UBE3D

gene
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Also known as DKFZp434A1520H10BHYJR141W

Summary

UBE3D (ubiquitin protein ligase E3D, HGNC:21381) is a protein-coding gene on chromosome 6q14.1, encoding E3 ubiquitin-protein ligase E3D (Q7Z6J8). E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. It is a selective cancer dependency (DepMap: 11.5% of cell lines).

Enables cyclin binding activity; ubiquitin protein ligase activity; and ubiquitin-like protein conjugating enzyme binding activity. Involved in protein autoubiquitination; protein monoubiquitination; and protein polyubiquitination. Part of ubiquitin ligase complex. Is active in cytosol.

Source: NCBI Gene 90025 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 73 total
  • Cancer dependency (DepMap): dependent in 11.5% of screened cell lines
  • MANE Select transcript: NM_198920

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21381
Approved symbolUBE3D
Nameubiquitin protein ligase E3D
Location6q14.1
Locus typegene with protein product
StatusApproved
AliasesDKFZp434A1520, H10BH, YJR141W
Ensembl geneENSG00000118420
Ensembl biotypeprotein_coding
OMIM612495
Entrez90025

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 nonsense_mediated_decay, 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000237186, ENST00000369746, ENST00000369747, ENST00000430071, ENST00000503942, ENST00000505226, ENST00000509102, ENST00000626828, ENST00000910309, ENST00000917834, ENST00000917835

RefSeq mRNA: 6 — MANE Select: NM_198920 NM_001304437, NM_001350602, NM_001350603, NM_001350604, NM_001410933, NM_198920

CCDS: CCDS34491, CCDS93953

Canonical transcript exons

ENST00000369747 — 10 exons

ExonStartEnd
ENSE000020502878306564283065841
ENSE000034751338305782683058022
ENSE000034894558295731282957450
ENSE000035025218289239082893042
ENSE000035686898301897383019136
ENSE000036178598304442883044659
ENSE000036240438305414883054238
ENSE000036334808302396983024038
ENSE000036504298303841683038485
ENSE000036927508302245383022561

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 93.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6539 / max 233.9773, expressed in 1681 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
745497.11231654
745481.4711515
745470.070531

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233693.20gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.92gold quality
bronchial epithelial cellCL:000232883.61gold quality
bronchusUBERON:000218582.27gold quality
right uterine tubeUBERON:000130281.67gold quality
olfactory segment of nasal mucosaUBERON:000538679.44gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.64gold quality
caudate nucleusUBERON:000187378.18gold quality
hypothalamusUBERON:000189877.81gold quality
oviduct epitheliumUBERON:000480477.81gold quality
putamenUBERON:000187477.15gold quality
Brodmann (1909) area 9UBERON:001354077.10gold quality
islet of LangerhansUBERON:000000676.77gold quality
cortical plateUBERON:000534376.47gold quality
calcaneal tendonUBERON:000370175.95gold quality
colonic epitheliumUBERON:000039775.94gold quality
right frontal lobeUBERON:000281075.78gold quality
fallopian tubeUBERON:000388975.60gold quality
nucleus accumbensUBERON:000188275.57gold quality
anterior cingulate cortexUBERON:000983575.53gold quality
dorsolateral prefrontal cortexUBERON:000983475.31gold quality
prefrontal cortexUBERON:000045175.30gold quality
C1 segment of cervical spinal cordUBERON:000646975.20gold quality
body of pancreasUBERON:000115075.11gold quality
mucosa of paranasal sinusUBERON:000503075.10gold quality
pancreasUBERON:000126475.00gold quality
palpebral conjunctivaUBERON:000181274.95gold quality
cerebellar hemisphereUBERON:000224574.54gold quality
cerebellar cortexUBERON:000212974.39gold quality
amygdalaUBERON:000187674.34gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting UBE3D, 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-3163100.0077.238605
HSA-MIR-428299.9975.366408
HSA-MIR-477599.9875.006394
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-651-3P99.9473.485177
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-202-3P99.8471.411290
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-1212499.6869.172700
HSA-MIR-561-3P99.6470.903647
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-106A-3P99.5367.58995
HSA-MIR-54399.5269.032595
HSA-MIR-136-5P99.5067.261153
HSA-MIR-142-5P99.4870.922416
HSA-MIR-5590-3P99.4870.912429
HSA-MIR-312399.4767.152693
HSA-MIR-942-5P99.4168.401977
HSA-MIR-584-3P99.3567.691082
HSA-MIR-442799.3470.331854
HSA-MIR-427999.1966.702437
HSA-MIR-548L99.0670.902560
HSA-MIR-511-5P98.9770.942268
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-382-3P98.8367.101074
HSA-MIR-501-5P98.7768.881328

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • The carboxyl terminal half of H10BH was able to bind cyclin B and ubiquitinylate cyclin B in vitro. (PMID:15749827)
  • A novel missense SNV, rs7739323, is strongly associated with age-related macular degeneration in an East Asian population. (PMID:25872646)
  • With the exception of associations of BEGAIN with severe and UBE3D with moderate chronic periodontitis (CP) , no other loci were associated with CP in ARIC or aggressive periodontitis in the German sample. (PMID:26962152)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioube3dENSDARG00000026178
mus_musculusUbe3dENSMUSG00000032415
rattus_norvegicusUbe3dENSRNOG00000010802
caenorhabditis_elegansWBGENE00022168

Protein

Protein identifiers

E3 ubiquitin-protein ligase E3DQ7Z6J8 (reviewed: Q7Z6J8)

Alternative names: HECT-type E3 ubiquitin transferase E3D, UbcH10-binding protein with a HECT-like domain, Ubiquitin-conjugating enzyme E2C-binding protein

All UniProt accessions (6): Q7Z6J8, D6RD24, D6RHY9, H0Y359, J3KMY4, Q4G0X5

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. Independently of its E3 ubiquitin-protein ligase activity, acts as an inhibitor of CPSF3 endonuclease activity by blocking CPSF3 active site.

Subunit / interactions. Interacts with UBE2C/UbcH10 (E2 ubiquitin-conjugating enzyme). In vitro, interacts with cyclin-B.

Subcellular location. Cytoplasm.

Post-translational modifications. Ubiquitinated by UBCH10 (E2 ubiquitin-conjugating enzyme).

Domain organisation. The C-terminal half (AA 188-389) is able to bind cyclin-B and shows a self-ubiquitination activity (mono-, poly, or multi-ubiquitination) in a HECT-like sequence dependent manner. The BRAT1-like motif mediates inhibition of the endonuclease activity of CPSF3 by forming hydrogen bond and hydrophobic interactions with the active site of CPSF3: Cys-144 coordinates one of the two active site zinc ions of CPSF3.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (6): NP_001291366, NP_001337531, NP_001337532, NP_001337533, NP_001397862, NP_944602* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019193UBQ-conj_enz_E2-bd_protFamily

Pfam: PF09814

UniProt features (11 total): sequence conflict 2, region of interest 2, sequence variant 2, initiator methionine 1, chain 1, short sequence motif 1, binding site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z6J8-F179.340.51

Functional residue map

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

Ligand- & substrate-binding residues (1): 144

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 122 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_PROTEIN_AUTOUBIQUITINATION, TGIF_01, GOBP_PROTEIN_MONOUBIQUITINATION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, STONER_ESOPHAGEAL_CARCINOGENESIS_DN, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, RIGGI_EWING_SARCOMA_PROGENITOR_UP, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_TRANSFERASE_COMPLEX, GOBP_PROTEOLYSIS

GO Biological Process (5): protein polyubiquitination (GO:0000209), protein monoubiquitination (GO:0006513), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein autoubiquitination (GO:0051865), protein ubiquitination (GO:0016567)

GO Molecular Function (7): ribonuclease inhibitor activity (GO:0008428), cyclin binding (GO:0030332), ubiquitin conjugating enzyme binding (GO:0031624), ubiquitin-like protein conjugating enzyme binding (GO:0044390), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (4): ubiquitin ligase complex (GO:0000151), nucleus (GO:0005634), cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Class I MHC mediated antigen processing & presentation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein ubiquitination3
cellular anatomical structure2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein modification by small protein conjugation1
RNA nuclease activity1
nuclease inhibitor activity1
protein binding1
ubiquitin-like protein conjugating enzyme binding1
enzyme binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
intracellular protein-containing complex1
transferase complex1
intracellular membrane-bounded organelle1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UBE3DUBE2CO00762935
UBE3DCBLL2Q8N7E2589
UBE3DARIH2O95376524
UBE3DPUDPQ08623450
UBE3DC6orf163Q5TEZ5447
UBE3DCSTF3Q12996443
UBE3DFBXO42Q6P3S6428
UBE3DNOL9Q5SY16396
UBE3DFCF1Q9Y324392
UBE3DCPSF3Q9UKF6391
UBE3DRWDD2AQ9UIY3386
UBE3DSNAPC3Q92966384
UBE3DCEP162Q5TB80377
UBE3DZNF668Q96K58377
UBE3DSMIM8Q96KF7373

IntAct

34 interactions, top by confidence:

ABTypeScore
CCM2KRIT1psi-mi:“MI:0914”(association)0.960
LMO1ZBTB43psi-mi:“MI:0914”(association)0.830
DNAAF2UBE3Dpsi-mi:“MI:0914”(association)0.780
UBE3DDNAAF2psi-mi:“MI:0915”(physical association)0.780
DNAAF2UBE3Dpsi-mi:“MI:0915”(physical association)0.780
CPSF3CPSF4psi-mi:“MI:0914”(association)0.640
MAGEA11UBE3Dpsi-mi:“MI:0915”(physical association)0.560
LMO3ZBTB43psi-mi:“MI:0914”(association)0.550
DEFA1MANBApsi-mi:“MI:0914”(association)0.530
FKBP6EEF2Kpsi-mi:“MI:0914”(association)0.530
KLHDC2PFDN1psi-mi:“MI:0914”(association)0.530
UBE3DSTIP1psi-mi:“MI:0914”(association)0.530
SLC31A1C2orf72psi-mi:“MI:0914”(association)0.530
C1QTNF9BPLOD3psi-mi:“MI:0914”(association)0.530
UBE3DPPP5Cpsi-mi:“MI:0915”(physical association)0.400
CPSF3P4HA2psi-mi:“MI:0914”(association)0.350
CCM2KRIT1psi-mi:“MI:0914”(association)0.350
MEMO1TARBP2psi-mi:“MI:0914”(association)0.350
CAPZBENAHpsi-mi:“MI:0914”(association)0.350
TCTN2TMEM131Lpsi-mi:“MI:0914”(association)0.350
NXPH1RAD51Cpsi-mi:“MI:0914”(association)0.350
LCN9C1QL1psi-mi:“MI:0914”(association)0.350
MEMO1HMBOX1psi-mi:“MI:0914”(association)0.350
LMO1LMX1Bpsi-mi:“MI:0914”(association)0.350
ATG101FIBPpsi-mi:“MI:2364”(proximity)0.270

BioGRID (70): UBE3D (Affinity Capture-MS), UBE3D (Affinity Capture-MS), UBE3D (Affinity Capture-MS), DNAAF2 (Affinity Capture-MS), UBE3D (Affinity Capture-MS), GTPBP2 (Affinity Capture-MS), SUFU (Affinity Capture-MS), UBE3D (Affinity Capture-MS), HSP90AB4P (Affinity Capture-MS), UBE3D (Affinity Capture-MS), UBE3D (Affinity Capture-MS), UBE3D (Affinity Capture-MS), STIP1 (Affinity Capture-MS), BORA (Affinity Capture-MS), TUBA4A (Affinity Capture-MS)

ESM2 similar proteins: A1KXW8, A6QL50, E1BGQ2, H0Y354, O94955, P47224, Q08326, Q0IIH8, Q1JQA1, Q1RMS8, Q1RMZ1, Q2TBU5, Q3T1H6, Q4R372, Q4R528, Q4R9C4, Q5F480, Q5F4A1, Q5I0G3, Q5RCQ0, Q5RFG8, Q5TFE4, Q5TYM5, Q641X7, Q6L9T8, Q6PIP5, Q7L622, Q7Z6J8, Q7ZX59, Q86X60, Q8BFZ8, Q8BKW4, Q8BM85, Q8BX13, Q8CEL2, Q8N5C7, Q8N635, Q8NHU2, Q8TCF1, Q8TCJ0

Diamond homologs: Q1JQA1, Q3T1H6, Q5RFG8, Q7Z6J8, Q8BX13

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign7
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3605 predictions. Top by Δscore:

VariantEffectΔscore
6:82936951:AGGT:Adonor_gain1.0000
6:83022560:ACC:Aacceptor_loss1.0000
6:83024039:C:CCacceptor_gain1.0000
6:83040612:ATT:Adonor_gain1.0000
6:83057824:A:ACdonor_gain1.0000
6:83057825:C:CCdonor_gain1.0000
6:83065640:ACC:Adonor_gain1.0000
6:83065641:CCC:Cdonor_gain1.0000
6:82893962:AC:Adonor_gain0.9900
6:82893963:CC:Cdonor_gain0.9900
6:82936951:A:ACdonor_gain0.9900
6:82936952:G:Cdonor_gain0.9900
6:82957306:GCTCA:Gdonor_loss0.9900
6:82957307:CTCAC:Cdonor_loss0.9900
6:82957308:TCACC:Tdonor_loss0.9900
6:82957309:CAC:Cdonor_loss0.9900
6:82957310:A:AGdonor_loss0.9900
6:82957311:C:CAdonor_loss0.9900
6:82957446:CAAGT:Cacceptor_gain0.9900
6:82957451:C:CCacceptor_gain0.9900
6:83019132:CATAG:Cacceptor_gain0.9900
6:83022447:TCTTA:Tdonor_loss0.9900
6:83022448:CTTA:Cdonor_loss0.9900
6:83022449:TTA:Tdonor_loss0.9900
6:83022450:TACCA:Tdonor_loss0.9900
6:83022451:A:Gdonor_loss0.9900
6:83022564:G:Cacceptor_loss0.9900
6:83038410:TCTTA:Tdonor_loss0.9900
6:83038411:CTTAC:Cdonor_loss0.9900
6:83038412:TTAC:Tdonor_loss0.9900

AlphaMissense

2549 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:83038458:A:GC209R0.988
6:83054182:A:GC111R0.985
6:83054180:G:CC111W0.983
6:83019133:A:GW284R0.980
6:83019133:A:TW284R0.980
6:83044601:A:GW142R0.980
6:83044601:A:TW142R0.980
6:83019004:A:CY327D0.979
6:82957379:A:GL361P0.978
6:83019009:A:TV325D0.978
6:83038449:A:GC212R0.975
6:83038456:A:CC209W0.975
6:83054173:A:GC114R0.975
6:83038448:C:GC212S0.974
6:83038449:A:TC212S0.974
6:83022489:G:CF270L0.973
6:83022489:G:TF270L0.973
6:83022490:A:GF270S0.973
6:83022491:A:GF270L0.973
6:83038457:C:TC209Y0.973
6:83019011:C:AK324N0.972
6:83019011:C:GK324N0.972
6:83022495:A:CF268L0.971
6:83022495:A:TF268L0.971
6:83022497:A:GF268L0.971
6:83054172:C:TC114Y0.970
6:83038433:C:TG217E0.969
6:83038457:C:GC209S0.969
6:83038458:A:TC209S0.969
6:82957437:A:GW342R0.968

dbSNP variants (sampled 300 via entrez): RS1000019849 (6:83056922 A>G), RS1000030866 (6:83009595 A>G), RS1000032400 (6:82921211 C>T), RS1000074211 (6:83015068 C>G), RS1000121421 (6:82928801 A>G), RS1000129946 (6:82943004 G>A), RS1000135404 (6:82951150 A>G), RS1000164450 (6:83000448 C>A,G), RS1000174916 (6:82989536 C>T), RS1000175441 (6:82992286 G>A,C,T), RS1000192978 (6:82958806 A>G,T), RS1000200839 (6:83044208 G>C), RS1000207826 (6:82903004 T>C), RS1000208453 (6:82905357 A>G,T), RS1000210533 (6:83032887 C>A,T)

Disease associations

OMIM: gene MIM:612495 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST003360_3Crohn’s disease2.000000e-11
GCST003901_8Cognitive decline (age-related)1.000000e-06
GCST006288_130Heel bone mineral density5.000000e-12
GCST006288_553Heel bone mineral density5.000000e-13
GCST006979_299Heel bone mineral density2.000000e-33
GCST009177_5Entorhinal cortical volume9.000000e-06
GCST010988_368Adult body size5.000000e-09
GCST012291_7Schizophrenia, bipolar disorder or recurrent major depressive disorder3.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density
EFO:0005092entorhinal cortical volume
EFO:0004952disease recurrence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects cotreatment, decreases expression, affects expression7
mercuric bromidedecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tetrachlorodibenzodioxindecreases expression2
Tretinoindecreases expression2
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aincreases expression1
trichostatin Adecreases expression1
beta-lapachonedecreases expression1
sodium arsenitedecreases expression1
zinc chromateaffects expression, increases abundance1
benzo(e)pyreneincreases methylation1
chromium hexavalent ionaffects expression, increases abundance1
entinostatincreases expression1
monomethylarsonous acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
Sunitinibincreases expression1
Vorinostatincreases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases expression1
Calcitriolaffects cotreatment, decreases expression1
Dexamethasoneincreases expression, affects cotreatment1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Indomethacinincreases expression, affects cotreatment1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.