DDB2

gene
On this page

Also known as DDBBUV-DDB2FLJ34321XPE

Summary

DDB2 (damage specific DNA binding protein 2, HGNC:2718) is a protein-coding gene on chromosome 11p11.2, encoding DNA damage-binding protein 2 (Q92466). Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively.

This gene encodes a protein that is necessary for the repair of ultraviolet light-damaged DNA. This protein is the smaller subunit of a heterodimeric protein complex that participates in nucleotide excision repair, and this complex mediates the ubiquitylation of histones H3 and H4, which facilitates the cellular response to DNA damage. This subunit appears to be required for DNA binding. Mutations in this gene cause xeroderma pigmentosum complementation group E, a recessive disease that is characterized by an increased sensitivity to UV light and a high predisposition for skin cancer development, in some cases accompanied by neurological abnormalities. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 1643 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): xeroderma pigmentosum group E (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 12
  • Clinical variants (ClinVar): 174 total — 9 pathogenic, 5 likely-pathogenic
  • Phenotypes (HPO): 64
  • Cancer driver (intOGen): activating (oncogene-like) across 2 cancer types
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_000107

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2718
Approved symbolDDB2
Namedamage specific DNA binding protein 2
Location11p11.2
Locus typegene with protein product
StatusApproved
AliasesDDBB, UV-DDB2, FLJ34321, XPE
Ensembl geneENSG00000134574
Ensembl biotypeprotein_coding
OMIM600811
Entrez1643

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 17 protein_coding, 5 retained_intron, 4 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000256996, ENST00000378600, ENST00000378601, ENST00000378603, ENST00000610805, ENST00000612309, ENST00000614394, ENST00000614825, ENST00000614884, ENST00000615695, ENST00000616278, ENST00000617022, ENST00000617847, ENST00000620515, ENST00000622090, ENST00000622878, ENST00000896514, ENST00000896515, ENST00000896516, ENST00000915750, ENST00000915751, ENST00000915752, ENST00000915753, ENST00000967663, ENST00000967664, ENST00000967665, ENST00000967666

RefSeq mRNA: 6 — MANE Select: NM_000107 NM_000107, NM_001300734, NM_001399874, NM_001399875, NM_001399876, NM_001399878

CCDS: CCDS73284, CCDS7927, CCDS91469

Canonical transcript exons

ENST00000256996 — 10 exons

ExonStartEnd
ENSE000008392384723457347234672
ENSE000008392394723475747234934
ENSE000009891014723281447232959
ENSE000010980024721497447215263
ENSE000010980054721633647216472
ENSE000011809444721685847217049
ENSE000034851544723527047235412
ENSE000035708994723880047239217
ENSE000036495464723783747238001
ENSE000036751334723813847238183

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 96.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.3030 / max 291.9871, expressed in 1809 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
11416717.26361697
11416614.65981787
1141651.8025973
1141680.4617194
1141690.080122
1141700.035311

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skin of abdomenUBERON:000141696.65gold quality
skin of legUBERON:000151196.60gold quality
right uterine tubeUBERON:000130296.44gold quality
right adrenal gland cortexUBERON:003582796.13gold quality
right adrenal glandUBERON:000123395.48gold quality
descending thoracic aortaUBERON:000234595.12gold quality
olfactory segment of nasal mucosaUBERON:000538694.98gold quality
zone of skinUBERON:000001494.74gold quality
granulocyteCL:000009494.61gold quality
left adrenal glandUBERON:000123494.52gold quality
ascending aortaUBERON:000149694.49gold quality
thoracic aortaUBERON:000151594.44gold quality
left adrenal gland cortexUBERON:003582594.31gold quality
tibial nerveUBERON:000132393.72gold quality
esophagus mucosaUBERON:000246993.71gold quality
endometrium epitheliumUBERON:000481193.64gold quality
vaginaUBERON:000099693.57gold quality
minor salivary glandUBERON:000183093.52gold quality
muscle layer of sigmoid colonUBERON:003580593.38gold quality
lower esophagus mucosaUBERON:003583493.35gold quality
ectocervixUBERON:001224993.20gold quality
apex of heartUBERON:000209893.17gold quality
body of pancreasUBERON:000115093.16gold quality
body of uterusUBERON:000985392.96gold quality
esophagusUBERON:000104392.94gold quality
right lobe of liverUBERON:000111492.75gold quality
adrenal glandUBERON:000236992.71gold quality
aortaUBERON:000094792.62gold quality
endocervixUBERON:000045892.55gold quality
rectumUBERON:000105292.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.66

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
BCL2Repression
SOD2Repression
XPAUnknown

Upstream regulators (CollecTRI, top): BRCA1, E2F1, E2F3, NF1, SP1, TP53, TP63

miRNA regulators (miRDB)

16 targeting DDB2, 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-4673100.0066.641490
HSA-MIR-480399.9871.993117
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-478499.1567.411733
HSA-MIR-128699.0966.231046
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-218-1-3P98.6367.97832
HSA-MIR-6728-3P98.6367.631534
HSA-MIR-3187-3P97.3865.80904
HSA-MIR-129196.2865.891224
HSA-MIR-6813-3P95.7863.78540
HSA-MIR-6775-3P95.7665.91982
HSA-MIR-6851-3P95.7365.11688
HSA-MIR-328-3P92.8264.37521

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • These results indicate that DDB2 is a modulator of UV-induced apoptosis, and that UV resistance can be overcome by inhibition of DDB2 (PMID:11852074)
  • These results demonstrate direct activation of the human DDB2 gene by p53. The corresponding region in the mouse DDB2 gene shared significant sequence identity with the human gene but was deficient for p53 binding and transcriptional activation. (PMID:11971958)
  • Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation (PMID:12034848)
  • findings substantiate the physical and functional connection between the hepatitis B virus X protein and the DDB1-DDB2 heterodimer, leading to the regulation of the pool of the viral protein (PMID:12050362)
  • These findings indicate that hepatitis B virus X protein acts through a pathway that involves a DDB2-independent nuclear function of DDB1 and that this activity will depend on the relative concentration of DDB1 and DDB2 in cells. (PMID:12151405)
  • BRCA1 upregulates DDB2, with some evidence that p53 is involved in its regulation. (PMID:12496474)
  • overexpression of DDB2 in V79 cell potentiates DNA repair and protects cells from UV-induced apoptosis and cytotoxicity. (PMID:12553360)
  • DDB2 and CSA are each integrated into nearly identical complexes via interaction with DDB1 (PMID:12732143)
  • DDB2p48 activates the recruitment of XPC to cyclobutane pyrimidine dimers and may be the initial recognition factor in the nucleotide excision repair pathway (PMID:12944386)
  • Data suggest that both before and after UV irradiation, DDB2 directly regulates p53 levels, while DDB2 expression is itself regulated by p53. (PMID:14560002)
  • identification of four DDB2 variants from HeLa cells (D1-D4) that are generated by alternative splicing (PMID:14751237)
  • DDB2 regulates TNF signaling-mediated apoptosis via cFLIP and contributes to acquired cross-resistance. (PMID:15644494)
  • UV-DDB interacts with XPC physically, and both are polyubiquitylated by the UV-DDB-ubiquitin ligase complex. (PMID:15882621)
  • DDB1-DDB2 protein complex recognizes DNA mismatches and lesions (PMID:16223728)
  • DDB2 has an intrinsic damaged DNA binding activity (PMID:16260596)
  • Monoubiquitinated histone H2A in native chromatin coimmunoprecipitates with the endogenous DDB1-CUL4A(DDB2) complex in response to UV irradiation. (PMID:16473935)
  • CUL-4A mediates the proteolytic degradation of DDB2 and this degradation event, initiated at the lesion sites, regulates damage recognition by XPC. (PMID:16527807)
  • DDB2 can bind to damaged DNA in vivo as a monomer, whereas Cul4A recruitment to damage sites depends on the fully assembled complex. (PMID:16951172)
  • Results suggest that the roles of p53 and nucleotide excision repair in the recovery from UV-induced replication are separable and DDB2-independent. (PMID:17630510)
  • A nonsense mutation 574CT (R192X) in DDB2 was found in association facial neoplasms in a form of xeroderma pigmentosum.The parents were heterozygous & the patient homozygous. (PMID:17660462)
  • provide genetic evidence linking the regulation of p21(Waf1/Cip1) to the nucleotide excision repair activity of DDB2 (PMID:17967871)
  • p53 determines the switch by regulating ddb2 and DNA double-strand breaks in antineoplastic agent treatment of glioblastoma multiforme. (PMID:18089819)
  • These findings demonstrate for the first time that DDB2 can play a role as oncogene and may become a promising candidate as a predictive marker in breast cancer. (PMID:18431487)
  • DDB1-CUL4B(DDB2) E3 ligase may have a distinctive function in modifying the chromatin structure at the site of UV lesions to promote efficient NER. (PMID:18593899)
  • p38 MAPK regulates chromatin remodeling as well as DDB2 degradation for facilitating NER factor assembly (PMID:18806262)
  • Results suggest a model in which UV-dependent degradation of DDB2 is important for the release of DDB1 from continuous association to unrepaired DNA and makes DDB1 available for its other DNA damage response functions. (PMID:18936169)
  • The structure DDB1-DDB2 complex shows the tightly localized probing of the photolesions, combined with proofreading in the photodimer pocket, enables DDB2 to detect lesions refractory to detection by other damage surveillance proteins. (PMID:19109893)
  • DDB2 exerts, at least in part, a control of breast cancer cell growth through its negative regulation of constitutive expression of the SOD2 gene. (PMID:19339246)
  • p53 is primarily protective against ultraviolet rays-induced apoptosis in primary human fibroblasts and this activity of p53 does not require DDB2. (PMID:19428372)
  • Results provide evidence for a new regulatory loop involving the NER protein DDB2, Mdm2, and p21(Waf1/Cip1) that is critical in deciding cell fate (apoptosis or arrest) upon DNA damage. (PMID:19541625)
  • Overexpression of DDB2 enhances the sensitivity of ovarian cancer cells to cisplatin by augmenting cellular apoptosis. (PMID:20013802)
  • Data show that XPC and Ku oppositely regulate the ubiquitin ligase activity of DDB2, and that DDB2 complex-mediated ubiquitylation plays a role in recruiting XPA to damaged sites. (PMID:20368362)
  • Damaged DNA-binding protein 2 (DDB2) protects against UV irradiation in human cells and Drosophila (PMID:20398405)
  • Multiple skin cancers in adults are associted with mutations in the XP-E (DDB2) DNA repair gene. (PMID:21107348)
  • Nucleotide excision repair proteins rapidly accumulate but fail to persist in human xeroderma pigmentosum XP-E (DDB2 mutant) cells. (PMID:21388382)
  • Studies indicate the modular architecture of DDB1-CUL4 in complex with DDB2, CSA and CDT2 in DNA repair of UV-induced DNA lesions. (PMID:21550341)
  • DDB2 subunit of UV-DDB associates transiently with the DNA-binding domain of XPC to fine-tune its engagement with CPD lesions (PMID:22039351)
  • study reports a new function of DDB2 in modulating chromatin structure at DNA lesions (PMID:22492724)
  • Findings indicate structural and conformational insights of the DDB1-CUL4A(DDB2) E3 ligase, with significant implications for the regulation and overall organization of the proteins responsible for initiation of nucleotide-excision repair (NER) pathway. (PMID:22822215)
  • DDB2 can inhibit cell growth rate in AR-expressing cells (LNCaP) but not in AR-null cells (PC3). (PMID:22846800)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioddb2ENSDARG00000041140
mus_musculusDdb2ENSMUSG00000002109
rattus_norvegicusDdb2ENSRNOG00000014071

Protein

Protein identifiers

DNA damage-binding protein 2Q92466 (reviewed: Q92466)

Alternative names: DDB p48 subunit, Damage-specific DNA-binding protein 2, UV-damaged DNA-binding protein 2

All UniProt accessions (6): A0A087WTQ7, A0A087WV56, A0A087WW71, A0A087WYT8, Q92466, A0A087X0X5

UniProt curated annotations — full annotation on UniProt →

Function. Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively. Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also functions as the substrate recognition module for the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB2-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB2-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. The DDB2-CUL4-ROC1 complex also ubiquitinates KAT7/HBO1 in response to DNA damage, leading to its degradation: recognizes KAT7/HBO1 following phosphorylation by ATR. Inhibits UV-damaged DNA repair. Inhibits UV-damaged DNA repair.

Subunit / interactions. Component of the UV-DDB complex which includes DDB1 and DDB2. The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1), which includes CUL4A or CUL4B, DDB1, DDB2 and RBX1. DDB2 may function as the substrate recognition module within this complex. The DDB1-CUL4-ROC1 complex may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. A large number of other DCX complexes may also exist in which an alternate substrate targeting subunit replaces DDB2. These targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Isoform D1 and isoform D2 do not interact with DDB1.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Ubiquitously expressed; with highest levels in corneal endothelium and lowest levels in brain. Isoform D1 is highly expressed in brain and heart. Isoform D2, isoform D3 and isoform D4 are weakly expressed.

Post-translational modifications. Phosphorylation by ABL1 negatively regulate UV-DDB activity. Ubiquitinated by CUL4A in response to UV irradiation. Ubiquitination appears to both impair DNA-binding and promotes ubiquitin-dependent proteolysis. Degradation of DDB2 at sites of DNA damage may be a prerequisite for their recognition by XPC and subsequent repair. CUL4A-mediated degradation appears to be promoted by ABL1. Ubiquitinated, leading to proteasomal degradation, and deubiquitinated by USP24. Deubiquitinated by USP44; leading to its stabilization on DNA lesions. Acetylated. Deacetylation by SIRT6 in response to UV stress facilitates nucleotide excision repair pathway (the NER pathway) transduction.

Disease relevance. Xeroderma pigmentosum complementation group E (XP-E) [MIM:278740] An autosomal recessive pigmentary skin disorder characterized by solar hypersensitivity of the skin, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities. The skin develops marked freckling and other pigmentation abnormalities. XP-E patients show a mild phenotype with minimal or no neurologic features. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The DWD box is required for interaction with DDB1. Interblade loops of the WD repeat region mediate most of the interaction with DNA. A hairpin between blades 5 and 6 inserts into DNA minor groove and mediates recognition of lesions and separation of the damaged and undamaged strands.

Induction. Expression is induced in response to treatment with IR or UV and this requires p53/TP53 activity.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the WD repeat DDB2/WDR76 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q92466-11yes
Q92466-2D1
Q92466-3D2
Q92466-4D3
Q92466-5D4

RefSeq proteins (6): NP_000098, NP_001287663, NP_001386803, NP_001386804, NP_001386805, NP_001386807 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR033312DDB2Family
IPR036322WD40_repeat_dom_sfHomologous_superfamily

Pfam: PF00400

UniProt features (91 total): strand 37, mutagenesis site 11, turn 10, repeat 7, splice variant 6, helix 5, region of interest 4, modified residue 4, sequence variant 4, chain 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
3I7LX-RAY DIFFRACTION2.8
4E54X-RAY DIFFRACTION2.85
4E5ZX-RAY DIFFRACTION3.22
3EI4X-RAY DIFFRACTION3.3
9J8WELECTRON MICROSCOPY3.38
6R8ZELECTRON MICROSCOPY3.9
6R91ELECTRON MICROSCOPY4.1
6R8YELECTRON MICROSCOPY4.3
6R90ELECTRON MICROSCOPY4.5
6R92ELECTRON MICROSCOPY4.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92466-F183.690.70

Functional residue map

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

Post-translational modifications (4): 24, 26, 35, 77

Mutagenesis-validated functional residues (11):

PositionPhenotype
35decreased acetylation levels.
40does not affect acetylation levels.
77decreased acetylation levels.
258impairs interaction with ddb1.
262impairs interaction with ddb1.
264impairs interaction with ddb1.
269impairs interaction with ddb1.
270impairs interaction with ddb1.
272impairs interaction with ddb1.
273impairs interaction with ddb1.
350impairs interaction with ddb1.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-5689880Ub-specific processing proteases
R-HSA-5696394DNA Damage Recognition in GG-NER
R-HSA-5696395Formation of Incision Complex in GG-NER
R-HSA-5696400Dual Incision in GG-NER
R-HSA-6796648TP53 Regulates Transcription of DNA Repair Genes
R-HSA-8951664Neddylation

MSigDB gene sets: 392 (showing top): REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER, E2F_Q4, E2F_Q4_01, LEE_NEURAL_CREST_STEM_CELL_DN, KANG_FLUOROURACIL_RESISTANCE_UP, MORF_RAB5A, GOBP_CELLULAR_RESPONSE_TO_UV, BASSO_B_LYMPHOCYTE_NETWORK, GOBP_CELLULAR_RESPONSE_TO_LIGHT_STIMULUS, ROVERSI_GLIOMA_COPY_NUMBER_UP, KAUFFMANN_DNA_REPAIR_GENES, GOBP_NUCLEOTIDE_EXCISION_REPAIR, E2F_Q3, CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN

GO Biological Process (10): protein polyubiquitination (GO:0000209), DNA repair (GO:0006281), nucleotide-excision repair (GO:0006289), pyrimidine dimer repair (GO:0006290), DNA damage response (GO:0006974), response to UV (GO:0009411), cellular response to UV (GO:0034644), protein autoubiquitination (GO:0051865), UV-damage excision repair (GO:0070914), protein ubiquitination (GO:0016567)

GO Molecular Function (5): DNA binding (GO:0003677), damaged DNA binding (GO:0003684), protein-containing complex binding (GO:0044877), ubiquitin-protein transferase activity (GO:0004842), protein binding (GO:0005515)

GO Cellular Component (10): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cell junction (GO:0030054), Cul4A-RING E3 ubiquitin ligase complex (GO:0031464), Cul4B-RING E3 ubiquitin ligase complex (GO:0031465), protein-containing complex (GO:0032991), Cul4-RING E3 ubiquitin ligase complex (GO:0080008), site of DNA damage (GO:0090734), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Global Genome Nucleotide Excision Repair (GG-NER)3
Deubiquitination1
Transcriptional Regulation by TP531
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
DNA repair3
protein ubiquitination2
binding2
chromosome2
Cul4-RING E3 ubiquitin ligase complex2
DNA metabolic process1
DNA damage response1
cellular response to stress1
response to light stimulus1
response to UV1
cellular response to light stimulus1
cellular response to UV1
protein modification by small protein conjugation1
nucleic acid binding1
DNA binding1
ubiquitin-like protein transferase activity1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular_component1
cullin-RING ubiquitin ligase complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1960 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DDB2DDB1Q16531999
DDB2CUL4AQ13619998
DDB2RBX1P62877996
DDB2XPAP23025972
DDB2RAD23BP54727857
DDB2CUL4BQ13620846
DDB2ERCC2P18074831
DDB2CETN2P41208830
DDB2DET1Q7L5Y6829
DDB2USP24Q9UPU5820
DDB2SMARCA4P51532806
DDB2XPCQ01831797
DDB2ERCC3P19447751
DDB2TP53P04637745
DDB2DTLQ9NZJ0745

IntAct

153 interactions, top by confidence:

ABTypeScore
DDB2DDB1psi-mi:“MI:0915”(physical association)0.970
DDB1DDB2psi-mi:“MI:0407”(direct interaction)0.970
DDB1DDB2psi-mi:“MI:0915”(physical association)0.970
DDB2DDB1psi-mi:“MI:0407”(direct interaction)0.970
CUL4BDDB1psi-mi:“MI:0914”(association)0.940
DDB1CUL4Apsi-mi:“MI:0914”(association)0.920
COPS5COPS2psi-mi:“MI:0914”(association)0.910
CUL4ADDB2psi-mi:“MI:0915”(physical association)0.900
DDB2CUL4Apsi-mi:“MI:0914”(association)0.900
COPS2GPS1psi-mi:“MI:0914”(association)0.860
COPS8COPS2psi-mi:“MI:0914”(association)0.850
CUL4BCOPS2psi-mi:“MI:0914”(association)0.790
CUL4BCUL4Apsi-mi:“MI:0914”(association)0.730
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730

BioGRID (515): DDB1 (Affinity Capture-Western), CUL4A (Affinity Capture-Western), CUL4B (Affinity Capture-Western), DDB2 (Biochemical Activity), CUL4A (Biochemical Activity), DDB2 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), PFDN4 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), CUL4B (Affinity Capture-MS), CUL4A (Affinity Capture-MS), DDB1 (Affinity Capture-MS)

ESM2 similar proteins: A2AKB9, A2RRH5, A2RUS2, O43379, O60336, P58742, Q08BB3, Q0VBY8, Q148I1, Q15334, Q3MHH0, Q3SZD4, Q3U3T8, Q499N3, Q4R3J7, Q4VBE8, Q5FW06, Q5QP82, Q5RCX2, Q5T6F0, Q5U4D9, Q5U4F6, Q5VW00, Q5ZJL7, Q63ZP7, Q6AX81, Q6AY87, Q6NS57, Q6NWH1, Q6P1M3, Q6P809, Q7Z5U6, Q80Y17, Q86W42, Q8AVS9, Q8BGW4, Q8BGZ3, Q8C5V5, Q8HXL3, Q8K4K5

Diamond homologs: A1CF18, A1CQI9, A2AKB9, A5DL92, A5DST9, A8IR43, A8X8C6, A9V790, B0XM00, B2VZH2, B6GZD3, B6QC06, B8N9H4, C5PFX0, D5GBI7, F1DLK1, F4IIK6, O42860, O74184, P0CS44, P0CS45, P38959, P41318, Q0CLJ4, Q0D0X6, Q0VBY8, Q17QU5, Q28I90, Q29HG9, Q2UGK1, Q2UGU1, Q2YDS1, Q499N3, Q4VBE8, Q4WLM7, Q54D08, Q5APF0, Q5FW06, Q5I0B4, Q5QP82

SIGNOR signaling

5 interactions.

AEffectBMechanism
PCSK7down-regulatesDDB2
USP24up-regulatesDDB2deubiquitination
DDB2“form complex”DDB2/DDB1binding
DDB2up-regulatesE2F1binding
ABL1down-regulatesDDB2phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 114 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
DNA Damage Recognition in GG-NER1453.3×9e-19
Prefoldin mediated transfer of substrate to CCT/TriC736.8×8e-08
Formation of TC-NER Pre-Incision Complex1336.7×2e-15
RHOBTB1 GTPase cycle531.7×3e-05
Formation of tubulin folding intermediates by CCT/TriC528.2×5e-05
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding527.2×5e-05
Recognition of DNA damage by PCNA-containing replication complex525.4×7e-05
Formation of Incision Complex in GG-NER723.7×1e-06

GO biological processes:

GO termPartnersFoldFDR
regulation of protein neddylation872.0×1e-11
protein neddylation960.8×4e-12
positive regulation of telomere maintenance via telomerase535.2×3e-05
intrinsic apoptotic signaling pathway517.2×6e-04
cellular response to UV617.1×1e-04
protein folding98.9×6e-05
ubiquitin-dependent protein catabolic process85.7×4e-03
protein ubiquitination145.6×3e-05

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 2 cancer types — AML, BLCA.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic9
Likely pathogenic5
Uncertain significance72
Likely benign39
Benign26

Top pathogenic / likely-pathogenic (14)

Variant IDHGVSClassification
1319564NM_000107.3(DDB2):c.574C>T (p.Arg192Ter)Pathogenic
1333388NM_000107.3(DDB2):c.1187C>A (p.Ser396Ter)Pathogenic
2062799NM_000107.3(DDB2):c.640C>T (p.Arg214Ter)Pathogenic
3067698NM_000107.3(DDB2):c.702+1G>TPathogenic
3366825NC_000011.9:g.(47238024_47238408)_(47254511_47256123)delPathogenic
3711370NM_000107.3(DDB2):c.1063C>T (p.Arg355Ter)Pathogenic
8787NM_000107.3(DDB2):c.730A>G (p.Lys244Glu)Pathogenic
8789NM_000107.3(DDB2):c.937C>T (p.Arg313Ter)Pathogenic
8790NM_000107.3(DDB2):c.919G>T (p.Asp307Tyr)Pathogenic
2431840NM_000107.3(DDB2):c.85dup (p.Glu29fs)Likely pathogenic
2576188NM_000107.3(DDB2):c.456+2T>CLikely pathogenic
3599767NM_000107.3(DDB2):c.970dup (p.Leu324fs)Likely pathogenic
4081306NM_000107.3(DDB2):c.880+1G>TLikely pathogenic
872377NM_000107.3(DDB2):c.457-2A>CLikely pathogenic

SpliceAI

1677 predictions. Top by Δscore:

VariantEffectΔscore
11:47215241:G:GTdonor_gain1.0000
11:47215244:GCTCT:Gdonor_gain1.0000
11:47215245:C:Gdonor_gain1.0000
11:47232960:G:GGdonor_gain1.0000
11:47234570:CA:Cacceptor_loss1.0000
11:47234571:A:AGacceptor_gain1.0000
11:47234572:G:GGacceptor_gain1.0000
11:47234572:G:GTacceptor_loss1.0000
11:47234572:GC:Gacceptor_gain1.0000
11:47234572:GCA:Gacceptor_gain1.0000
11:47234572:GCAT:Gacceptor_gain1.0000
11:47234572:GCATC:Gacceptor_gain1.0000
11:47234670:GAG:Gdonor_gain1.0000
11:47234673:G:GGdonor_gain1.0000
11:47234673:G:Tdonor_loss1.0000
11:47235269:GCTT:Gacceptor_gain1.0000
11:47235409:CAAGG:Cdonor_loss1.0000
11:47235410:AAGGT:Adonor_loss1.0000
11:47235412:GGTG:Gdonor_loss1.0000
11:47235413:G:GAdonor_loss1.0000
11:47235414:T:Adonor_loss1.0000
11:47237814:T:TAacceptor_gain1.0000
11:47237835:A:AGacceptor_gain1.0000
11:47237836:G:GGacceptor_gain1.0000
11:47237836:GGCA:Gacceptor_gain1.0000
11:47237953:G:Tdonor_gain1.0000
11:47237997:GTTCG:Gdonor_gain1.0000
11:47237998:T:Gdonor_gain1.0000
11:47238007:GCT:Gdonor_gain1.0000
11:47215257:GGC:Gdonor_gain0.9900

AlphaMissense

2817 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:47237843:T:AW344R0.997
11:47237843:T:CW344R0.997
11:47237877:G:CR355P0.997
11:47216948:T:AW119R0.996
11:47216948:T:CW119R0.996
11:47234862:T:AW270R0.996
11:47234862:T:CW270R0.996
11:47234926:T:AV291D0.996
11:47235327:G:CR313P0.995
11:47216988:A:TK132I0.994
11:47234838:T:CS262P0.994
11:47234839:C:TS262F0.994
11:47216984:T:CS131P0.993
11:47235389:T:CF334L0.993
11:47235391:C:AF334L0.993
11:47235391:C:GF334L0.993
11:47216976:C:AA128D0.992
11:47234638:G:TG223V0.992
11:47234839:C:AS262Y0.992
11:47235300:T:CL304P0.992
11:47216931:G:CR113T0.991
11:47216932:G:CR113S0.991
11:47216932:G:TR113S0.991
11:47216989:A:CK132N0.991
11:47216989:A:TK132N0.991
11:47234836:C:AA261D0.991
11:47238148:T:CF400S0.991
11:47216931:G:TR113M0.990
11:47234833:C:AT260K0.990
11:47234835:G:CA261P0.990

dbSNP variants (sampled 300 via entrez): RS1000400312 (11:47224284 G>C,T), RS1000547724 (11:47231151 A>C), RS1000796690 (11:47230361 C>T), RS1000848691 (11:47224532 G>A,C), RS1001044620 (11:47237149 G>C), RS1001143751 (11:47222951 G>A), RS1001195558 (11:47214174 C>G,T), RS1001226693 (11:47213455 G>A), RS1001343139 (11:47224897 T>G), RS1001467664 (11:47227734 A>G), RS1001498614 (11:47227407 A>G), RS1001513565 (11:47216036 G>GTTC), RS1001671776 (11:47220692 T>C), RS1001804565 (11:47226126 A>G), RS1001957754 (11:47221685 T>C)

Disease associations

OMIM: gene MIM:600811 | disease phenotypes: MIM:278740, MIM:278700, MIM:167000

GenCC curated gene-disease

DiseaseClassificationInheritance
xeroderma pigmentosum group EDefinitiveAutosomal recessive
xeroderma pigmentosumSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
xeroderma pigmentosum group EDefinitiveAR

Mondo (3): xeroderma pigmentosum group E (MONDO:0010213), xeroderma pigmentosum (MONDO:0019600), ovarian cancer (MONDO:0008170)

Orphanet (3): Xeroderma pigmentosum (Orphanet:910), Rare ovarian cancer (Orphanet:213500), OBSOLETE: Xeroderma pigmentosum complementation group E (Orphanet:276261)

HPO phenotypes

64 total (30 of 64 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000135Hypogonadism
HP:0000164Abnormality of the dentition
HP:0000252Microcephaly
HP:0000365Hearing impairment
HP:0000407Sensorineural hearing impairment
HP:0000486Strabismus
HP:0000491Keratitis
HP:0000498Blepharitis
HP:0000509Conjunctivitis
HP:0000518Cataract
HP:0000524Conjunctival telangiectasia
HP:0000613Photophobia
HP:0000621Entropion
HP:0000648Optic atrophy
HP:0000656Ectropion
HP:0000958Dry skin
HP:0000962Hyperkeratosis
HP:0000963Thin skin
HP:0000992Cutaneous photosensitivity
HP:0000995Melanocytic nevus
HP:0001009Telangiectasia
HP:0001029Poikiloderma
HP:0001034Hypermelanotic macule
HP:0001053Hypopigmented skin patches
HP:0001059Pterygium
HP:0001072Thickened skin
HP:0001249Intellectual disability
HP:0001250Seizure

GWAS associations

12 associations (top):

StudyTraitp-value
GCST002329_2Acne (severe)4.000000e-09
GCST004521_165Autism spectrum disorder or schizophrenia3.000000e-08
GCST005232_56Neuroticism1.000000e-16
GCST006940_125Neurociticism4.000000e-10
GCST006942_9Feeling lonely2.000000e-09
GCST006943_11Feeling miserable6.000000e-10
GCST007825_4Alzheimer’s disease or fasting glucose levels (pleiotropy)3.000000e-16
GCST010002_238Refractive error2.000000e-14
GCST010244_64Triglyceride levels2.000000e-31
GCST011348_26High density lipoprotein cholesterol levels1.000000e-08
GCST90002389_462Lymphocyte percentage of white cells2.000000e-13
GCST90002394_465Monocyte percentage of white cells2.000000e-19

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement
EFO:0007865loneliness measurement
EFO:0009598feeling miserable measurement
EFO:0004530triglyceride measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007993lymphocyte percentage of leukocytes
EFO:0007989monocyte percentage of leukocytes

MeSH disease descriptors (3)

DescriptorNameTree numbers
D010051Ovarian NeoplasmsC04.588.322.455; C12.050.351.500.056.630.705; C12.050.351.937.418.685; C12.100.250.056.630.705; C12.900.418.685; C19.344.410; C19.391.630.705
D014983Xeroderma PigmentosumC04.834.867; C16.131.831.936; C16.320.850.970; C17.800.600.925; C17.800.621.936; C17.800.804.936; C17.800.827.970; C18.452.284.975
C564732Xeroderma Pigmentosum, Complementation Group E (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects expression, affects cotreatment, increases expression12
sodium arseniteincreases abundance, affects expression, affects cotreatment, decreases expression10
Cisplatinaffects expression, increases expression, affects cotreatment, decreases expression7
Aflatoxin B1affects expression, affects cotreatment, increases expression7
Cadmium Chloridedecreases expression, increases expression6
Arsenicaffects methylation, decreases expression, affects cotreatment, increases abundance4
Fluorouracilaffects response to substance, increases expression, increases reaction4
Tobacco Smoke Pollutionaffects expression, decreases expression, increases expression4
Valproic Acidaffects expression, decreases expression4
Cyclosporinedecreases expression, increases expression4
Resveratrolaffects cotreatment, increases expression3
bisphenol Aaffects expression, decreases expression2
trichostatin Aaffects cotreatment, decreases expression2
dibenzo(a,l)pyreneincreases expression2
pifithrindecreases reaction, increases expression2
monomethylarsonous aciddecreases expression2
Estradioldecreases expression, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression2
Particulate Matterdecreases expression, increases abundance2
aristolochic acid Iincreases expression1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amineincreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
pradimicin-IRDdecreases expression, affects expression, affects response to substance1
benzo(b)fluorantheneaffects cotreatment, increases expression1
deoxynivalenolincreases expression1
VX-agentincreases expression1
Nonidet P-40decreases expression1
decabromobiphenyl etherdecreases expression1
tris(2-butoxyethyl) phosphateaffects expression1

Cellosaurus cell lines

20 cell lines: 11 finite cell line, 5 cancer cell line, 3 transformed cell line, 1 telomerase immortalized cell line

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

CellosaurusNameCategorySex
CVCL_7327GM01646Transformed cell lineFemale
CVCL_B1PVAbcam HeLa DDB2 KOCancer cell lineFemale
CVCL_B8EKAbcam HCT 116 DDB2 KOCancer cell lineMale
CVCL_B8UNAbcam MCF-7 DDB2 KOCancer cell lineFemale
CVCL_B9GTAbcam A-549 DDB2 KOCancer cell lineMale
CVCL_F028GM01389Finite cell lineFemale
CVCL_F496XP2ROFinite cell lineFemale
CVCL_F497XP3RO LCLTransformed cell lineFemale
CVCL_KT50HeLa SilenciX DDB2Cancer cell lineFemale
CVCL_M225CW3-XPETransformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00190697PHASE4COMPLETEDA Study of LY353381 (Arzoxifene) for Patients Who Benefitted From This Drug in Other Oncology Trials and Wished to Continue Treatment
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00727961PHASE4COMPLETEDA Study to Evaluate Efficacy and Tolerance of Caelyx in Patients With Epithelial Ovarian Cancer. (Study P04072)(COMPLETED)
NCT00740116PHASE4COMPLETEDTranexamic Acid in Surgery of Advanced Ovarian Cancer
NCT00817479PHASE4COMPLETEDTumor Gene Expression in Women With Ovarian Cancer
NCT01432015PHASE4COMPLETEDFosaprepitant Versus Aprepitant in the Prevention of Chemotherapy Induced Nausea and Vomiting
NCT01706120PHASE4UNKNOWNStudy of Clinical and Biological Prognostic Factors in Patients With Ovarian Cancer Receiving Carboplatin +Paclitaxel With Bevacizumab
NCT01932125PHASE4COMPLETEDAn Interventional Study of Avastin (Bevacizumab) in Patients With Advanced/Metastatic Epithelial Ovarian Cancer, Fallopian Tube Cancer or Primary Peritoneal Cancer
NCT01953107PHASE4COMPLETEDOral Iron vs. Placebo in Newly Diagnosed Gynecologic Oncology Patients Who Are Surgical Candidates.
NCT02035345PHASE4TERMINATEDSlowed Carboplatin Infusion for Ovarian Cancer Patients Receiving Carboplatin Re-Treatment
NCT02243059PHASE4WITHDRAWNMagnetic Resonance Imaging for Lymph Node Staging in Ovarian Cancer
NCT03164980PHASE4TERMINATEDQoL-Comparison Between Trabectedin/PLD and Pt-based Therapy in Patients With Pt-sensitive Recurrent Ovarian Cancer
NCT03384511PHASE4COMPLETEDThe Use of 18F-ALF-NOTA-PRGD2 PET/CT Scan to Predict the Efficacy and Adverse Events of Apatinib in Malignancies.
NCT03543462PHASE4COMPLETEDDiaphragmatic Resection And Gynecological Ovarian Neoplasm
NCT03752216PHASE4COMPLETEDNIraparib and Quality of LifE is a Longitudinal Study Evaluating in Real Life the Tolerability of Niraparib.
NCT03858166PHASE4TERMINATEDEfficacy and Safety of PEG-rhG-CSF Secondary Prophylaxis vs. Therapeutic Administration in Patients With Ovarian Cancer
NCT04024254PHASE4COMPLETEDA Study of Serum Folate Levels in Patients Treated With Olaparib
NCT04330040PHASE4COMPLETEDProspective Multicentre Phase-IV Clinical Trial of Olaparib in Indian Patients With Ovarian and Metastatic Breast Cancer
NCT04352439PHASE4COMPLETEDAspirin for Prevention of Venous Thromboembolism Among Ovarian Cancer Patients Receiving Neoadjuvant Chemotherapy
NCT05187208PHASE4UNKNOWNPARP Inhibitor Oral Maintenance in Low-Risk Ovarian Cancer
NCT05606692PHASE4RECRUITINGInfluences of Propofol and Sevoflurane Anesthesia in Ovarian Cancer (Anesthetics)
NCT05926336PHASE4RECRUITINGThe Effects of Using Different Anesthetics on the Prognosis of Primary Tumors and Its Mechanism of Action
NCT06412120PHASE4RECRUITINGStudy Evaluating Safety, Tolerability, and Metabolism of Niraparib
NCT06871787PHASE4NOT_YET_RECRUITINGNear-Infrared Fluorescence Imaging With Indocyanine Green to Evaluate Bowel Anastomoses in Gynecologic Oncology Surgery
NCT06887933PHASE4NOT_YET_RECRUITINGA Trial to Evaluate the Safety of Niraparib Tablets in Adult Female Participants With Advanced or Relapsed Epithelial Ovarian Cancer
NCT07469202PHASE4NOT_YET_RECRUITINGCYTALUX Dose Extension Study
NCT00001806PHASE3COMPLETEDMethods in Education for Breast Cancer Genetics
NCT00002477PHASE3UNKNOWNAdjuvant Chemotherapy Compared With Observation in Treating Patients With Resected Early Stage Ovarian Epithelial Cancer
NCT00002568PHASE3COMPLETEDCombination Chemotherapy With or Without Surgery in Treating Patients With Stage III Ovarian Epithelial Cancer
NCT00002641PHASE3COMPLETEDSurgery With or Without Chemotherapy in Treating Patients With Soft Tissue Sarcoma
NCT00002717PHASE3COMPLETEDPaclitaxel and Cisplatin in Treating Patients With Stage III or Stage IV Ovarian Cancer or Primary Peritoneal Cancer
NCT00002764PHASE3COMPLETEDSurgery With or Without Combination Chemotherapy in Treating Patients With Lung Metastases From Soft Tissue Sarcoma
NCT00002819PHASE3TERMINATEDChemotherapy With or Without Peripheral Stem Cell Transplantation in Treating Patients With Persistent Ovarian Epithelial Cancer
NCT00002894PHASE3COMPLETEDPlatinum-based Chemotherapy With or Without Paclitaxel in Treating Patients With Relapsed Ovarian Cancer
NCT00002895PHASE3COMPLETEDEarly Chemotherapy Based on CA 125 Level Alone Compared With Delayed Chemotherapy in Treating Patients With Recurrent Ovarian Epithelial , Fallopian Tube, or Primary Peritoneal Cancer
NCT00003120PHASE3COMPLETEDS9701 Paclitaxel in Treating Patients With Advanced Ovarian, Fallopian Tube, or Primary Peritoneal Cancer in Remission
NCT00003214PHASE3COMPLETEDChemosensitivity Testing to Assign Treatment for Patients With Stage III or Stage IV Ovarian Cancer
NCT00003322PHASE3COMPLETEDCombination Chemotherapy in Treating Patients With Primary Peritoneal or Stage III Epithelial Ovarian Cancer
NCT00003636PHASE3COMPLETEDChemotherapy Plus Surgery in Treating Patients With Stage III or Stage IV Ovarian, Peritoneal, or Fallopian Tube Cancer
NCT00003644PHASE3COMPLETEDCarboplatin Plus Paclitaxel With or Without Continued Low-Dose Paclitaxel in Treating Patients With Early-Stage Ovarian Cancer