DDI1

gene
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Also known as FLJ36017

Summary

DDI1 (DDI proteasomal shuttling factor 1, HGNC:18961) is a protein-coding gene on chromosome 11q22.3, encoding Protein DDI1 homolog 1 (Q8WTU0). Probable aspartic protease.

Predicted to enable aspartic-type endopeptidase activity. Involved in several processes, including cellular response to hydroxyurea; regulation of DNA stability; and regulation of protein stability.

Source: NCBI Gene 414301 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 79 total
  • MANE Select transcript: NM_001001711

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18961
Approved symbolDDI1
NameDDI proteasomal shuttling factor 1
Location11q22.3
Locus typegene with protein product
StatusApproved
AliasesFLJ36017
Ensembl geneENSG00000170967
Ensembl biotypeprotein_coding
OMIM620870
Entrez414301

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000302259

RefSeq mRNA: 1 — MANE Select: NM_001001711 NM_001001711

CCDS: CCDS31660

Canonical transcript exons

ENST00000302259 — 1 exons

ExonStartEnd
ENSE00001407353104036640104039196

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 99.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1072 / max 118.6354, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1164520.06363
1164510.04363

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001999.13gold quality
left testisUBERON:000453385.43gold quality
right testisUBERON:000453485.14gold quality
testisUBERON:000047383.21gold quality
adult organismUBERON:000702381.52gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047377.52gold quality
tibialis anteriorUBERON:000138569.03silver quality
pancreatic ductal cellCL:000207966.00silver quality
sural nerveUBERON:001548859.60silver quality
deltoidUBERON:000147657.09gold quality
ileal mucosaUBERON:000033157.04silver quality
epithelial cell of pancreasCL:000008355.38gold quality
cardiac muscle of right atriumUBERON:000337954.34gold quality
left ventricle myocardiumUBERON:000656654.23gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
bone marrow cellCL:000209250.82gold quality
myocardiumUBERON:000234950.25gold quality
colonic epitheliumUBERON:000039748.94gold quality
tendon of biceps brachiiUBERON:000818848.54silver quality
quadriceps femorisUBERON:000137747.76gold quality
nasal cavity epitheliumUBERON:000538447.03gold quality
adrenal tissueUBERON:001830346.73gold quality
cerebellar vermisUBERON:000472046.54gold quality
skin of hipUBERON:000155446.43silver quality
calcaneal tendonUBERON:000370146.12silver quality
skeletal muscle tissueUBERON:000113445.51gold quality
vastus lateralisUBERON:000137945.40gold quality
tendonUBERON:000004344.90silver quality
muscle tissueUBERON:000238544.78gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting DDI1, 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-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-223-3P99.9970.141140
HSA-MIR-512-3P99.9767.351049
HSA-MIR-60799.9773.625593
HSA-MIR-570-3P99.9672.414910
HSA-MIR-314399.9371.963104
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-544A99.8468.661965
HSA-MIR-205299.7969.372031
HSA-MIR-1213099.7565.47452
HSA-MIR-808499.7369.571760
HSA-MIR-320299.6667.702737
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-6758-3P99.5767.551078
HSA-MIR-106A-3P99.5367.58995
HSA-MIR-186-3P99.5166.241685
HSA-MIR-4761-5P99.5166.69804
HSA-MIR-391599.4568.491905
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-4735-5P99.4368.491780
HSA-MIR-372-5P99.4169.112299
HSA-MIR-425199.4069.193363
HSA-MIR-431299.3467.30511
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-580-5P99.2870.941776
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-205499.2068.891699
HSA-MIR-3940-5P99.1465.26493

Literature-anchored findings (GeneRIF, showing 1)

  • Using human neuroblastoma SH-SY5Y cells in culture, we also observed that human DDI1 is ubiquitinated by UBE3A, without being targeted for degradation (PMID:29788202)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioddi2ENSDARG00000006477
mus_musculusDdi1ENSMUSG00000047619
rattus_norvegicusDdi1ENSRNOG00000022081
drosophila_melanogasterrngoFBGN0030753
caenorhabditis_elegansWBGENE00015308

Paralogs (4): NRIP2 (ENSG00000053702), UBAC2 (ENSG00000134882), NRIP3 (ENSG00000175352), DDI2 (ENSG00000197312)

Protein

Protein identifiers

Protein DDI1 homolog 1Q8WTU0 (reviewed: Q8WTU0)

All UniProt accessions (1): Q8WTU0

UniProt curated annotations — full annotation on UniProt →

Function. Probable aspartic protease. Seems to act as a proteasomal shuttle which links the proteasome and replication fork proteins like RTF2. Required, with DDI2, for cellular survival following replication stress. Together or redudantly with DDI2, removes RTF2 from stalled forks to allow cell cycle progression after replication stress and maintains genome integrity.

Activity regulation. Inhibited by the proteinase inhibitors amprenavir, indinavir, lopinavir, isovaleryl pepstatin, ritonavir and saquinavir.

Similarity. Belongs to the DDI1 family.

RefSeq proteins (1): NP_001001711* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000626Ubiquitin-like_domDomain
IPR019103Peptidase_aspartic_DDI1-typeDomain
IPR021109Peptidase_aspartic_dom_sfHomologous_superfamily
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR033882DDI1_NDomain
IPR057273Ddi1/2_HDDDomain

Pfam: PF00240, PF09668, PF24669

UniProt features (30 total): strand 9, helix 5, sequence conflict 4, sequence variant 3, region of interest 2, turn 2, compositionally biased region 2, chain 1, domain 1, active site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3S8IX-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WTU0-F178.270.48

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): 260

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, chr11q22, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CELLULAR_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_ACTIVITY, GOMF_ASPARTIC_TYPE_PEPTIDASE_ACTIVITY, GOBP_RESPONSE_TO_HYDROXYUREA, MIR6833_3P, MIR4768_5P, MIR580_5P, MIR7113_5P

GO Biological Process (5): proteasomal protein catabolic process (GO:0010498), regulation of protein stability (GO:0031647), cellular response to hydroxyurea (GO:0072711), regulation of DNA stability (GO:0097752), proteolysis (GO:0006508)

GO Molecular Function (4): aspartic-type endopeptidase activity (GO:0004190), protein binding (GO:0005515), peptidase activity (GO:0008233), hydrolase activity (GO:0016787)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of biological quality2
protein catabolic process1
response to hydroxyurea1
cellular response to nitrogen compound1
protein metabolic process1
endopeptidase activity1
aspartic-type peptidase activity1
binding1
hydrolase activity1
catalytic activity, acting on a protein1
catalytic activity1

Protein interactions and networks

STRING

944 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DDI1ADRM1Q16186815
DDI1PSMD4P55036783
DDI1UBQLN1Q9UMX0783
DDI1UBQLN2Q9UHD9764
DDI1RAD23AP54725654
DDI1NGLY1Q96IV0595
DDI1PSMD2Q13200588
DDI1UBE3AP78355561
DDI1NFE2L1Q14494550
DDI1SPRTNQ9H040536
DDI1PSMD14O00487507
DDI1SEM1Q6ZVN7505
DDI1RTF2Q9BY42496
DDI1RAD23BP54727489
DDI1USP14P54578453

IntAct

93 interactions, top by confidence:

ABTypeScore
DDI1CCL28psi-mi:“MI:0915”(physical association)0.830
CCL28DDI1psi-mi:“MI:0915”(physical association)0.830
CYGBDDI1psi-mi:“MI:0915”(physical association)0.720
KLHL42DDI1psi-mi:“MI:0915”(physical association)0.720
DDI1KLHL42psi-mi:“MI:0915”(physical association)0.720
DDI1CYGBpsi-mi:“MI:0915”(physical association)0.720
SFXN1DDI1psi-mi:“MI:0915”(physical association)0.590
DDI1UBE2Kpsi-mi:“MI:0915”(physical association)0.560
UBE2KDDI1psi-mi:“MI:0915”(physical association)0.560
DDI1MAS1psi-mi:“MI:0915”(physical association)0.560
DDI1DDI1psi-mi:“MI:0915”(physical association)0.560
MAS1DDI1psi-mi:“MI:0915”(physical association)0.560
USP2DDI1psi-mi:“MI:0915”(physical association)0.560
SDSDDI1psi-mi:“MI:0915”(physical association)0.560
TRAF2DDI1psi-mi:“MI:0915”(physical association)0.560
DDI1FAM161Bpsi-mi:“MI:0915”(physical association)0.560
DDI1RPP25psi-mi:“MI:0915”(physical association)0.560

BioGRID (89): DDI1 (Two-hybrid), DDI1 (Two-hybrid), DDI1 (Two-hybrid), DDI1 (Two-hybrid), UBC (Reconstituted Complex), DDI1 (Affinity Capture-MS), DDI1 (Affinity Capture-MS), USP47 (Affinity Capture-MS), NRIP3 (Affinity Capture-MS), RSC1A1 (Affinity Capture-MS), PHC3 (Affinity Capture-MS), DDI1 (Two-hybrid), CCL28 (Two-hybrid), DDI1 (Affinity Capture-MS), NRIP3 (Affinity Capture-MS)

ESM2 similar proteins: A0JPP7, E9Q4Z2, F1N2W9, F1QDI9, O12940, O35815, O60784, O70593, O88746, O88978, O88984, O95453, P54252, P54731, P58797, P69341, Q0VGM9, Q1RMR5, Q28BP9, Q2HJD0, Q2T9Z1, Q32LM2, Q3TDN2, Q5BK32, Q5R752, Q5RC51, Q5RJZ1, Q68FJ8, Q6AZH6, Q6GQ69, Q6H1L8, Q6R005, Q6TH22, Q7ZU92, Q7ZYA7, Q80W98, Q8BJU0, Q8CFK2, Q8UUU2, Q8VD33

Diamond homologs: A0JPP7, A1CDT9, A1DCU5, A2ADY9, I7HUG0, P0CS14, P0CS15, P40087, Q0CJ13, Q0U3Y6, Q10256, Q17569, Q1DNB9, Q1EBV4, Q2H085, Q2T9Z1, Q2USD7, Q497D6, Q4WGS4, Q54JB0, Q5AY89, Q5TDH0, Q6BK42, Q6CFI3, Q6CNS3, Q6FQE9, Q6TH22, Q754R2, Q7S906, Q7ZYA7, Q8WTU0, Q95JI3, Q9DAF3, Q9BQI9, P0C273, P0C275, P0C276, P0CG82, P0CH10, P0CH11

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance71
Likely benign4
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

221 predictions. Top by Δscore:

VariantEffectΔscore
11:104036839:A:ACdonor_gain0.9400
11:104036840:C:CCdonor_gain0.9400
11:104037016:GCCTC:Gacceptor_gain0.9300
11:104037019:T:TGacceptor_gain0.9000
11:104037045:C:CCacceptor_gain0.9000
11:104037960:T:Gacceptor_gain0.8500
11:104036833:CCGT:Cdonor_gain0.8400
11:104036865:G:GCdonor_gain0.8300
11:104036861:CGAGG:Cdonor_gain0.8100
11:104037020:C:Aacceptor_gain0.8100
11:104037044:A:ACacceptor_gain0.8100
11:104036834:CGTG:Cdonor_gain0.7400
11:104036911:T:TAdonor_gain0.7200
11:104037994:C:CTacceptor_gain0.7200
11:104037765:CAGTG:Cdonor_gain0.7100
11:104037959:T:TGacceptor_gain0.7100
11:104037017:CCTC:Cacceptor_gain0.6900
11:104037581:T:TAdonor_gain0.6800
11:104036829:A:ACdonor_gain0.6700
11:104036826:CTGA:Cdonor_gain0.6600
11:104036827:TGAT:Tdonor_gain0.6600
11:104036859:T:Adonor_gain0.6600
11:104037015:GGCCT:Gacceptor_gain0.6600
11:104036775:G:GGdonor_gain0.6400
11:104038271:A:Cacceptor_gain0.6400
11:104036774:A:AGdonor_gain0.6300
11:104036831:C:Tdonor_gain0.6300
11:104036867:C:Tdonor_gain0.6300
11:104037562:A:Cdonor_gain0.6200
11:104038269:CCA:Cacceptor_gain0.6200

AlphaMissense

2592 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:104037598:T:AV259D0.999
11:104037868:T:CL349P0.998
11:104037592:C:AA257D0.996
11:104037602:C:AD260E0.996
11:104037602:C:GD260E0.996
11:104037640:C:AA273D0.996
11:104037691:C:AA290D0.996
11:104037534:T:CF238L0.995
11:104037536:T:AF238L0.995
11:104037536:T:GF238L0.995
11:104037600:G:CD260H0.995
11:104037601:A:CD260A0.995
11:104037601:A:GD260G0.995
11:104037601:A:TD260V0.995
11:104037727:T:AV302D0.995
11:104037817:T:CL332P0.995
11:104037826:T:AL335H0.995
11:104037826:T:CL335P0.995
11:104037840:T:CC340R0.995
11:104037564:T:CC248R0.994
11:104037724:G:CR301P0.994
11:104037813:G:CG331R0.994
11:104037814:G:AG331D0.994
11:104037853:T:CL344S0.994
11:104037868:T:AL349Q0.994
11:104037900:T:CF360L0.994
11:104037902:T:AF360L0.994
11:104037902:T:GF360L0.994
11:104037729:C:GH303D0.993
11:104037868:T:GL349R0.993

dbSNP variants (sampled 300 via entrez): RS1000987835 (11:104037027 G>A), RS1001438638 (11:104036680 C>A,T), RS1002223509 (11:104036466 T>A,C,G), RS1002998066 (11:104034767 C>G,T), RS1003303067 (11:104039431 T>A,C), RS1004933366 (11:104036088 A>G), RS1005601577 (11:104038453 T>A,C), RS1006051597 (11:104034962 T>TA), RS1006173918 (11:104039410 G>GA), RS1006682114 (11:104036216 GA>G), RS1008677639 (11:104035941 A>G), RS1009354209 (11:104038361 C>T), RS1009403637 (11:104038128 C>T), RS1009643869 (11:104036769 C>A), RS1012300769 (11:104036663 A>G)

Disease associations

OMIM: gene MIM:620870 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): premature menopause (MONDO:0001119)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST009391_1168Metabolite levels8.000000e-06
GCST009391_1194Metabolite levels2.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0010460anthranilic acid measurement
EFO:0009765alanine measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008594Menopause, PrematureC12.050.351.500.056.630.250; C12.100.250.056.630.250; G08.686.157.500.500; G08.686.841.249.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases methylation1
CGP 52608affects binding, increases reaction1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00417066PHASE4COMPLETEDFlexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693PHASE4COMPLETEDEvaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616PHASE4COMPLETEDEstrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501PHASE4UNKNOWNEffects of ADSC Therapy in Women With POF
NCT02783937PHASE4COMPLETEDFilgrastim for Premature Ovarian Insufficiency
NCT03535480PHASE4UNKNOWNAutologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00140998PHASE3COMPLETEDEstrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00001951PHASE2COMPLETEDHormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019PHASE2WITHDRAWNEffects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494PHASE2COMPLETEDGnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852PHASE2SUSPENDEDThe Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467PHASE2UNKNOWNPrevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982PHASE2COMPLETEDThe Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT02912104PHASE1COMPLETEDA Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695PHASE1COMPLETEDInovium Ovarian Rejuvenation Trials
NCT04815213PHASE1ACTIVE_NOT_RECRUITINGThe Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367PHASE1COMPLETEDEffects of UCA-PSCs in Women With POF
NCT06132542PHASE1UNKNOWNAutologous ADMSC Transplantation in Patients With POI
NCT00948857PHASE2/PHASE3TERMINATEDDehydroepiandrosterone (DHEA) Treatment and Premature Ovarian Failure (POF)
NCT04031456PHASE2/PHASE3RECRUITINGAutologous PRP Infusion May Restore Ovarian Function and May Promote Folliculogenesis in POI Patients
NCT02043743PHASE1/PHASE2UNKNOWNAutologous Stem Cells Transplantation in Patients With Idiopathic and Drug Induced Premature Ovarian Failure
NCT02062931PHASE1/PHASE2UNKNOWNAutologous Mesenchymal Stem Cells Transplantation In Women With Premature Ovarian Failure
NCT02151890PHASE1/PHASE2COMPLETEDPregnancy After Stem Cell Transplantation in Premature Ovarian Failure
NCT02372474PHASE1/PHASE2COMPLETEDIt is a Real The First Baby Of Autologous Stem Cell Therapy in Premature Ovarian Failure
NCT02603744PHASE1/PHASE2UNKNOWNAutologous Adipose Derived Mesenchymal Stromal Cells Transplantation in Women With Premature Ovarian Failure (POF)
NCT02644447PHASE1/PHASE2COMPLETEDTransplantation of HUC-MSCs With Injectable Collagen Scaffold for POF
NCT03069209PHASE1/PHASE2UNKNOWNAutologous Bone Marrow-Derived Stem Cell Transplantation in Patients With Premature Ovarian Failure (POF)
NCT03985462PHASE1/PHASE2WITHDRAWNVery Small Embryonic-like Stem Cells for Ovary
NCT04009473PHASE1/PHASE2UNKNOWNStem Cell Therapy and Growth Factor Ovarian in Vitro Activation
NCT04071574PHASE1/PHASE2COMPLETEDComparative Study on the Efficacy of Ovarian Stimulation Protocols on the Success Rate of ICSI in Female Infertility
NCT04922398PHASE1/PHASE2UNKNOWNOvarian Injection of PRP (Platelet -Rich Plasma) Vs Normal Saline in Premature Ovarian Insufficiency
NCT05462379PHASE1/PHASE2ACTIVE_NOT_RECRUITINGAutologous Heterotopic Fresh Ovarian Graft in Woman With LACC Eligible for Pelvic Radiotherapy Treatment.
NCT06202547PHASE1/PHASE2UNKNOWNIntra-ovarian Injection of MSC-EVs in Idiopathic Premature Ovarian Failure
NCT01129947EARLY_PHASE1WITHDRAWNThe Use of DHEA in Women With Premature Ovarian Failure
NCT05522634EARLY_PHASE1UNKNOWNA Clinical Study of Chinese Herbal Compound TJAOA101 in the Treatment of Premature Ovarian Insufficiency
NCT07308327EARLY_PHASE1ACTIVE_NOT_RECRUITINGThe Influence of Gut Microbiota on Ovarian Function: A Single-center, Randomized,Double Blind, Parallel-controlled, Exploratory Clinical Trial
NCT00001275Not specifiedCOMPLETEDOvarian Follicle Function in Patients With Primary Ovarian Failure
NCT00001306Not specifiedCOMPLETEDSteroid Therapy in Autoimmune Premature Ovarian Failure
NCT00006156Not specifiedCOMPLETEDFeasibility Study for Development of an Early Test for Ovarian Failure
NCT00119925Not specifiedUNKNOWN‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): premature menopause