DTX3

gene
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Also known as FLJ34766RNF154

Summary

DTX3 (deltex E3 ubiquitin ligase 3, HGNC:24457) is a protein-coding gene on chromosome 12q13.3, encoding E3 ubiquitin-protein ligase DTX3 (Q8N9I9). Functions as an ubiquitin ligase protein, and regulates Notch signaling.

DTX3 functions as an E3 ubiquitin ligase (Takeyama et al., 2003 [PubMed 12670957]).

Source: NCBI Gene 196403 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 39 total
  • MANE Select transcript: NM_178502

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24457
Approved symbolDTX3
Namedeltex E3 ubiquitin ligase 3
Location12q13.3
Locus typegene with protein product
StatusApproved
AliasesFLJ34766, RNF154
Ensembl geneENSG00000178498
Ensembl biotypeprotein_coding
OMIM613142
Entrez196403

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 31 protein_coding

ENST00000337737, ENST00000548198, ENST00000548478, ENST00000548804, ENST00000549583, ENST00000550300, ENST00000550596, ENST00000551632, ENST00000551835, ENST00000884287, ENST00000884288, ENST00000884289, ENST00000884290, ENST00000884291, ENST00000884292, ENST00000884293, ENST00000884294, ENST00000884295, ENST00000884296, ENST00000884297, ENST00000939591, ENST00000939592, ENST00000939593, ENST00000939594, ENST00000939595, ENST00000939596, ENST00000939597, ENST00000939598, ENST00000946644, ENST00000946645, ENST00000946646

RefSeq mRNA: 3 — MANE Select: NM_178502 NM_001286245, NM_001286246, NM_178502

CCDS: CCDS41800, CCDS66410

Canonical transcript exons

ENST00000337737 — 7 exons

ExonStartEnd
ENSE000012615705760852057608737
ENSE000013548755760686557607613
ENSE000013883555760557157605731
ENSE000015315345760619057606252
ENSE000015315385760482457604858
ENSE000035363655760644357606518
ENSE000038465205760907757609802

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 98.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.5535 / max 172.2434, expressed in 1494 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
12628612.66301488
1262840.8414497
1262830.5246293
1262850.4460267
1262870.078429

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489098.75gold quality
cerebellar hemisphereUBERON:000224598.63gold quality
cerebellar cortexUBERON:000212998.58gold quality
adenohypophysisUBERON:000219697.99gold quality
right frontal lobeUBERON:000281097.89gold quality
cerebellumUBERON:000203797.86gold quality
pituitary glandUBERON:000000797.80gold quality
cortical plateUBERON:000534397.55gold quality
right uterine tubeUBERON:000130297.49gold quality
endothelial cellCL:000011597.39gold quality
left ovaryUBERON:000211997.30gold quality
body of uterusUBERON:000985397.26gold quality
right ovaryUBERON:000211897.19gold quality
anterior cingulate cortexUBERON:000983597.09gold quality
cingulate cortexUBERON:000302797.05gold quality
nucleus accumbensUBERON:000188296.93gold quality
esophagogastric junction muscularis propriaUBERON:003584196.93gold quality
lower esophagus muscularis layerUBERON:003583396.85gold quality
lower esophagusUBERON:001347396.83gold quality
muscle layer of sigmoid colonUBERON:003580596.78gold quality
caudate nucleusUBERON:000187396.75gold quality
ganglionic eminenceUBERON:000402396.65gold quality
endocervixUBERON:000045896.61gold quality
apex of heartUBERON:000209896.61gold quality
amygdalaUBERON:000187696.40gold quality
left uterine tubeUBERON:000130396.32gold quality
mucosa of stomachUBERON:000119996.29gold quality
primary visual cortexUBERON:000243695.93gold quality
dorsolateral prefrontal cortexUBERON:000983495.89gold quality
right coronary arteryUBERON:000162595.84gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting DTX3, 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-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-444799.8567.812900
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-808099.8267.521342
HSA-MIR-44899.7972.372103
HSA-MIR-430699.7270.503630
HSA-MIR-449999.6267.291470
HSA-MIR-447299.5666.081478
HSA-MIR-486-3P99.5166.821901
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-608199.4866.071446
HSA-MIR-127599.4767.902749
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-491-5P99.1365.981468
HSA-MIR-328-5P99.0864.651000
HSA-MIR-6868-5P99.0665.691284
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-6885-5P98.7164.33902
HSA-MIR-6878-5P98.4967.912142
HSA-MIR-6511A-5P98.1367.471770
HSA-MIR-4665-5P97.9167.691536
HSA-MIR-432997.6866.261003
HSA-MIR-6892-5P97.2768.60847
HSA-MIR-60297.0961.68156
HSA-MIR-4690-3P97.0264.72981

Literature-anchored findings (GeneRIF, showing 5)

  • It is reported that BBAP and the human family of DTX proteins (DTX1, DTX2, and DTX3) function as E3 ligases based on their capacity for self-ubiquitination. (PMID:12670957)
  • We show here that both molecules (Deltex (DTX) and AIP4) interact and partially colocalize to endocytic vesicles, and that AIP4 targets DTX for lysosomal degradation. (PMID:17028573)
  • DTX3, a novel E3 ligase for NOTCH2 was identified, and promoted its ubiquitination and degradation. DTX3 overexpression suppressed the proliferation and tumorigenicity of human oesophageal carcinoma cells. The analysis of tissue samples from patients revealed that the expression of DTX3 was low in esophageal cancer cells. (PMID:31854042)
  • DTX3 copy number increase in breast cancer: a study of associations to molecular subtype, proliferation and prognosis. (PMID:33616774)
  • Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway. (PMID:36614304)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriodtx3ENSDARG00000025766
mus_musculusDtx3ENSMUSG00000040415
rattus_norvegicusDtx3ENSRNOG00000005129

Paralogs (4): DTX2 (ENSG00000091073), DTX4 (ENSG00000110042), DTX1 (ENSG00000135144), DTX3L (ENSG00000163840)

Protein

Protein identifiers

E3 ubiquitin-protein ligase DTX3Q8N9I9 (reviewed: Q8N9I9)

Alternative names: Protein deltex-3, RING finger protein 154, RING-type E3 ubiquitin transferase DTX3

All UniProt accessions (6): A0A0C4DGI8, A0A1Y8EH36, Q8N9I9, F8VUZ4, F8VV96, H0YHF9

UniProt curated annotations — full annotation on UniProt →

Function. Functions as an ubiquitin ligase protein, and regulates Notch signaling. By promoting the ubiquitination and subsequent degradation of target proteins, it can block activation of the Notch signaling pathway, potentially acting as a tumor suppressor in human cancers. Involved in the angiogenic EPHB4 kinase degradation in cancer cell.

Subunit / interactions. Homodimer. May form a heterodimers with other members of the Deltex family. Interacts with NOTCH1.

Subcellular location. Cytoplasm. Nucleus.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the Deltex family.

Isoforms (3)

UniProt IDNamesCanonical?
Q8N9I9-11, DTX3Ayes
Q8N9I9-22, DTX3B
Q8N9I9-33, DTX3C

RefSeq proteins (3): NP_001273174, NP_001273175, NP_848597* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR017907Znf_RING_CSConserved_site
IPR039396Deltex_CDomain
IPR039398Deltex_famFamily
IPR039399Deltex_C_sfHomologous_superfamily

Pfam: PF13923, PF18102

UniProt features (6 total): splice variant 2, chain 1, zinc finger region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N9I9-F183.280.55

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CAGCTG_AP4_Q5, MARTINEZ_RB1_TARGETS_DN, DOANE_RESPONSE_TO_ANDROGEN_DN, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_REGULATION_OF_NOTCH_SIGNALING_PATHWAY, AFP1_Q6, RYTTCCTG_ETS2_B, CCCNNGGGAR_OLF1_01, MARTINEZ_RB1_AND_TP53_TARGETS_UP, AP2GAMMA_01, TGGAAA_NFAT_Q4_01, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY

GO Biological Process (3): Notch signaling pathway (GO:0007219), regulation of Notch signaling pathway (GO:0008593), protein ubiquitination (GO:0016567)

GO Molecular Function (5): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cell surface receptor signaling pathway1
Notch signaling pathway1
regulation of signal transduction1
protein modification by small protein conjugation1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1

Protein interactions and networks

STRING

496 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DTX3PARP9Q8IXQ6837
DTX3ANK2Q01484652
DTX3ANK3Q12955639
DTX3ANK1P16157636
DTX3DVL3Q92997559
DTX3UBE2D1P51668547
DTX3AMBRA1Q9C0C7406
DTX3CIRSRQ86X95400
DTX3METTL6Q8TCB7396
DTX3DCAF13Q9NV06378
DTX3MRPS23Q9Y3D9377
DTX3LFNGQ8NES3376
DTX3C22orf15Q8WYQ4369
DTX3NOTCH4Q99466358
DTX3SYAP1Q96A49355

IntAct

121 interactions, top by confidence:

ABTypeScore
UBE2KDTX3psi-mi:“MI:0915”(physical association)0.720
DTX3UBE2Kpsi-mi:“MI:0915”(physical association)0.720
DTX3UBE2D1psi-mi:“MI:0915”(physical association)0.670
UBE2D3DTX3psi-mi:“MI:0915”(physical association)0.670
DTX3UBE2L6psi-mi:“MI:0915”(physical association)0.670
UBE2D4DTX3psi-mi:“MI:0915”(physical association)0.670
UBE2D1DTX3psi-mi:“MI:0915”(physical association)0.670
DTX3TRAF4psi-mi:“MI:0915”(physical association)0.670
UBE2L6DTX3psi-mi:“MI:0915”(physical association)0.670
DTX3UBE2D4psi-mi:“MI:0915”(physical association)0.670
TRAF4DTX3psi-mi:“MI:0915”(physical association)0.670
FYNDTX3psi-mi:“MI:0915”(physical association)0.600
DTX3FYNpsi-mi:“MI:0915”(physical association)0.600
UBASH3BDTX3psi-mi:“MI:0915”(physical association)0.560
TRIP10DTX3psi-mi:“MI:0915”(physical association)0.560
DTX3ZMYND19psi-mi:“MI:0915”(physical association)0.560
DTX3PARP11psi-mi:“MI:0915”(physical association)0.560
PTK6DTX3psi-mi:“MI:0915”(physical association)0.560
UBASH3ADTX3psi-mi:“MI:0915”(physical association)0.560
DTX3NFKBIDpsi-mi:“MI:0915”(physical association)0.560
BAG3DTX3psi-mi:“MI:0915”(physical association)0.560
EPM2AIP1DTX3psi-mi:“MI:0915”(physical association)0.560
FAM90A1DTX3psi-mi:“MI:0915”(physical association)0.560
YES1DTX3psi-mi:“MI:0915”(physical association)0.560
DTX3psi-mi:“MI:0915”(physical association)0.560
NCK2DTX3psi-mi:“MI:0915”(physical association)0.560

BioGRID (151): DTX3 (Two-hybrid), DTX3 (Two-hybrid), FARSB (Affinity Capture-MS), NARFL (Affinity Capture-MS), NDUFAF5 (Affinity Capture-MS), CHFR (Affinity Capture-MS), ITSN1 (Affinity Capture-MS), MAPK9 (Affinity Capture-MS), NMD3 (Affinity Capture-MS), NDUFS6 (Affinity Capture-MS), RNF114 (Affinity Capture-MS), CHFR (Affinity Capture-MS), NARFL (Affinity Capture-MS), NMD3 (Affinity Capture-MS), ITSN1 (Affinity Capture-MS)

ESM2 similar proteins: A1L1K1, A2ARM1, A2AVJ5, A4IFC9, A7E305, G5EGQ2, O08653, O36006, O43435, O46080, O95343, P13481, P28702, P28704, P56423, P56424, P56645, P61260, P97499, Q02556, Q07820, Q2NL16, Q32N92, Q5E9R0, Q5REG4, Q5SQI0, Q5TJF7, Q5U2W6, Q5U2Y1, Q61010, Q62233, Q6MZQ0, Q80V91, Q86Y01, Q86YD1, Q8AW93, Q8BIG4, Q8HYS5, Q8N9I9, Q91VU8

Diamond homologs: Q23985, Q3UIR3, Q5REG4, Q61010, Q80V91, Q86UW9, Q86Y01, Q8N9I9, Q8R3P2, Q8TDB6, Q6PDK8, Q8AW93, Q9Y2E6, Q07G17, Q2KJ29, Q3KNV8, Q80Z37, Q8BTQ0, Q9NS56, B4F6W9, F1LP64, G5E870, Q13670, F4KGU4, Q2EMV9, Q9NS91, Q9QXK2

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”DTX3ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 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
Synthesis of active ubiquitin: roles of E1 and E2 enzymes886.7×6e-12
Negative regulators of DDX58/IFIH1 signaling548.0×4e-06
Regulation of TNFR1 signaling639.5×8e-07
E3 ubiquitin ligases ubiquitinate target proteins528.5×4e-05
Antigen processing: Ubiquitination & Proteasome degradation1314.2×3e-10

GO biological processes:

GO termPartnersFoldFDR
protein K11-linked ubiquitination761.0×2e-09
protein monoubiquitination538.2×1e-05
protein K48-linked ubiquitination933.7×8e-10
protein K63-linked ubiquitination529.7×3e-05
protein modification process527.1×5e-05
protein polyubiquitination1025.6×8e-10
ubiquitin-dependent protein catabolic process914.8×6e-07
protein ubiquitination76.4×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1305 predictions. Top by Δscore:

VariantEffectΔscore
12:57604856:GAG:Gdonor_gain1.0000
12:57604858:GGTA:Gdonor_loss1.0000
12:57606519:G:GGdonor_gain1.0000
12:57607586:G:GGdonor_gain1.0000
12:57607610:GGGG:Gdonor_gain1.0000
12:57607611:GGG:Gdonor_gain1.0000
12:57607611:GGGG:Gdonor_gain1.0000
12:57607612:GGG:Gdonor_gain1.0000
12:57608671:G:GTdonor_gain1.0000
12:57608717:C:Gdonor_gain1.0000
12:57608725:G:GTdonor_gain1.0000
12:57608735:GCT:Gdonor_gain1.0000
12:57608736:C:Gdonor_gain1.0000
12:57608738:G:GGdonor_gain1.0000
12:57604854:GAGAG:Gdonor_gain0.9900
12:57604859:G:GGdonor_gain0.9900
12:57606107:G:GTdonor_gain0.9900
12:57606112:G:GTdonor_gain0.9900
12:57606112:G:Tdonor_gain0.9900
12:57606188:A:AGacceptor_gain0.9900
12:57606189:G:GAacceptor_gain0.9900
12:57606189:GTCCT:Gacceptor_gain0.9900
12:57606432:C:Aacceptor_gain0.9900
12:57606441:A:AGacceptor_gain0.9900
12:57606441:A:Gacceptor_loss0.9900
12:57606442:G:GGacceptor_gain0.9900
12:57606515:CAAAG:Cdonor_loss0.9900
12:57606517:AA:Adonor_gain0.9900
12:57606517:AAGT:Adonor_loss0.9900
12:57606518:AGTAA:Adonor_loss0.9900

AlphaMissense

2212 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:57607353:T:CC164R1.000
12:57607355:C:GC164W1.000
12:57607362:T:AC167S1.000
12:57607362:T:CC167R1.000
12:57607363:G:CC167S1.000
12:57607401:T:AC180S1.000
12:57607401:T:CC180R1.000
12:57607402:G:CC180S1.000
12:57607413:T:CF184L1.000
12:57607414:T:CF184S1.000
12:57607415:C:AF184L1.000
12:57607415:C:GF184L1.000
12:57607416:T:CC185R1.000
12:57607425:T:AC188S1.000
12:57607425:T:CC188R1.000
12:57607426:G:CC188S1.000
12:57607458:T:AC199S1.000
12:57607458:T:CC199R1.000
12:57607459:G:AC199Y1.000
12:57607459:G:CC199S1.000
12:57607467:T:AC202S1.000
12:57607467:T:CC202R1.000
12:57607468:G:CC202S1.000
12:57607495:G:TG211V1.000
12:57607582:T:AI240N1.000
12:57607587:T:CY242H1.000
12:57607610:G:CQ249H1.000
12:57607610:G:TQ249H1.000
12:57608547:T:GY260D1.000
12:57608563:G:CR265P1.000

dbSNP variants (sampled 300 via entrez): RS1000700275 (12:57607160 G>C,T), RS1001378807 (12:57610282 G>A), RS1001638897 (12:57603538 A>C), RS1001900918 (12:57605200 A>C,G), RS1002192094 (12:57606510 A>G), RS1002931301 (12:57603463 T>C), RS1003193296 (12:57605082 C>T), RS1003268092 (12:57604892 G>A), RS1003970140 (12:57606687 A>G), RS1004226437 (12:57606155 G>A), RS1004503996 (12:57607750 T>G), RS1004802818 (12:57609660 T>C,G), RS1004979544 (12:57604104 ACAC>A,ACACCAC), RS1006708007 (12:57604233 G>C), RS1007170108 (12:57604533 G>C)

Disease associations

OMIM: gene MIM:613142 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression4
sodium arsenitedecreases expression, increases expression2
(+)-JQ1 compounddecreases expression2
nickel sulfatedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
enzalutamideaffects expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Zoledronic Acidincreases expression1
Glyphosateincreases expression1
Acroleinaffects cotreatment, decreases expression1
Benzo(a)pyreneincreases methylation1
Diethylhexyl Phthalatedecreases expression1
Doxorubicinaffects expression1
Estradioldecreases expression1
Hydrogen Peroxideaffects expression1
Nickeldecreases expression1
Ozoneaffects cotreatment, decreases expression1
Tetrachlorodibenzodioxinincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Aflatoxin B1decreases methylation1
Gold Compoundsincreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chlorideincreases expression1

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B1QGAbcam HeLa DTX3 KOCancer cell lineFemale
CVCL_D7NWUbigene A-549 DTX3 KOCancer cell lineMale
CVCL_D9DNUbigene HEK293 DTX3 KOTransformed cell lineFemale
CVCL_E0BWUbigene HeLa DTX3 KOCancer cell lineFemale

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.