DDX51

gene
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Summary

DDX51 (DEAD-box helicase 51, HGNC:20082) is a protein-coding gene on chromosome 12q24.33, encoding ATP-dependent RNA helicase DDX51 (Q8N8A6). ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits. It is a common-essential gene (DepMap: required in 96.6% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in membrane.

Source: NCBI Gene 317781 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 186 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 96.6% of screened cell lines (common-essential)
  • MANE Select transcript: NM_175066

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20082
Approved symbolDDX51
NameDEAD-box helicase 51
Location12q24.33
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000185163
Ensembl biotypeprotein_coding
Entrez317781

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 5 retained_intron

ENST00000329073, ENST00000397333, ENST00000462829, ENST00000541489, ENST00000545991, ENST00000546058, ENST00000864667, ENST00000919064, ENST00000919065, ENST00000919066, ENST00000960080, ENST00000960081, ENST00000960082

RefSeq mRNA: 1 — MANE Select: NM_175066 NM_175066

CCDS: CCDS41865

Canonical transcript exons

ENST00000397333 — 15 exons

ExonStartEnd
ENSE00001301508132143993132144319
ENSE00001302733132142728132142878
ENSE00001324623132143695132143909
ENSE00001528235132136594132139298
ENSE00003473661132139635132139769
ENSE00003473703132142119132142190
ENSE00003480365132140098132140199
ENSE00003528149132139861132139924
ENSE00003534230132142277132142422
ENSE00003536349132140620132140735
ENSE00003577993132140831132141020
ENSE00003620265132141275132141420
ENSE00003627912132140423132140539
ENSE00003656622132141850132141956
ENSE00003677605132141498132141606

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 90.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.0562 / max 229.1759, expressed in 1779 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13419113.05621779

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489090.22gold quality
right frontal lobeUBERON:000281090.02gold quality
cerebellar hemisphereUBERON:000224589.76gold quality
cerebellar cortexUBERON:000212989.66gold quality
cerebellumUBERON:000203789.65gold quality
pituitary glandUBERON:000000789.55gold quality
left ovaryUBERON:000211989.37gold quality
right uterine tubeUBERON:000130289.08gold quality
apex of heartUBERON:000209888.91gold quality
right ovaryUBERON:000211888.82gold quality
body of pancreasUBERON:000115088.69gold quality
ovaryUBERON:000099288.46gold quality
adenohypophysisUBERON:000219688.30gold quality
granulocyteCL:000009488.29gold quality
left uterine tubeUBERON:000130388.04gold quality
body of uterusUBERON:000985387.44gold quality
spleenUBERON:000210687.18gold quality
frontal cortexUBERON:000187086.81gold quality
right testisUBERON:000453486.72gold quality
right lobe of thyroid glandUBERON:000111986.67gold quality
tibial nerveUBERON:000132386.65gold quality
ectocervixUBERON:001224986.58gold quality
nucleus accumbensUBERON:000188286.57gold quality
mucosa of transverse colonUBERON:000499186.56gold quality
left testisUBERON:000453386.47gold quality
dorsolateral prefrontal cortexUBERON:000983486.46gold quality
brainUBERON:000095586.44gold quality
anterior cingulate cortexUBERON:000983586.40gold quality
endocervixUBERON:000045886.36gold quality
body of stomachUBERON:000116186.30gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting DDX51, 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-150-5P99.9966.691976
HSA-MIR-548P99.9872.253784
HSA-MIR-512-3P99.9767.351049
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-302E99.9670.742669
HSA-MIR-218-5P99.9372.222103
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-197699.7465.481127
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-6832-5P99.5864.821132
HSA-MIR-608199.4866.071446
HSA-MIR-1211399.3267.541072
HSA-MIR-3064-5P99.2666.131497
HSA-MIR-3085-3P99.2666.161490
HSA-MIR-6504-5P99.2665.951487
HSA-MIR-797499.2465.481137
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-66199.0965.942062
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-181A-2-3P98.9167.601168
HSA-MIR-4716-5P98.8268.571168
HSA-MIR-314998.7767.131639
HSA-MIR-390898.7567.311160
HSA-MIR-475298.7168.04833

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • these data suggest that DDX51 aids cell cancer proliferation by regulating multiple signaling pathways (PMID:27198888)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioddx51ENSDARG00000025854
mus_musculusDdx51ENSMUSG00000029504
rattus_norvegicusDdx51ENSRNOG00000037480
drosophila_melanogasterDbp73DFBGN0004556
caenorhabditis_elegansWBGENE00022792

Paralogs (38): DDX20 (ENSG00000064703), DDX3Y (ENSG00000067048), DDX1 (ENSG00000079785), DDX43 (ENSG00000080007), DDX18 (ENSG00000088205), DDX24 (ENSG00000089737), DDX17 (ENSG00000100201), DDX49 (ENSG00000105671), DDX50 (ENSG00000107625), DDX5 (ENSG00000108654), DDX25 (ENSG00000109832), DDX6 (ENSG00000110367), DDX55 (ENSG00000111364), DDX59 (ENSG00000118197), DDX54 (ENSG00000123064), DDX39A (ENSG00000123136), DDX27 (ENSG00000124228), DDX31 (ENSG00000125485), DDX56 (ENSG00000136271), EIF4A3 (ENSG00000141543), DDX46 (ENSG00000145833), DDX4 (ENSG00000152670), EIF4A2 (ENSG00000156976), DDX19B (ENSG00000157349), EIF4A1 (ENSG00000161960), DDX21 (ENSG00000165732), DDX19A (ENSG00000168872), TDRD12 (ENSG00000173809), DDX23 (ENSG00000174243), DDX10 (ENSG00000178105), DDX28 (ENSG00000182810), DDX41 (ENSG00000183258), DDX53 (ENSG00000184735), DDX42 (ENSG00000198231), DDX39B (ENSG00000198563), DDX47 (ENSG00000213782), DDX3X (ENSG00000215301), DDX52 (ENSG00000278053)

Protein

Protein identifiers

ATP-dependent RNA helicase DDX51Q8N8A6 (reviewed: Q8N8A6)

Alternative names: DEAD box protein 51

All UniProt accessions (1): Q8N8A6

UniProt curated annotations — full annotation on UniProt →

Function. ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits.

Subcellular location. Nucleus. Nucleolus.

Domain organisation. The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Similarity. Belongs to the DEAD box helicase family. DDX51/DBP6 subfamily.

RefSeq proteins (1): NP_778236* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000629RNA-helicase_DEAD-box_CSConserved_site
IPR001650Helicase_C-likeDomain
IPR011545DEAD/DEAH_box_helicase_domDomain
IPR014001Helicase_ATP-bdDomain
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF00270, PF00271

Catalyzed reactions (Rhea), 1 shown:

  • ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (28 total): sequence variant 8, compositionally biased region 5, sequence conflict 4, modified residue 3, domain 2, short sequence motif 2, initiator methionine 1, chain 1, binding site 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N8A6-F174.640.37

Functional residue map

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

Ligand- & substrate-binding residues (1): 256–263

Post-translational modifications (3): 2, 83, 103

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 158 (showing top): GOBP_RIBOSOME_BIOGENESIS, SHEPARD_CRASH_AND_BURN_MUTANT_UP, CREBP1_Q2, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, CREB_Q4, E4F1_Q6, ATF3_Q6, CREB_Q2_01, ATF4_Q2, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, BURTON_ADIPOGENESIS_4, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, ATF_01, CREBP1CJUN_01, CREB_01

GO Biological Process (2): rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (8): RNA binding (GO:0003723), RNA helicase activity (GO:0003724), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), helicase activity (GO:0004386), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ATP-dependent activity2
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
ribonucleoprotein complex biogenesis1
nucleic acid binding1
helicase activity1
ATP-dependent activity, acting on RNA1
catalytic activity, acting on RNA1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
ribonucleoside triphosphate phosphatase activity1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
nucleic acid conformation isomerase activity1
catalytic activity, acting on a nucleic acid1
catalytic activity1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

2843 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DDX51CFAP45Q9UL16600
DDX51NOL10Q9BSC4563
DDX51NOL9Q5SY16541
DDX51RRP9O43818525
DDX51PDCD11Q14690522
DDX51RBM34P42696517
DDX51URB1O60287505
DDX51PPANQ9NQ55484
DDX51A0A0B4J1V8A0A0B4J1V8483
DDX51WRAP73Q9P2S5471
DDX51NOP58Q9Y2X3468
DDX51WDR36Q8NI36466
DDX51GTPBP4Q9BZE4462
DDX51RRP8O43159458
DDX51NOP56O00567448

IntAct

127 interactions, top by confidence:

ABTypeScore
NEUROG3GXYLT2psi-mi:“MI:0914”(association)0.640
MECP2KPNA3psi-mi:“MI:0914”(association)0.640
ILF3ADARpsi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
PLEKHO1UBA6psi-mi:“MI:0914”(association)0.530
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
ZNF512ZNF724psi-mi:“MI:0914”(association)0.530
RBM34NVLpsi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
RSBN1SETD1Apsi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
RPL18ARRP8psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
CASQ2PES1psi-mi:“MI:0914”(association)0.530
CCDC59GAPDHSpsi-mi:“MI:0914”(association)0.530
SRPK2RRP9psi-mi:“MI:0914”(association)0.530
GTF3C2C1QBPpsi-mi:“MI:0914”(association)0.530
RRP8MAGEB2psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530

BioGRID (146): DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Co-fractionation), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS), DDX51 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8Y7D0, A1L020, A2ARS0, A6NDN8, G1T8A2, O70418, O75426, P29473, P29597, P49897, P49898, P52824, P55073, P62861, P62862, P70313, P79209, Q08097, Q08DF2, Q148R9, Q1LZC5, Q28969, Q39491, Q4R327, Q566C8, Q5SPX3, Q62600, Q6DN07, Q6H5L4, Q6N063, Q6NXT1, Q6QN11, Q6ZS82, Q758T2, Q7L9B9, Q86SG2, Q8C2K5, Q8MJG0, Q8N8A6, Q8TD08

Diamond homologs: A1CIQ5, A1CKJ0, A1CR32, A1CW14, A1D405, A1D6X9, A2QA23, A2RB17, A2XKG2, A3LNR6, A3LS22, A3LSJ2, A3LSN3, A4QYM6, A4RGD1, A5D7C1, A5DID7, A5DK47, A5DLE0, A5DQF1, A5DS77, A5DY34, A5E726, A6QRQ7, A6RUH2, A6RW56, A6ZSB3, A6ZSX1, A7EML8, A7F4L5, A7TFZ9, A7TS37, O22907, P0CR00, P0CR01, P25888, P26802, P34580, P38712, P53734

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 142 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
Peptide chain elongation1316.7×9e-11
Viral mRNA Translation1316.7×9e-11
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1316.5×9e-11
Selenocysteine synthesis1315.8×1e-10
Eukaryotic Translation Termination1315.8×1e-10
Response of EIF2AK4 (GCN2) to amino acid deficiency1415.7×6e-11
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1315.5×1e-10
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1315.5×1e-10

GO biological processes:

GO termPartnersFoldFDR
ribosomal large subunit biogenesis827.3×1e-07
cytoplasmic translation1419.9×8e-12
rRNA processing1314.2×4e-09
positive regulation of miRNA transcription613.4×7e-04
ribosomal small subunit biogenesis712.3×3e-04
RNA processing711.8×4e-04
translation1411.1×1e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance152
Likely benign16
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3244436NC_000012.11:g.(?132414268)(133263901_?)delPathogenic

SpliceAI

2456 predictions. Top by Δscore:

VariantEffectΔscore
12:132139630:CTTA:Cdonor_loss1.0000
12:132139631:TTA:Tdonor_loss1.0000
12:132139632:TACCT:Tdonor_loss1.0000
12:132139633:A:AGdonor_loss1.0000
12:132140092:GCTCA:Gdonor_loss1.0000
12:132140093:CTCAC:Cdonor_loss1.0000
12:132140094:TCACC:Tdonor_loss1.0000
12:132140095:CA:Cdonor_loss1.0000
12:132140096:A:ACdonor_gain1.0000
12:132140096:AC:Adonor_gain1.0000
12:132140097:C:CTdonor_gain1.0000
12:132140097:CC:Cdonor_gain1.0000
12:132140418:CTCA:Cdonor_loss1.0000
12:132140419:TCACA:Tdonor_loss1.0000
12:132140420:CA:Cdonor_loss1.0000
12:132140421:A:ACdonor_gain1.0000
12:132140421:AC:Adonor_loss1.0000
12:132140421:ACAG:Adonor_gain1.0000
12:132140422:C:CCdonor_gain1.0000
12:132140422:CA:Cdonor_gain1.0000
12:132140422:CAG:Cdonor_gain1.0000
12:132140422:CAGC:Cdonor_gain1.0000
12:132140433:T:TAdonor_gain1.0000
12:132140434:C:Adonor_gain1.0000
12:132140535:AGAGC:Aacceptor_gain1.0000
12:132140536:GAGC:Gacceptor_gain1.0000
12:132140538:GC:Gacceptor_gain1.0000
12:132140538:GCCTA:Gacceptor_loss1.0000
12:132140539:CC:Cacceptor_gain1.0000
12:132140540:C:CCacceptor_gain1.0000

AlphaMissense

4262 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:132140098:C:GR592P0.998
12:132140190:G:CS561R0.998
12:132140190:G:TS561R0.998
12:132140192:T:GS561R0.998
12:132140102:G:CH591D0.997
12:132140646:G:CF510L0.997
12:132140646:G:TF510L0.997
12:132140648:A:GF510L0.997
12:132141410:T:AE372V0.997
12:132141553:A:GL350P0.997
12:132139915:C:AR595S0.996
12:132139915:C:GR595S0.996
12:132141401:C:GR375P0.996
12:132141569:C:GA345P0.996
12:132141404:T:AD374V0.995
12:132141405:C:GD374H0.995
12:132141408:C:GA373P0.995
12:132141410:T:GE372A0.995
12:132141499:A:GL368P0.995
12:132141556:C:GR349P0.995
12:132142153:A:GL285P0.995
12:132139916:C:GR595T0.994
12:132140136:G:CN579K0.994
12:132140136:G:TN579K0.994
12:132140177:C:GA566P0.994
12:132140651:A:GC509R0.994
12:132140703:C:AK491N0.994
12:132140703:C:GK491N0.994
12:132142126:G:TA294D0.994
12:132142332:A:TV254D0.994

dbSNP variants (sampled 300 via entrez): RS1000269617 (12:132142812 G>A,C,T), RS1000521431 (12:132143414 C>G,T), RS1000575013 (12:132140616 T>C), RS1000819124 (12:132143415 G>A), RS1000922669 (12:132136931 T>A), RS1001138798 (12:132136612 T>C), RS1001199394 (12:132143663 C>A,G,T), RS1001421656 (12:132140003 C>T), RS1001533438 (12:132144202 C>A,T), RS1001689037 (12:132143688 G>A,T), RS1002039657 (12:132143241 A>G), RS1002239931 (12:132144650 G>A,C,T), RS1002371281 (12:132143368 C>T), RS1002520205 (12:132138904 C>G,T), RS1002700673 (12:132141781 C>A,G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615083

GenCC curated gene-disease

Mondo (1): colorectal cancer, susceptibility to, 12 (MONDO:0014038)

Orphanet (1): Attenuated familial adenomatous polyposis (Orphanet:220460)

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST005951_3Body mass index6.000000e-09
GCST007059_15Response to antidepressants (symptom improvement)5.000000e-06
GCST007060_6Response to SSRI (symptom remission)3.000000e-06
GCST008163_561Height2.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0005658response to selective serotonin reuptake inhibitor

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
sodium arseniteincreases abundance, increases expression2
Tretinoindecreases expression2
Valproic Acidaffects expression, increases methylation2
FR900359increases phosphorylation1
tamibaroteneaffects expression1
di-n-butylphosphoric acidaffects expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
Arsenicincreases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Cisplatindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradiolincreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Phenobarbitalaffects expression1
Phthalic Acidsdecreases expression1
Plant Extractsdecreases expression1
Potassium Dichromateincreases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Thiramdecreases expression1
Cyclosporineincreases expression1
Asbestos, Crocidolitedecreases expression1
Cadmium Chloridedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): colorectal cancer, susceptibility to, 12