RWDD3

gene
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Also known as DKFZP566K023RSUME

Summary

RWDD3 (RWD domain containing 3, HGNC:21393) is a protein-coding gene on chromosome 1p21.3, encoding RWD domain-containing protein 3 (Q9Y3V2). Enhancer of SUMO conjugation.

Involved in negative regulation of NF-kappaB transcription factor activity; positive regulation of hypoxia-inducible factor-1alpha signaling pathway; and positive regulation of protein sumoylation. Predicted to be located in cytoplasm and nucleus.

Source: NCBI Gene 25950 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 36 total
  • MANE Select transcript: NM_015485

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21393
Approved symbolRWDD3
NameRWD domain containing 3
Location1p21.3
Locus typegene with protein product
StatusApproved
AliasesDKFZP566K023, RSUME
Ensembl geneENSG00000122481
Ensembl biotypeprotein_coding
OMIM615875
Entrez25950

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000263893, ENST00000370202, ENST00000460571, ENST00000473397, ENST00000492639, ENST00000495272, ENST00000497058, ENST00000885950, ENST00000885951, ENST00000930351, ENST00000930352, ENST00000930353, ENST00000930354, ENST00000930355

RefSeq mRNA: 5 — MANE Select: NM_015485 NM_001128142, NM_001199682, NM_001278247, NM_001278248, NM_015485

CCDS: CCDS41357, CCDS44177

Canonical transcript exons

ENST00000370202 — 4 exons

ExonStartEnd
ENSE000014520589523421095234315
ENSE000034591379524675695247225
ENSE000036117969524421195244698
ENSE000036621869524654295246657

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 93.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1266 / max 110.7990, expressed in 1800 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
412611.94061789
41252.18601212

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endometriumUBERON:000129593.85gold quality
body of pancreasUBERON:000115093.62gold quality
calcaneal tendonUBERON:000370192.63gold quality
right lobe of liverUBERON:000111492.15gold quality
nucleus accumbensUBERON:000188291.76gold quality
amygdalaUBERON:000187691.71gold quality
putamenUBERON:000187491.45gold quality
olfactory segment of nasal mucosaUBERON:000538691.31gold quality
temporal lobeUBERON:000187191.27gold quality
caudate nucleusUBERON:000187391.05gold quality
corpus callosumUBERON:000233691.01gold quality
adenohypophysisUBERON:000219690.93gold quality
heart left ventricleUBERON:000208490.91gold quality
uterusUBERON:000099590.77gold quality
apex of heartUBERON:000209890.66gold quality
metanephros cortexUBERON:001053390.64gold quality
C1 segment of cervical spinal cordUBERON:000646990.60gold quality
spinal cordUBERON:000224090.55gold quality
Ammon’s hornUBERON:000195490.41gold quality
substantia nigraUBERON:000203890.29gold quality
fundus of stomachUBERON:000116090.26gold quality
Brodmann (1909) area 9UBERON:001354090.26gold quality
heartUBERON:000094890.22gold quality
right adrenal gland cortexUBERON:003582790.20gold quality
pituitary glandUBERON:000000790.16gold quality
mucosa of transverse colonUBERON:000499189.99gold quality
muscle layer of sigmoid colonUBERON:003580589.95gold quality
right lobe of thyroid glandUBERON:000111989.94gold quality
hypothalamusUBERON:000189889.82gold quality
pancreasUBERON:000126489.80gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting RWDD3, 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-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-569699.9872.364487
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-990299.8969.152250
HSA-MIR-391999.8769.452489
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-425599.7267.701541
HSA-MIR-472999.6972.184233
HSA-MIR-447099.6669.351767
HSA-MIR-6516-3P99.6568.571238
HSA-MIR-312899.5067.851258
HSA-MIR-889-3P99.4069.762103
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-4796-5P99.3470.06810
HSA-MIR-570198.9769.541502
HSA-MIR-124-5P98.1167.651095
HSA-MIR-4670-3P97.3768.351378

Literature-anchored findings (GeneRIF, showing 14)

  • RSUME plays a central role in the regulation of sumoylation and, hence, several critical regulatory pathways in mammalian cells [RSUME]. (PMID:17956732)
  • BMP-4 and RSUME may be interesting targets for inhibiting steps involved in pituitary tumorigenesis. (PMID:19407504)
  • RSUME critically regulates HIF-1a and VEGF-A production and thus might play an important role in pituitary tumour neovascularisation (PMID:22009797)
  • this study failed to replicate a GWAS reporting an association between the 2 SNPs rs2296308 in RWDD3 and rs1829 in the intron of TECTA and time to neuropathy in ovarian cancer patients treated with paclitaxel (PMID:22877241)
  • a degree of redundancy of the RSUME variants on the SUMO pathway (PMID:23469069)
  • RSUME interacts with glucocorticoid receptor and increases its SUMOylation and transcriptional activity, pointing to SUMO conjugation as the cause for transcriptional stimulation. (PMID:23508108)
  • RSUME is expressed in VHL tumors and inhibits VHL and regulates its tumor suppressor function. (PMID:25500545)
  • the present report suggest that the association of RWDD3 and TECTA with paclitaxel-induced peripheral neuropathy may have been a false positive signal (PMID:25549536)
  • an important role of RSUME in cancer and inflammation (PMID:26297826)
  • RSUME has a role in tumorigenesis and metastasis of pancreatic neuroendocrine tumors (PMID:27506944)
  • RSUME affects post-transcriptional expression of HIF-1a by regulating VEGF-A secretion and pituitary adenoma cells invasiveness. (PMID:27989771)
  • We found that PTTG overexpression in pituitary tumor cells is explained by its protein stabilization, is regulated by RSUME and accounts for PTTG tumor abundance and pathogenic action. There is no evidence so far that this mechanism operates in normal cells. This finding puts in a central role the protein stabilization-overexpression of proto-oncogenes as major regulators of cellular dysfunction. (PMID:29622689)
  • The results show RSUME involvement in von Hippel-Lindau mutants deregulation that leads to the angiogenic phenotype of renal cell carcinoma tumors. (PMID:30890701)
  • Impact of RSUME Actions on Biomolecular Modifications in Physio-Pathological Processes. (PMID:35528020)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusRwdd3ENSMUSG00000028133
rattus_norvegicusRwdd3ENSRNOG00000029893

Protein

Protein identifiers

RWD domain-containing protein 3Q9Y3V2 (reviewed: Q9Y3V2)

Alternative names: RWD domain-containing sumoylation enhancer

All UniProt accessions (1): Q9Y3V2

UniProt curated annotations — full annotation on UniProt →

Function. Enhancer of SUMO conjugation. Via its interaction with UBE2I/UBC9, increases SUMO conjugation to proteins by promoting the binding of E1 and E2 enzymes, thioester linkage between SUMO and UBE2I/UBC9 and transfer of SUMO to specific target proteins which include HIF1A, PIAS, NFKBIA, NR3C1 and TOP1. Isoform 1 and isoform 2 positively regulate the NF-kappa-B signaling pathway by enhancing the sumoylation of NF-kappa-B inhibitor alpha (NFKBIA), promoting its stabilization which consequently leads to an increased inhibition of NF-kappa-B transcriptional activity. Isoform 1 and isoform 2 negatively regulate the hypoxia-inducible factor-1 alpha (HIF1A) signaling pathway by increasing the sumoylation of HIF1A, promoting its stabilization, transcriptional activity and the expression of its target gene VEGFA during hypoxia. Isoform 2 promotes the sumoylation and transcriptional activity of the glucocorticoid receptor NR3C1 and enhances the interaction of SUMO1 and NR3C1 with UBE2I/UBC9. Has no effect on ubiquitination.

Subunit / interactions. Isoform 1 and isoform 2 interact with UBE2I/UBC9. Isoform 1 shows a greater interaction with NFKBIA and HIF1A as compared to isoform 2. Isoform 2 interacts with NCOA2 and NR3C1.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Isoform 1 and isoform 2 are expressed in glioma tumors (at protein level). Expressed in a wide number of tissues with highest expression in cerebellum, pituitary, heart, kidney, liver, stomach, pancreas, prostate and spleen. Low levels in thalamus, spinal cord, esophagus, thymus, lung and peripheral blood leukocytes. A higher level expression seen in pituitary tumors as compared to the pituitary gland.

Domain organisation. The RWD domain is required for the sumoylation enhancement activity.

Induction. Induced by hypoxia and heat shock.

Isoforms (4)

UniProt IDNamesCanonical?
Q9Y3V2-11yes
Q9Y3V2-22
Q9Y3V2-33
Q9Y3V2-44

RefSeq proteins (5): NP_001121614, NP_001186611, NP_001265176, NP_001265177, NP_056300* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006575RWD_domDomain
IPR016135UBQ-conjugating_enzyme/RWDHomologous_superfamily
IPR038840RWDD3Family

Pfam: PF05773

UniProt features (26 total): helix 5, strand 5, turn 4, splice variant 4, region of interest 2, sequence variant 2, chain 1, domain 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
4Y1LX-RAY DIFFRACTION2.7
2EBKSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y3V2-F182.310.26

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
61–62abolishes enhancement of nfkbia and nr3c1 sumoylation. no effect on nr3c1 transcriptional activity.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-3065678SUMO is transferred from E1 to E2 (UBE2I, UBC9)
R-HSA-2990846SUMOylation
R-HSA-3215018Processing and activation of SUMO
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 126 (showing top): GOBP_REGULATION_OF_PROTEIN_SUMOYLATION, GOBP_PEPTIDYL_LYSINE_MODIFICATION, DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS, GOBP_NEGATIVE_REGULATION_OF_NF_KAPPAB_TRANSCRIPTION_FACTOR_ACTIVITY, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, GOBP_RESPONSE_TO_OXYGEN_LEVELS, GOBP_PROTEIN_SUMOYLATION, GOBP_NEGATIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, SCHLOSSER_SERUM_RESPONSE_DN, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_SUMOYLATION

GO Biological Process (3): obsolete negative regulation of NF-kappaB transcription factor activity (GO:0032088), positive regulation of protein sumoylation (GO:0033235), positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)

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

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Processing and activation of SUMO1
Post-translational protein modification1
SUMOylation1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein sumoylation1
regulation of protein sumoylation1
positive regulation of protein modification by small protein conjugation or removal1
hypoxia-inducible factor-1alpha signaling pathway1
regulation of hypoxia-inducible factor-1alpha signaling pathway1
positive regulation of intracellular signal transduction1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

308 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RWDD3UBE2IP50550829
RWDD3SENP1Q9P0U3542
RWDD3RANBP2P49792503
RWDD3SUMO1P55856446
RWDD3S4R434S4R434445
RWDD3VHLP40337399
RWDD3NUTM2FA1L443398
RWDD3SUMO2P55855391
RWDD3TLCD4Q96MV1369
RWDD3GGHQ92820366
RWDD3HIF1AQ16665364
RWDD3CBX4O00257349
RWDD3SUMO4Q6EEV6348
RWDD3BRD3OSA0A1B0GUI7348
RWDD3PIAS4Q8N2W9325

IntAct

9 interactions, top by confidence:

ABTypeScore
UBE2ISUMO1psi-mi:“MI:0914”(association)0.950
UBE2IRWDD3psi-mi:“MI:0407”(direct interaction)0.610
UBE2IRWDD3psi-mi:“MI:0915”(physical association)0.610
RWDD3UBE2Ipsi-mi:“MI:0403”(colocalization)0.610
UBE2IRWDD3psi-mi:“MI:0403”(colocalization)0.610
RWDD3SUMO1psi-mi:“MI:0407”(direct interaction)0.440
RWDD3NFKBIApsi-mi:“MI:0407”(direct interaction)0.440
RWDD3HIF1Apsi-mi:“MI:0915”(physical association)0.400

BioGRID (15): RWDD3 (Affinity Capture-RNA), RWDD3 (Reconstituted Complex), RWDD3 (Affinity Capture-Western), VHL (Affinity Capture-Western), HIF1A (Affinity Capture-Western), RWDD3 (Reconstituted Complex), RWDD3 (Affinity Capture-MS), RWDD3 (Affinity Capture-MS), RWDD3 (Affinity Capture-Western), RWDD3 (Affinity Capture-MS), RWDD3 (Cross-Linking-MS (XL-MS)), SUMO1 (Affinity Capture-Western), UBE2I (Affinity Capture-Western), NFKBIA (Affinity Capture-Western), HIF1A (Affinity Capture-Western)

ESM2 similar proteins: A0JMU5, A1A5P5, A3KN24, A6QLC7, A9ULH0, B2RXC1, B5DF07, B6DMK2, B6NXD5, O60678, O70467, O75417, P0C7N0, Q08B12, Q14AI0, Q19QT9, Q28ES8, Q2KI89, Q32LH3, Q32NV1, Q32PH0, Q3EBC8, Q4R6P2, Q5E9U4, Q5R629, Q5RDC7, Q5XGG3, Q5ZI89, Q5ZJM3, Q641F8, Q68F70, Q6DHJ1, Q6GMB0, Q6GPP1, Q6NU25, Q6PBV4, Q6PD74, Q7Z392, Q8BP74, Q8BSA9

Diamond homologs: A3KN24, A9ULH0, P0C7N0, Q5RDC7, Q6PBV4, Q8VIL2, Q9Y3V2

SIGNOR signaling

1 interactions.

AEffectBMechanism
RWDD3up-regulatesHIF1Asumoylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance30
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

782 predictions. Top by Δscore:

VariantEffectΔscore
1:95234249:G:GTdonor_gain0.9900
1:95234297:G:GTdonor_gain0.9900
1:95234297:G:Tdonor_gain0.9900
1:95234311:CTCAG:Cdonor_loss0.9900
1:95234313:CAG:Cdonor_loss0.9900
1:95234314:AGGTG:Adonor_loss0.9900
1:95234315:GG:Gdonor_loss0.9900
1:95234316:GT:Gdonor_loss0.9900
1:95234317:T:Adonor_loss0.9900
1:95244717:T:Gdonor_gain0.9900
1:95246744:T:Aacceptor_loss0.9900
1:95246751:TGCA:Tacceptor_loss0.9900
1:95246752:GCA:Gacceptor_loss0.9900
1:95246753:CAG:Cacceptor_loss0.9900
1:95244209:A:AGacceptor_gain0.9700
1:95244210:G:GGacceptor_gain0.9700
1:95244634:G:GTdonor_gain0.9700
1:95246754:A:AGacceptor_gain0.9500
1:95246755:G:GGacceptor_gain0.9500
1:95244710:T:Gdonor_gain0.9400
1:95246740:CTTTT:Cacceptor_loss0.9400
1:95234300:GTGC:Gdonor_gain0.9300
1:95234301:TGCT:Tdonor_gain0.9300
1:95234302:GCTG:Gdonor_gain0.9300
1:95234303:C:CGdonor_gain0.9300
1:95244210:GA:Gacceptor_gain0.9300
1:95243745:G:Tdonor_gain0.9200
1:95241984:T:TAacceptor_gain0.9100
1:95244198:G:Aacceptor_gain0.9100
1:95234294:TGGG:Tdonor_gain0.9000

AlphaMissense

1757 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:95244609:T:AW162R0.987
1:95244609:T:CW162R0.987
1:95246545:T:CY193H0.970
1:95246811:T:CF249L0.970
1:95246813:T:AF249L0.970
1:95246813:T:GF249L0.970
1:95244588:T:CY155H0.968
1:95244640:T:CL172P0.964
1:95244673:T:CL183P0.962
1:95246545:T:GY193D0.962
1:95246546:A:CY193S0.962
1:95246577:T:AD203E0.962
1:95246577:T:GD203E0.962
1:95246766:T:CF234L0.962
1:95246768:T:AF234L0.962
1:95246768:T:GF234L0.962
1:95246606:A:TE213V0.961
1:95246604:A:CK212N0.959
1:95246604:A:TK212N0.959
1:95244569:C:AH148Q0.958
1:95244569:C:GH148Q0.958
1:95244611:G:CW162C0.958
1:95244611:G:TW162C0.958
1:95244575:A:CR150S0.956
1:95244575:A:TR150S0.956
1:95246800:T:CL245S0.954
1:95244634:G:AG170E0.950
1:95244645:T:CF174L0.950
1:95244647:C:AF174L0.950
1:95244647:C:GF174L0.950

dbSNP variants (sampled 300 via entrez): RS1000049754 (1:95240946 G>A), RS1000081823 (1:95241278 G>A), RS1000149480 (1:95234568 C>T), RS1000287364 (1:95240565 C>T), RS1000452458 (1:95246440 A>G), RS1000500931 (1:95234369 G>C,T), RS1000696279 (1:95244644 G>A,C), RS1000770002 (1:95244984 G>C,T), RS1001023436 (1:95239034 A>T), RS1001233522 (1:95240247 C>T), RS1001348796 (1:95233172 G>A), RS1001784331 (1:95234205 G>A,C,T), RS1001816918 (1:95234452 G>A,C), RS1001965101 (1:95239848 A>G), RS1002008000 (1:95234611 C>A)

Disease associations

OMIM: gene MIM:615875 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST001838_4Palmitic acid (16:0) levels3.000000e-11
GCST001840_7Stearic acid (18:0) levels2.000000e-15
GCST002701_35Verbal declarative memory9.000000e-06
GCST002759_11Motion sickness4.000000e-14
GCST004616_110Platelet distribution width4.000000e-09
GCST007327_129Smoking status (ever vs never smokers)3.000000e-09
GCST007576_304Chronotype7.000000e-09
GCST008811_27Alcohol consumption (drinks per week)2.000000e-08
GCST011125_14Caffeine consumption from coffee9.000000e-11
GCST011494_5Daytime nap1.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004874memory performance
EFO:0006805word list delayed recall measurement
EFO:0006928motion sickness
EFO:0007984platelet component distribution width
EFO:0004318smoking behavior
EFO:0008328chronotype measurement
EFO:0006781coffee consumption measurement
EFO:0007828daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolaffects expression, decreases expression2
Cyclosporinedecreases expression2
dicrotophosdecreases expression1
bufotalindecreases expression1
triphenyl phosphateaffects expression1
trichostatin Aaffects expression1
methylparabendecreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
scriptaiddecreases expression1
suberoyl bis-hydroxamic aciddecreases expression1
bisphenol Sincreases expression, affects cotreatment1
SB939 compounddecreases expression1
Sunitinibdecreases expression1
Vorinostatdecreases expression1
Air Pollutantsincreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Camptothecinincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinincreases expression, affects cotreatment1
Methotrexateincreases expression1
Niclosamidedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Aciddecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1
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.