DDA1

gene
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Also known as PCIA1MGC2594

Summary

DDA1 (DET1 and DDB1 associated 1, HGNC:28360) is a protein-coding gene on chromosome 19p13.11, encoding DET1- and DDB1-associated protein 1 (Q9BW61). Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It is a selective cancer dependency (DepMap: 21.3% of cell lines).

Involved in protein polyubiquitination. Part of Cul4-RING E3 ubiquitin ligase complex.

Source: NCBI Gene 79016 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 15 total
  • Cancer dependency (DepMap): dependent in 21.3% of screened cell lines
  • MANE Select transcript: NM_024050

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28360
Approved symbolDDA1
NameDET1 and DDB1 associated 1
Location19p13.11
Locus typegene with protein product
StatusApproved
AliasesPCIA1, MGC2594
Ensembl geneENSG00000130311
Ensembl biotypeprotein_coding
Entrez79016

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000359866, ENST00000593466, ENST00000594501, ENST00000596582, ENST00000596925, ENST00000858242, ENST00000935014

RefSeq mRNA: 1 — MANE Select: NM_024050 NM_024050

CCDS: CCDS12357

Canonical transcript exons

ENST00000359866 — 5 exons

ExonStartEnd
ENSE000008955051731433817314389
ENSE000008955091731593417315995
ENSE000013226781730956317309657
ENSE000014000321731954617323298
ENSE000035164911731402317314103

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 96.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 67.1690 / max 288.0773, expressed in 1825 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
17449367.16901825

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
anterior cingulate cortexUBERON:000983596.60gold quality
cingulate cortexUBERON:000302796.53gold quality
prefrontal cortexUBERON:000045196.51gold quality
left testisUBERON:000453396.29gold quality
right testisUBERON:000453496.17gold quality
monocyteCL:000057696.09gold quality
mononuclear cellCL:000084295.97gold quality
right frontal lobeUBERON:000281095.83gold quality
stromal cell of endometriumCL:000225595.47gold quality
leukocyteCL:000073895.41gold quality
amygdalaUBERON:000187695.06gold quality
mucosa of transverse colonUBERON:000499194.77gold quality
dorsolateral prefrontal cortexUBERON:000983494.60gold quality
C1 segment of cervical spinal cordUBERON:000646994.51gold quality
nucleus accumbensUBERON:000188294.29gold quality
frontal cortexUBERON:000187094.24gold quality
testisUBERON:000047394.05gold quality
hypothalamusUBERON:000189894.02gold quality
caudate nucleusUBERON:000187393.99gold quality
apex of heartUBERON:000209893.96gold quality
popliteal arteryUBERON:000225093.92gold quality
tibial arteryUBERON:000761093.92gold quality
neocortexUBERON:000195093.91gold quality
Brodmann (1909) area 9UBERON:001354093.83gold quality
left adrenal glandUBERON:000123493.71gold quality
right adrenal gland cortexUBERON:003582793.61gold quality
aortaUBERON:000094793.60gold quality
left coronary arteryUBERON:000162693.52gold quality
adult organismUBERON:000702393.51gold quality
thoracic aortaUBERON:000151593.48gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.95
E-MTAB-6386no192.56
E-GEOD-110499no106.26
E-GEOD-125970no3.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

150 targeting DDA1, 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-4533100.0069.482758
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4673100.0066.641490
HSA-MIR-5692A100.0074.406850
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4455100.0065.481587
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4692100.0067.322066
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-451499.9967.101870
HSA-MIR-607799.9968.042299
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-512-3P99.9767.351049
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 21.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • PCIA1 gene expression correlates with tumor formation, invasion and metastasis (PMID:17557237)
  • Cells depleted of Dda1 spontaneously accumulated double-stranded DNA breaks in a similar way to Cul4A-, Cul4B- or Wdr23-depleted cells, indicating that Dda1 interacts physically and functionally with cullin-RING E3 ligases complexes. (PMID:19295130)
  • Data indicate that DET1- and DDB1-associated protein 1 (DDA1)-mediated tumor progression is associated with the activation of the NF-kappa B (NFkappaB)/COP9 signalosome 2(CSN2)/glycogen synthase kinase3beta (GSK3beta) pathway. (PMID:26942699)
  • the c-Abl non-receptor kinase phosphorylates DDB1 at residue Tyr-316 to recruit a small regulatory protein, DDA1, leading to increased substrate ubiquitination (PMID:28087699)
  • The results indicate that DDA1 promotes lung cancer progression, potentially through promoting cyclins and cell cycle progression. (PMID:28211159)
  • surveyed the spectrum of G protein coupling of dDA1 and Damb, and we confirmed that both receptors can couple to Gs to stimulate cAMP synthesis (PMID:29166600)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriodda1ENSDARG00000076074
mus_musculusDda1ENSMUSG00000074247
rattus_norvegicusDda1ENSRNOG00000039417
drosophila_melanogasterCG31855FBGN0051855

Protein

Protein identifiers

DET1- and DDB1-associated protein 1Q9BW61 (reviewed: Q9BW61)

Alternative names: Placenta cross-immune reaction antigen 1

All UniProt accessions (1): Q9BW61

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. In the DCX complexes, acts as a scaffolding subunit required to stabilize the complex.

Subunit / interactions. Component of numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which consist of a core of DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1. Component of the DCX(DCAF15) complex, also named CLR4(DCAF15) complex, composed of DCAF15, DDB1, cullin-4 (CUL4A or CUL4B), DDA1 and RBX1. Part of the DDD core complex containing DET1, DDA1 and DDB1; the DDD core complex recruits a specific UBE2E enzyme, such as UBE2E1, UBE2E2 UBE2E3, to form specific DDD-E2 complexes.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the DDA1 family.

RefSeq proteins (1): NP_076955* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR018276DDA1_domDomain
IPR033575DDA1-likeFamily

Pfam: PF10172

UniProt features (15 total): turn 3, modified residue 3, helix 2, strand 2, compositionally biased region 2, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

30 structures.

PDBMethodResolution (Å)
9BZ0ELECTRON MICROSCOPY1.9
8G46ELECTRON MICROSCOPY2.2
6UD7X-RAY DIFFRACTION2.3
6UE5X-RAY DIFFRACTION2.61
8TL6ELECTRON MICROSCOPY2.63
9LTJELECTRON MICROSCOPY2.65
9BJZELECTRON MICROSCOPY2.83
6PAIX-RAY DIFFRACTION2.9
6Q0RX-RAY DIFFRACTION2.9
6Q0VX-RAY DIFFRACTION2.9
6Q0WX-RAY DIFFRACTION2.9
9DHDELECTRON MICROSCOPY2.9
9LTOELECTRON MICROSCOPY2.92
9LTLELECTRON MICROSCOPY2.93
9LTRELECTRON MICROSCOPY3.03
9C5UELECTRON MICROSCOPY3.05
6DSZX-RAY DIFFRACTION3.09
8ROYELECTRON MICROSCOPY3.1
9LTWELECTRON MICROSCOPY3.25
9LTZELECTRON MICROSCOPY3.26
8ROXELECTRON MICROSCOPY3.3
9S3RELECTRON MICROSCOPY3.3
9C5VELECTRON MICROSCOPY3.36
8QH5ELECTRON MICROSCOPY3.4
9FD2ELECTRON MICROSCOPY3.4
6SJ7ELECTRON MICROSCOPY3.54
9LU1ELECTRON MICROSCOPY3.62
9W90ELECTRON MICROSCOPY3.7
9M0YELECTRON MICROSCOPY4.25
9LULELECTRON MICROSCOPY4.99

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BW61-F167.250.00

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 (3): 2, 33, 95

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8951664Neddylation

MSigDB gene sets: 167 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, MODULE_169, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GTTAAAG_MIR302B, GGGTGGRR_PAX4_03, RICKMAN_METASTASIS_DN, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_REGULATION_OF_NATURAL_KILLER_CELL_ACTIVATION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION

GO Biological Process (4): protein polyubiquitination (GO:0000209), positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436), protein ubiquitination (GO:0016567), regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)

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

GO Cellular Component (2): nucleoplasm (GO:0005654), Cul4-RING E3 ubiquitin ligase complex (GO:0080008)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
proteasome-mediated ubiquitin-dependent protein catabolic process2
protein ubiquitination1
regulation of proteasomal ubiquitin-dependent protein catabolic process1
positive regulation of proteasomal protein catabolic process1
positive regulation of ubiquitin-dependent protein catabolic process1
protein modification by small protein conjugation1
regulation of proteasomal protein catabolic process1
regulation of ubiquitin-dependent protein catabolic process1
binding1
nuclear lumen1
cellular anatomical structure1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DDA1DDB1Q16531992
DDA1DET1Q7L5Y6978
DDA1CUL4AQ13619970
DDA1DCAF15Q66K64832
DDA1CUL4BQ13620821
DDA1RBM39Q14498771
DDA1DCAF1Q9Y4B6745
DDA1RBX1P62877559
DDA1HLTFQ14527478
DDA1GPATCH8Q9UKJ3475
DDA1ENY2Q9NPA8449
DDA1EME2A4GXA9444
DDA1DCAF17Q5H9S7425
DDA1MUS81Q96NY9418
DDA1TET2Q6N021376

IntAct

158 interactions, top by confidence:

ABTypeScore
FOSL2JUNpsi-mi:“MI:0914”(association)0.930
LLGL2PRKCIpsi-mi:“MI:0914”(association)0.890
CUL4BCOPS2psi-mi:“MI:0914”(association)0.790
DDA1DDB1psi-mi:“MI:0407”(direct interaction)0.780
RFXANKRFXAPpsi-mi:“MI:0914”(association)0.780
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
CUL4ACOPS2psi-mi:“MI:0914”(association)0.640
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
DDA1AGTRAPpsi-mi:“MI:0915”(physical association)0.560
DDA1CMTM5psi-mi:“MI:0915”(physical association)0.560
CMTM5DDA1psi-mi:“MI:0915”(physical association)0.560
PKNOX2DDA1psi-mi:“MI:0915”(physical association)0.560
RDH10DDA1psi-mi:“MI:0915”(physical association)0.560
PRKNDDA1psi-mi:“MI:0915”(physical association)0.560
DCAF11GNPATpsi-mi:“MI:0914”(association)0.530
PRKCZIPO5psi-mi:“MI:0914”(association)0.530

BioGRID (758): DDB1 (Affinity Capture-Western), CUL4A (Affinity Capture-Western), CUL4B (Affinity Capture-Western), DDA1 (Two-hybrid), CMTM5 (Two-hybrid), DDA1 (Affinity Capture-Western), DDA1 (Affinity Capture-Western), DDA1 (Affinity Capture-Western), DET1 (Affinity Capture-Western), DDA1 (Affinity Capture-MS), DDA1 (Affinity Capture-MS), DDB1 (Co-fractionation), VPRBP (Co-fractionation), DDA1 (Two-hybrid), DDA1 (Affinity Capture-MS)

ESM2 similar proteins: A3CEM4, A6NGY3, A9CB88, B2ZCQ0, B3LVF9, B3P0Q4, B4HEN5, B4K843, B4LY66, B4N943, B4PST7, B4QZV5, C9K7C7, F4KIH4, O16224, O41804, O70903, O89085, O89945, O91087, P03238, P0A3T0, P0A3T1, P12597, P13623, P24103, P27970, P28953, P28989, P33632, P36356, P36713, P50785, P55924, P56280, P85112, Q09340, Q09410, Q12379, Q5E9A9

Diamond homologs: Q5BL73, Q5E9A9, Q5RD86, Q5U550, Q5ZK14, Q7T2A3, Q9BW61, Q9D9Z5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 173 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-NER1025.5×1e-09
Formation of TC-NER Pre-Incision Complex1018.9×2e-08
Recognition of DNA damage by PCNA-containing replication complex517.0×1e-03
Dual Incision in GG-NER613.9×7e-04
Formation of Incision Complex in GG-NER613.6×7e-04
Transcription-Coupled Nucleotide Excision Repair (TC-NER)511.9×5e-03
Neddylation2611.0×2e-17
Dual incision in TC-NER69.3×4e-03

GO biological processes:

GO termPartnersFoldFDR
regulation of protein neddylation530.8×1e-04
protein neddylation523.1×4e-04
protein ubiquitination349.3×2e-20
proteasome-mediated ubiquitin-dependent protein catabolic process206.9×6e-09
protein polyubiquitination96.8×9e-04
ubiquitin-dependent protein catabolic process115.4×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance13
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

547 predictions. Top by Δscore:

VariantEffectΔscore
19:17309654:GATG:Gdonor_gain1.0000
19:17309655:ATGG:Adonor_loss1.0000
19:17309656:TGGT:Tdonor_loss1.0000
19:17309657:GGT:Gdonor_loss1.0000
19:17309663:G:GTdonor_gain1.0000
19:17314021:A:AGacceptor_gain1.0000
19:17314021:AGGC:Aacceptor_loss1.0000
19:17314022:G:GGacceptor_gain1.0000
19:17314022:GGC:Gacceptor_gain1.0000
19:17314022:GGCA:Gacceptor_gain1.0000
19:17314104:G:GGdonor_gain1.0000
19:17314104:GTGA:Gdonor_loss1.0000
19:17314336:A:AGacceptor_gain1.0000
19:17314337:G:GTacceptor_gain1.0000
19:17314337:GA:Gacceptor_gain1.0000
19:17314337:GAACC:Gacceptor_gain1.0000
19:17314388:GA:Gdonor_gain1.0000
19:17314390:G:GGdonor_gain1.0000
19:17315996:G:GAdonor_loss1.0000
19:17315997:T:Gdonor_loss1.0000
19:17319536:T:Aacceptor_gain1.0000
19:17319542:CCAG:Cacceptor_loss1.0000
19:17319544:A:AGacceptor_gain1.0000
19:17319544:AGA:Aacceptor_loss1.0000
19:17319544:AGAAC:Aacceptor_gain1.0000
19:17319545:G:GGacceptor_gain1.0000
19:17319545:GA:Gacceptor_gain1.0000
19:17319545:GAA:Gacceptor_gain1.0000
19:17319545:GAAC:Gacceptor_gain1.0000
19:17319545:GAACG:Gacceptor_gain1.0000

AlphaMissense

665 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:17315937:T:AI47N1.000
19:17315937:T:GI47S1.000
19:17315946:A:TE50V1.000
19:17315958:T:AI54N1.000
19:17315958:T:CI54T1.000
19:17315958:T:GI54S1.000
19:17315961:T:AL55H1.000
19:17315961:T:CL55P1.000
19:17315964:T:AL56Q1.000
19:17315964:T:CL56P1.000
19:17315966:C:AR57S1.000
19:17315969:T:GY58D1.000
19:17315973:T:AL59Q1.000
19:17315973:T:CL59P1.000
19:17314042:T:CL8P0.999
19:17314065:T:CF16L0.999
19:17314066:T:CF16S0.999
19:17314067:T:AF16L0.999
19:17314067:T:GF16L0.999
19:17314356:T:GY35D0.999
19:17315937:T:CI47T0.999
19:17315956:C:AN53K0.999
19:17315956:C:GN53K0.999
19:17315957:A:TI54F0.999
19:17315966:C:GR57G0.999
19:17315967:G:CR57P0.999
19:17315970:A:CY58S0.999
19:17315975:C:GH60D0.999
19:17315979:A:CQ61P0.999
19:17315982:A:CQ62P0.999

dbSNP variants (sampled 300 via entrez): RS1000018641 (19:17312285 G>T), RS1000310237 (19:17309251 A>T), RS1000345753 (19:17314047 G>A), RS1000689099 (19:17312932 G>A), RS1000760897 (19:17313259 G>A,C), RS1001273889 (19:17318548 G>A), RS1001381720 (19:17307941 C>G), RS1001424651 (19:17313205 G>A), RS1001478947 (19:17313713 G>A), RS1001551197 (19:17313965 T>C), RS1001705172 (19:17318241 A>G,T), RS1001737667 (19:17323540 A>G), RS1001771880 (19:17323275 CAA>C), RS1001772206 (19:17308183 G>A), RS1001888098 (19:17312850 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001795_14Systemic lupus erythematosus1.000000e-06
GCST007394_2Mitochondrial DNA copy number1.000000e-14

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006312mitochondrial DNA measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutionincreases expression2
Valproic Aciddecreases methylation, increases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Adecreases methylation1
beta-lapachoneincreases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
bisphenol Sincreases expression, affects cotreatment1
Resveratroldecreases expression, affects cotreatment1
Temozolomideincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Manganeseincreases expression, affects cotreatment, increases abundance1
Methotrexateincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, 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.