HECTD3

gene
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Also known as FLJ21156

Summary

HECTD3 (HECT domain E3 ubiquitin protein ligase 3, HGNC:26117) is a protein-coding gene on chromosome 1p34.1, encoding E3 ubiquitin-protein ligase HECTD3 (Q5T447). E3 ubiquitin ligases accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

The protein encoded by this gene transfers ubiquitin from an E2 ubiquitin-conjugating enzyme to targeted substrates, leading to the degradation of those substrates. The encoded protein has been shown to transfer ubiquitin to TRIOBP to facilitate cell cycle progression, and to STX8.

Source: NCBI Gene 79654 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 130 total
  • MANE Select transcript: NM_024602

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26117
Approved symbolHECTD3
NameHECT domain E3 ubiquitin protein ligase 3
Location1p34.1
Locus typegene with protein product
StatusApproved
AliasesFLJ21156
Ensembl geneENSG00000126107
Ensembl biotypeprotein_coding
OMIM618638
Entrez79654

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 17 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000372168, ENST00000372172, ENST00000466423, ENST00000484564, ENST00000486132, ENST00000486296, ENST00000487488, ENST00000875134, ENST00000875135, ENST00000875136, ENST00000875137, ENST00000875138, ENST00000875139, ENST00000875140, ENST00000875141, ENST00000875142, ENST00000875143, ENST00000875144, ENST00000875145, ENST00000927793, ENST00000949667, ENST00000949668

RefSeq mRNA: 1 — MANE Select: NM_024602 NM_024602

CCDS: CCDS41318

Canonical transcript exons

ENST00000372172 — 21 exons

ExonStartEnd
ENSE000009575274500599745006116
ENSE000010463714500914445009226
ENSE000010463774500998645010121
ENSE000010463784500824045008321
ENSE000010463844500853645008701
ENSE000010463884500721945007271
ENSE000010463924501020145010293
ENSE000010463954500741345007595
ENSE000012181894500936945009482
ENSE000012181944500956845009683
ENSE000014078014501054645010706
ENSE000019180034501088945011324
ENSE000034928664500460045004806
ENSE000034970964500669245006795
ENSE000035082504500695145007015
ENSE000035361474500424845004377
ENSE000035492804500406045004134
ENSE000035918024500366945003740
ENSE000036590044500385545003936
ENSE000036732644500579445005883
ENSE000038480904500254845003576

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 96.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.9826 / max 205.4568, expressed in 1808 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1210617.89621808
121050.086430

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033196.54gold quality
mucosa of transverse colonUBERON:000499196.49gold quality
transverse colonUBERON:000115795.25gold quality
small intestine Peyer’s patchUBERON:000345495.21gold quality
body of pancreasUBERON:000115095.07gold quality
small intestineUBERON:000210894.72gold quality
rectumUBERON:000105294.29gold quality
skin of legUBERON:000151194.05gold quality
duodenumUBERON:000211493.84gold quality
right lobe of liverUBERON:000111493.54gold quality
skin of abdomenUBERON:000141693.50gold quality
mucosa of stomachUBERON:000119993.39gold quality
minor salivary glandUBERON:000183093.28gold quality
metanephros cortexUBERON:001053392.99gold quality
saliva-secreting glandUBERON:000104492.96gold quality
body of stomachUBERON:000116192.94gold quality
right adrenal gland cortexUBERON:003582792.92gold quality
right adrenal glandUBERON:000123392.70gold quality
intestineUBERON:000016092.65gold quality
right lobe of thyroid glandUBERON:000111992.63gold quality
right coronary arteryUBERON:000162592.55gold quality
granulocyteCL:000009492.51gold quality
colonUBERON:000115592.49gold quality
tibial nerveUBERON:000132392.41gold quality
right ovaryUBERON:000211892.41gold quality
large intestineUBERON:000005992.33gold quality
right hemisphere of cerebellumUBERON:001489092.33gold quality
jejunal mucosaUBERON:000039992.29gold quality
descending thoracic aortaUBERON:000234592.29gold quality
left adrenal glandUBERON:000123492.24gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.92
E-MTAB-6386no193.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting HECTD3, 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-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-6748-5P100.0065.811057
HSA-MIR-453499.9966.581907
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-211099.9666.681930
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-808299.9567.271170
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-129799.9173.413162
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-1211999.8768.351653
HSA-MIR-132199.8465.301811
HSA-MIR-473999.8465.251832
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-430799.8270.453374
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-378G99.7164.901106

Literature-anchored findings (GeneRIF, showing 6)

  • All these findings suggest that HECTD3 may facilitate cell cycle progression via regulating ubiquitination and degradation of Tara. (PMID:18194665)
  • Overexpression of MALT1 partially rescues HECTD3 depletion-induced apoptosis. (PMID:23358872)
  • HECTD3 as a tumor suppressor modulating the activity of this important oncogenic signaling pathway. (PMID:28636940)
  • This review describes the progress in the recent studies of HECTD3 in cancer and other diseases. [review] (PMID:31637449)
  • HECTD3 regulates the tumourigenesis of glioblastoma by polyubiquitinating PARP1 and activating EGFR signalling pathway. (PMID:36088509)
  • E3 ubiquitin ligase HECTD3 is a tumor suppressor and mediates the polyubiquitination of SLC7A11 to promote ferroptosis in colon cancer. (PMID:37422058)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohectd3ENSDARG00000038905
mus_musculusHectd3ENSMUSG00000046861
rattus_norvegicusHectd3ENSRNOG00000018363

Protein

Protein identifiers

E3 ubiquitin-protein ligase HECTD3Q5T447 (reviewed: Q5T447)

Alternative names: HECT domain-containing protein 3, HECT-type E3 ubiquitin transferase HECTD3

All UniProt accessions (1): Q5T447

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin ligases accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of TRIOBP and its subsequent proteasomal degradation, thus facilitating cell cycle progression by regulating the turn-over of TRIOBP. Mediates also ubiquitination of STX8.

Subunit / interactions. Interacts with TRIOBP. Interacts with STX8.

Subcellular location. Cytoplasm. Perinuclear region.

Pathway. Protein modification; protein ubiquitination.

Isoforms (2)

UniProt IDNamesCanonical?
Q5T447-11yes
Q5T447-22

RefSeq proteins (1): NP_078878* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000569HECT_domDomain
IPR004939APC_su10/DOC_domDomain
IPR008979Galactose-bd-like_sfHomologous_superfamily
IPR035983Hect_E3_ubiquitin_ligaseHomologous_superfamily
IPR042469HECTD3Family

Pfam: PF00632, PF03256

Enzyme classification (BRENDA):

  • EC 2.3.2.26 — HECT-type E3 ubiquitin transferase (BRENDA: 14 organisms, 64 substrates, 19 inhibitors, 5 Km, 5 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
[UBC5B]-L-LYSINE0.0046–0.0375

UniProt features (10 total): domain 2, modified residue 2, splice variant 2, initiator methionine 1, chain 1, active site 1, mutagenesis site 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
9R6VX-RAY DIFFRACTION1.61
9R85ELECTRON MICROSCOPY3.04
9R8TELECTRON MICROSCOPY6.06
9R94ELECTRON MICROSCOPY6.38

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5T447-F184.480.49

Functional residue map

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

Catalytic / active sites (1): 823 (glycyl thioester intermediate)

Post-translational modifications (2): 2, 12

Mutagenesis-validated functional residues (1):

PositionPhenotype
823loss of ubiquitin-ligase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 132 (showing top): GCM_GSPT1, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GCM_ZNF198, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, chr1p34, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, PARENT_MTOR_SIGNALING_UP, GOBP_PROTEOLYSIS, GOMF_SYNTAXIN_BINDING

GO Biological Process (2): protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (5): ubiquitin-protein transferase activity (GO:0004842), syntaxin binding (GO:0019905), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (2): perinuclear region of cytoplasm (GO:0048471), 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
cellular anatomical structure2
protein modification by small protein conjugation1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
ubiquitin-like protein transferase activity1
SNARE binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

1185 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HECTD3KIAA2013Q8IYS2552
HECTD3DHRS7Q9Y394461
HECTD3GGT7Q9UJ14414
HECTD3NOTOA8MTQ0369
HECTD3VITQ6UXI7367
HECTD3ADAM19Q9H013353
HECTD3PLS1Q14651346
HECTD3MTDHQ86UE4332
HECTD3DTX3Q8N9I9307
HECTD3GPR75O95800305
HECTD3PKDCCQ504Y2303
HECTD3WWC2Q6AWC2300
HECTD3TRIP12Q14669296
HECTD3RNF114Q9Y508280
HECTD3PSME4Q14997266

IntAct

152 interactions, top by confidence:

ABTypeScore
EIF4E2GIGYF1psi-mi:“MI:0914”(association)0.730
MAVSRIPK2psi-mi:“MI:0914”(association)0.580
PPLHECTD3psi-mi:“MI:0915”(physical association)0.560
YJU2BRCCD1psi-mi:“MI:0914”(association)0.530
RBFAMETTL15psi-mi:“MI:0914”(association)0.530
ODAD4GNPATpsi-mi:“MI:0914”(association)0.530
SERPINA5ZZEF1psi-mi:“MI:0914”(association)0.530
CPA6PPM1Gpsi-mi:“MI:0914”(association)0.530
ANGPT2ZZEF1psi-mi:“MI:0914”(association)0.530
GASTZZEF1psi-mi:“MI:0914”(association)0.530
FOSL2ZZEF1psi-mi:“MI:0914”(association)0.530
CAVIN1ZZEF1psi-mi:“MI:0914”(association)0.530
TRMT10CZZEF1psi-mi:“MI:0914”(association)0.530
POGLUT1ZZEF1psi-mi:“MI:0914”(association)0.530
MRPS24ZZEF1psi-mi:“MI:0914”(association)0.530
CHRDL1ZZEF1psi-mi:“MI:0914”(association)0.530
PARD6BZZEF1psi-mi:“MI:0914”(association)0.530
COPS7BZZEF1psi-mi:“MI:0914”(association)0.530
WFDC10AZZEF1psi-mi:“MI:0914”(association)0.530
CLEC3AZZEF1psi-mi:“MI:0914”(association)0.530
MRPS34ZZEF1psi-mi:“MI:0914”(association)0.530
GREM2ZZEF1psi-mi:“MI:0914”(association)0.530

BioGRID (203): HECTD3 (Two-hybrid), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0K9RDW0, A1L4V7, A2Y8B9, A3BN26, A6NHR9, B4FTR7, B8B0E2, B9EYZ1, F4I933, F4J117, O35099, O49931, O81360, P03271, P03272, P03273, P93236, P93740, Q0DST9, Q0DVX2, Q0JCU7, Q0WL81, Q3U487, Q56X76, Q5E9N5, Q5M721, Q5QLS7, Q5T447, Q5VRY0, Q5VS72, Q60649, Q69TY5, Q6ATB4, Q6K9C1, Q6YSY5, Q7X745, Q8H4D4, Q8IZ73, Q8S2E5, Q8W519

Diamond homologs: B4F6W9, C6KTB7, E1B7Q7, F1LP64, F1RCR6, G5E870, Q14669, Q15751, Q3U487, Q5T447, D3ZEF4, O43149, O95714, Q14999, Q4U2R1, Q5RCJ3, Q5SSH7, Q80TT8, Q8IWT3, Q8VE73, Q9VR91, A2A5Z6, A6NED2, A9JRZ0, D3ZBM7, D3ZGQ5, E1C656, F1N6G5, F2Z461, F8W2M1, O74881, O75592, O95199, P0C5Y8, P14199, P18754, P23800, P34664, Q15034, Q1LZE1

SIGNOR signaling

8 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”HECTD3ubiquitination
HECTD3“down-regulates quantity by destabilization”TRIOBPpolyubiquitination
HECTD3“down-regulates quantity by destabilization”STX8polyubiquitination
HECTD3“down-regulates activity”CASP8polyubiquitination
HECTD3“up-regulates quantity by stabilization”MALT1polyubiquitination
HECTD3“down-regulates quantity by destabilization”RAF1polyubiquitination
HECTD3“down-regulates activity”CASP9polyubiquitination
ERK1/2“up-regulates activity”HECTD3phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 149 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
Mitochondrial translation initiation812.1×4e-05
Mitochondrial translation elongation812.1×4e-05
Mitochondrial ribosome-associated quality control811.7×4e-05
Mitochondrial translation711.5×2e-04
Mitochondrial translation termination810.5×7e-05
Translation96.7×5e-04

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation811.1×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance105
Likely benign5
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2812 predictions. Top by Δscore:

VariantEffectΔscore
1:45003575:CA:Cacceptor_gain1.0000
1:45003577:C:CCacceptor_gain1.0000
1:45003664:CCCA:Cdonor_loss1.0000
1:45003666:CAC:Cdonor_loss1.0000
1:45003668:C:Gdonor_loss1.0000
1:45003851:TCA:Tdonor_loss1.0000
1:45003852:CAC:Cdonor_loss1.0000
1:45003853:A:ACdonor_gain1.0000
1:45003853:A:ATdonor_loss1.0000
1:45003853:AC:Adonor_gain1.0000
1:45003853:ACC:Adonor_gain1.0000
1:45003853:ACCC:Adonor_gain1.0000
1:45003854:C:CCdonor_gain1.0000
1:45003854:CC:Cdonor_gain1.0000
1:45003854:CCC:Cdonor_gain1.0000
1:45003854:CCCC:Cdonor_gain1.0000
1:45003854:CCCCA:Cdonor_gain1.0000
1:45003932:GTCCT:Gacceptor_gain1.0000
1:45003935:CT:Cacceptor_gain1.0000
1:45003937:C:CCacceptor_gain1.0000
1:45003938:T:Aacceptor_loss1.0000
1:45004055:CTGA:Cdonor_loss1.0000
1:45004056:TGAC:Tdonor_loss1.0000
1:45004057:GACCG:Gdonor_loss1.0000
1:45004058:A:ACdonor_gain1.0000
1:45004058:A:Cdonor_loss1.0000
1:45004059:C:CCdonor_gain1.0000
1:45004130:CCGGG:Cacceptor_gain1.0000
1:45004131:CGGG:Cacceptor_gain1.0000
1:45004131:CGGGC:Cacceptor_gain1.0000

AlphaMissense

5576 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:45003514:T:AD855V1.000
1:45003515:C:GD855H1.000
1:45003520:T:AD853V1.000
1:45003523:A:TI852N1.000
1:45003531:G:CC849W1.000
1:45003532:C:TC849Y1.000
1:45003533:A:GC849R1.000
1:45003541:G:TA846D1.000
1:45003553:A:GL842P1.000
1:45003701:G:CC823W1.000
1:45003702:C:TC823Y1.000
1:45003703:A:GC823R1.000
1:45003717:G:TP818H1.000
1:45003718:G:AP818S1.000
1:45003903:C:AG794V1.000
1:45003903:C:TG794D1.000
1:45003904:C:GG794R1.000
1:45003909:A:TV792D1.000
1:45003911:A:CF791L1.000
1:45003911:A:TF791L1.000
1:45003912:A:GF791S1.000
1:45003913:A:GF791L1.000
1:45003918:A:GL789P1.000
1:45003930:C:GR785P1.000
1:45004077:A:GL777P1.000
1:45004259:A:GL754P1.000
1:45005859:A:GW624R1.000
1:45005859:A:TW624R1.000
1:45006026:C:AG606W1.000
1:45006026:C:GG606R1.000

dbSNP variants (sampled 300 via entrez): RS1000689718 (1:45010979 G>A), RS1000869341 (1:45007634 A>G), RS1001053303 (1:45012627 T>C), RS1001647308 (1:45012776 G>A), RS1001840437 (1:45013217 T>C), RS1001908940 (1:45011268 C>T), RS1001953903 (1:45011740 C>A,G,T), RS1002303555 (1:45008350 A>G), RS1002331523 (1:45008089 T>C), RS1002685942 (1:45009765 G>A,C), RS1002774560 (1:45002309 C>T), RS1002785985 (1:45003173 G>A,C), RS1003856792 (1:45005561 G>A,C), RS1003918163 (1:45011652 A>T), RS1004430579 (1:45011462 C>G)

Disease associations

OMIM: gene MIM:618638 | 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

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression5
sodium arseniteincreases abundance, increases expression2
aristolochic acid Iincreases expression1
2,4,6-tribromophenolincreases expression1
trichostatin Aaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
pentabrominated diphenyl ether 100decreases expression1
Sunitinibincreases expression1
Air Pollutantsincreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Atrazineincreases expression1
Cadmiumdecreases expression, increases abundance1
Carcinogensdecreases expression1
Coumestroldecreases expression1
Doxorubicindecreases expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinincreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Particulate Matterincreases abundance, increases expression1

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.