0.350
CAMKVAP3B1psi-mi:“MI:0914”(association)0.350
EDAAP3B1psi-mi:“MI:0914”(association)0.350
IQCF1TBC1D4psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
KLRC1METTL15psi-mi:“MI:0914”(association)0.350
PLCD3AP3B1psi-mi:“MI:0914”(association)0.350
LYPD4PIK3C2Apsi-mi:“MI:0914”(association)0.350
TCEAL9DIRAS1psi-mi:“MI:0914”(association)0.350
DHDHZNF185psi-mi:“MI:0914”(association)0.350
TUBBVWA8psi-mi:“MI:0914”(association)0.350

BioGRID (41): AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), AP3S2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3D1 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), MEOX2 (Two-hybrid), AP3M2 (Affinity Capture-MS), AP3M2 (Affinity Capture-MS), AP3S2 (Affinity Capture-MS)

ESM2 similar proteins: A2RV18, A4IG72, A7MB11, B8APQ0, D3ZAA9, E2RED8, E9PY46, F4I562, O00189, O43304, O89043, P33611, P47795, P47823, P53676, P53677, P53678, Q0J649, Q10QS7, Q13144, Q14168, Q14181, Q24K11, Q29RY8, Q2PWT8, Q3UR70, Q499N2, Q4R6Q7, Q58D13, Q5E9X5, Q5R478, Q5ZMP7, Q64350, Q8BJ63, Q8CHW4, Q8R2R9, Q8WUH2, Q93Y22, Q96RY7, Q9D0T2

Diamond homologs: F4I562, P47795, P53676, P53677, P53678, Q00776, Q24K11, Q5R478, Q5ZMP7, Q8R2R9, Q9GPF1, Q9HFE5, Q9JKC8, Q9Y2T2, D3ZRP6, P35585, P35602, P38700, Q2KJ81, Q32Q06, Q3SYW1, Q54HS9, Q9BXS5, Q9WVP1, Q9Y6Q5

SIGNOR signaling

1 interactions.

AEffectBMechanism
AP3M2“form complex”“Neuronal AP-3”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 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
Membrane Trafficking511.6×1e-03
Vesicle-mediated transport510.9×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance48
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
687703GRCh37/hg19 8p11.21(chr8:41761813-42107108)x1Pathogenic

SpliceAI

1810 predictions. Top by Δscore:

VariantEffectΔscore
8:42155967:A:AGacceptor_gain1.0000
8:42158108:CACAG:Cdonor_loss1.0000
8:42158109:ACAGG:Adonor_loss1.0000
8:42158110:CAGGT:Cdonor_loss1.0000
8:42158111:AGGTA:Adonor_loss1.0000
8:42158114:T:Gdonor_loss1.0000
8:42165415:T:TAacceptor_gain1.0000
8:42165558:GAA:Gdonor_gain1.0000
8:42165561:G:GGdonor_gain1.0000
8:42167162:A:AGacceptor_gain1.0000
8:42167162:AGTCT:Aacceptor_gain1.0000
8:42167163:G:GAacceptor_gain1.0000
8:42167163:GT:Gacceptor_gain1.0000
8:42167163:GTCT:Gacceptor_gain1.0000
8:42167163:GTCTG:Gacceptor_gain1.0000
8:42167279:G:GTdonor_gain1.0000
8:42169040:G:GTdonor_gain1.0000
8:42169040:G:Tdonor_gain1.0000
8:42169064:G:GTdonor_gain1.0000
8:42169080:G:Tdonor_gain1.0000
8:42153104:AG:Adonor_loss0.9900
8:42153105:GGTGA:Gdonor_loss0.9900
8:42153106:GT:Gdonor_loss0.9900
8:42153107:T:Gdonor_loss0.9900
8:42154614:A:AGacceptor_gain0.9900
8:42154615:G:GGacceptor_gain0.9900
8:42154615:GA:Gacceptor_gain0.9900
8:42155968:A:Gacceptor_gain0.9900
8:42157936:ATCAG:Aacceptor_gain0.9900
8:42157937:T:Gacceptor_gain0.9900

AlphaMissense

2763 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:42162334:T:AW167R1.000
8:42162334:T:CW167R1.000
8:42165097:G:AG204R1.000
8:42165097:G:CG204R1.000
8:42165097:G:TG204W1.000
8:42165098:G:AG204E1.000
8:42165140:T:CL218P1.000
8:42165467:T:AV237D1.000
8:42167675:T:AW341R1.000
8:42167675:T:CW341R1.000
8:42158017:T:CL117P0.999
8:42158026:G:AG120D0.999
8:42158056:T:CL130P0.999
8:42158095:T:AV143D0.999
8:42162336:G:CW167C0.999
8:42162336:G:TW167C0.999
8:42162338:G:CR168P0.999
8:42162371:C:AA179D0.999
8:42162389:A:TE185V0.999
8:42162400:G:CA189P0.999
8:42165122:T:CL212P0.999
8:42165134:C:AP216Q0.999
8:42165146:T:CL220P0.999
8:42165463:T:CC236R0.999
8:42165464:G:AC236Y0.999
8:42165465:T:GC236W0.999
8:42165481:T:AW242R0.999
8:42165481:T:CW242R0.999
8:42165512:C:AP252H0.999
8:42165512:C:GP252R0.999

dbSNP variants (sampled 300 via entrez): RS1000094092 (8:42165220 A>C,T), RS1000140452 (8:42165702 G>A), RS1000249424 (8:42163986 C>G), RS1000330404 (8:42151795 A>G,T), RS1000359130 (8:42153087 C>G,T), RS1000372924 (8:42152908 C>T), RS1000443093 (8:42164844 G>A), RS1000578318 (8:42153676 A>G,T), RS1000635156 (8:42169067 G>A,T), RS1000883960 (8:42170890 G>A,C), RS1001050183 (8:42152038 T>A), RS1001149095 (8:42163943 G>T), RS1001298824 (8:42157757 T>C), RS1001313185 (8:42156906 C>G), RS1001332055 (8:42170287 C>T)

Disease associations

OMIM: gene MIM:610469 | disease phenotypes: MIM:615592

GenCC curated gene-disease

Mondo (1): severe combined immunodeficiency due to IKK2 deficiency (MONDO:0014267)

Orphanet (1): Combined immunodeficiency due to IKBKB deficiency (Orphanet:397787)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006988_102Blond vs. brown/black hair color2.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0003924hair color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cisplatinaffects expression, affects cotreatment, increases expression3
Valproic Acidaffects cotreatment, increases expression, decreases methylation3
sodium arsenitedecreases expression, increases expression2
Acetaminophenincreases expression2
Benzo(a)pyrenedecreases methylation, increases expression2
Nickelincreases expression2
Cyclosporineincreases expression, increases methylation2
alpha phellandreneincreases expression1
bisphenol Aaffects cotreatment, increases methylation1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
Decitabineaffects expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutants, Occupationalaffects expression1
Benzeneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Estradiolaffects cotreatment, decreases expression1
Ethyl Methanesulfonatedecreases expression1
Indomethacinaffects cotreatment, increases expression1
Methyl Methanesulfonatedecreases expression1
Progesteroneaffects cotreatment, decreases expression1
Quercetinincreases expression1
Tretinoindecreases expression1
Tunicamycinincreases expression1

Clinical trials (associated diseases)

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