DDX52

Summary

DDX52 (DExD-box helicase 52, HGNC:20038) is a protein-coding gene on chromosome 17q12, encoding Probable ATP-dependent RNA helicase DDX52 (Q9Y2R4). Required for efficient ribosome biogenesis. It is a selective cancer dependency (DepMap: 75.8% of cell lines).

Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA. Located in membrane.

Source: NCBI Gene 11056 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 105 total — 5 pathogenic
• Cancer dependency (DepMap): dependent in 75.8% of screened cell lines
• MANE Select transcript: NM_007010

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20038
Approved symbol	DDX52
Name	DExD-box helicase 52
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	ROK1
Ensembl gene	ENSG00000278053
Ensembl biotype	protein_coding
OMIM	612500
Entrez	11056

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 4 nonsense_mediated_decay, 4 protein_coding, 3 retained_intron

ENST00000612255, ENST00000613633, ENST00000614307, ENST00000616646, ENST00000617633, ENST00000619418, ENST00000620209, ENST00000622140, ENST00000869764, ENST00000939768, ENST00000965049

RefSeq mRNA: 2 — MANE Select: NM_007010 NM_001291476, NM_007010

CCDS: CCDS11323

Canonical transcript exons

ENST00000615769 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.1642 / max 780.7782, expressed in 1808 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165481	31.5717	1805
165482	1.5161	970
165479	0.0585	10
165483	0.0178	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	92.18	gold quality
endometrium	UBERON:0001295	92.10	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.54	gold quality
adrenal tissue	UBERON:0018303	88.13	gold quality
ganglionic eminence	UBERON:0004023	87.00	gold quality
islet of Langerhans	UBERON:0000006	86.92	gold quality
ventricular zone	UBERON:0003053	86.19	gold quality
rectum	UBERON:0001052	85.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.48	gold quality
smooth muscle tissue	UBERON:0001135	85.19	gold quality
calcaneal tendon	UBERON:0003701	85.07	gold quality
tonsil	UBERON:0002372	85.01	gold quality
pancreas	UBERON:0001264	85.00	gold quality
corpus callosum	UBERON:0002336	84.96	gold quality
duodenum	UBERON:0002114	84.45	gold quality
stromal cell of endometrium	CL:0002255	84.35	gold quality
esophagus mucosa	UBERON:0002469	84.35	gold quality
body of pancreas	UBERON:0001150	84.29	gold quality
mucosa of transverse colon	UBERON:0004991	84.12	gold quality
monocyte	CL:0000576	83.70	gold quality
leukocyte	CL:0000738	83.68	gold quality
vermiform appendix	UBERON:0001154	83.55	gold quality
muscle tissue	UBERON:0002385	83.09	gold quality
esophagus	UBERON:0001043	83.07	gold quality
placenta	UBERON:0001987	83.05	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.05	gold quality
cortical plate	UBERON:0005343	82.99	gold quality
small intestine	UBERON:0002108	82.98	gold quality
skeletal muscle tissue	UBERON:0001134	82.91	gold quality
gastrocnemius	UBERON:0001388	82.88	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-4850	no	301.55
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 75.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• Knockdown of DEAD-box RNA helicase 52 (DDX52) suppresses the proliferation of melanoma cells in vitro and of nude mouse xenografts by targeting c-Myc. (PMID:34233596)
• DDX52 gene expression in LUAD tissues indicates potential as a prognostic biomarker and therapeutic target. (PMID:37833424)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ddx52	ENSDARG00000100505
mus_musculus	Ddx52	ENSMUSG00000020677
drosophila_melanogaster	ais	FBGN0036754
caenorhabditis_elegans	ddx-52	WBGENE00011032

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), DDX51 (ENSG00000185163), DDX42 (ENSG00000198231), DDX39B (ENSG00000198563), DDX47 (ENSG00000213782), DDX3X (ENSG00000215301)

Protein

Protein identifiers

Probable ATP-dependent RNA helicase DDX52 — Q9Y2R4 (reviewed: Q9Y2R4)

Alternative names: ATP-dependent RNA helicase ROK1-like, DEAD box protein 52

All UniProt accessions (5): A0A087WTD6, A0A087X069, A0A087X121, A0A087X1P7, Q9Y2R4

UniProt curated annotations — full annotation on UniProt →

Function. Required for efficient ribosome biogenesis. May control cell cycle progression by regulating translation of mRNAs that contain a terminal oligo pyrimidine (TOP) motif in their 5’ UTRs, such as GTPBP4.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the DEAD box helicase family. DDX52/ROK1 subfamily.

RefSeq proteins (2): NP_001278405, NP_008941* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001650	Helicase_C-like	Domain
IPR011545	DEAD/DEAH_box_helicase_dom	Domain
IPR014001	Helicase_ATP-bd	Domain
IPR014014	RNA_helicase_DEAD_Q_motif	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR044764	DDX52/Rok1_DEADc	Domain
IPR050079	DEAD_box_RNA_helicase	Family

Pfam: PF00270, PF00271

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (38 total): helix 11, strand 10, sequence conflict 3, domain 2, modified residue 2, turn 2, region of interest 2, short sequence motif 2, chain 1, sequence variant 1, compositionally biased region 1, binding site 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3DKP	X-RAY DIFFRACTION	2.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2R4-F1	76.69	0.39

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): 209–216

Post-translational modifications (2): 39, 15

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 152 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER, GOBP_MATURATION_OF_SSU_RRNA, MORF_RAD51L3, PUJANA_CHEK2_PCC_NETWORK, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, MORF_PRKCA, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, RASHI_RESPONSE_TO_IONIZING_RADIATION_6, MORF_ATF2, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR

GO Biological Process (1): maturation of SSU-rRNA (GO:0030490)

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 (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), membrane (GO:0016020), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ATP-dependent activity	2
nuclear lumen	2
cellular anatomical structure	2
rRNA processing	1
ribosomal small subunit biogenesis	1
nucleic acid binding	1
helicase activity	1
ATP-dependent activity, acting on RNA	1
catalytic activity, acting on RNA	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
nucleic acid conformation isomerase activity	1
catalytic activity, acting on a nucleic acid	1
catalytic activity	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2033 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DDX52	PDCD11	Q14690	917
DDX52	RRP7A	Q9Y3A4	744
DDX52	BMS1	Q14692	732
DDX52	NAT10	Q9H0A0	716
DDX52	DHX15	O43143	710
DDX52	UTP23	Q9BRU9	674
DDX52	RCL1	Q9Y2P8	667
DDX52	KRR1	Q13601	665
DDX52	PIGW	Q7Z7B1	653
DDX52	ABT1	Q9ULW3	646
DDX52	TADA2A	O75478	637
DDX52	NOL6	Q9H6R4	628
DDX52	MRM1	Q6IN84	624
DDX52	BYSL	Q13895	614
DDX52	AATF	Q9NY61	612

IntAct

99 interactions, top by confidence:

A	B	Type	Score
MED29	MED19	psi-mi:“MI:0914”(association)	0.890
MED9	MED19	psi-mi:“MI:0914”(association)	0.790
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
CHCHD4	SSNA1	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
FGF3	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
RRP8	NVL	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
RSBN1	SETD1A	psi-mi:“MI:0914”(association)	0.530
FOXM1	PES1	psi-mi:“MI:0914”(association)	0.500
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
DDX52	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
DDX52	HMGN2	psi-mi:“MI:0915”(physical association)	0.400
DDX52	H1-0	psi-mi:“MI:0915”(physical association)	0.400
DDX52	H2BC5	psi-mi:“MI:0915”(physical association)	0.400
DDX52	EDF1	psi-mi:“MI:0915”(physical association)	0.400
HLCS	DDX52	psi-mi:“MI:0915”(physical association)	0.370
PMP22	DDX52	psi-mi:“MI:0915”(physical association)	0.370
DDX52	AP4M1	psi-mi:“MI:0915”(physical association)	0.370
FOXL1	IFRD1	psi-mi:“MI:0914”(association)	0.350
FOXL2	RTCA	psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
MYC	ILVBL	psi-mi:“MI:0914”(association)	0.350

BioGRID (204): DDX52 (Affinity Capture-MS), DDX52 (Affinity Capture-MS), DDX52 (Affinity Capture-MS), DDX52 (Affinity Capture-MS), DDX52 (Affinity Capture-MS), DDX52 (Co-fractionation), DDX52 (Co-fractionation), DDX52 (Co-fractionation), DDX52 (Co-fractionation), DDX52 (Co-fractionation), DDX52 (Co-fractionation), IMP4 (Co-fractionation), KIAA0020 (Co-fractionation), NOC4L (Co-fractionation), NOL10 (Co-fractionation)

ESM2 similar proteins: A2VD92, A5D7C1, A5DIX5, A5E1N2, A6ZU15, O16102, O74393, P23394, P45818, P54823, Q07886, Q09775, Q0DBS1, Q0IHV9, Q0IIK5, Q10202, Q19614, Q4R7L5, Q55CP6, Q5NVJ8, Q5T1V6, Q5XH91, Q641Y8, Q6AZV7, Q6C024, Q6CDS6, Q6CKI1, Q6FM43, Q7FGZ2, Q84T03, Q86TM3, Q8GXD6, Q90WU3, Q91VN6, Q91VR5, Q92499, Q9C551, Q9DBN9, Q9DF35, Q9FLB0

Diamond homologs: A1CNK1, A1D1E3, A2QAB5, A3GHW9, A4RMV8, A5D7C1, A5DBI5, A5DIX5, A5E1N2, A6ZQJ1, A6ZU15, A7EGL7, A7TT88, P0CR04, P0CR05, P0CR06, P0CR07, P10081, P10630, P25888, P45818, Q09775, Q0CMB0, Q0JM17, Q14240, Q1E306, Q2HCV7, Q2UQW3, Q38F76, Q3SZ65, Q4E162, Q4IPI1, Q4R4Y9, Q4WRH5, Q56XG6, Q5BET6, Q5JK84, Q5K5B6, Q5R4X1, Q5RKI1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 135 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:

Pathway	Partners	Fold	FDR
rRNA modification in the nucleus and cytosol	6	12.3×	2e-03
Regulation of PD-L1(CD274) transcription	7	8.4×	4e-03
Major pathway of rRNA processing in the nucleolus and cytosol	11	7.5×	1e-04
Estrogen-dependent gene expression	8	6.7×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal large subunit biogenesis	7	26.1×	6e-06
ribosomal small subunit biogenesis	6	11.5×	3e-03
RNA polymerase II preinitiation complex assembly	5	11.4×	1e-02
positive regulation of transcription initiation by RNA polymerase II	5	11.4×	1e-02
rRNA processing	9	10.7×	6e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	80
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1180528	GRCh37/hg19 17q12(chr17:34815466-36249366)x3	Pathogenic
1711449	GRCh37/hg19 17q12(chr17:34842544-36104875)x3	Pathogenic
32491	GRCh38/hg38 17q12(chr17:36500215-37889296)x3	Pathogenic
375218	GRCh37/hg19 17q12(chr17:34815072-36192492)x1	Pathogenic
58695	GRCh37/hg19 17q12(chr17:35958761-36224189)x3	Pathogenic

SpliceAI

2857 predictions. Top by Δscore:

Variant	Effect	Δscore
17:37618290:A:AC	donor_gain	1.0000
17:37618291:C:CC	donor_gain	1.0000
17:37618392:T:TC	acceptor_gain	1.0000
17:37621392:CTTTA:C	donor_loss	1.0000
17:37621393:TTTA:T	donor_loss	1.0000
17:37621394:TTAC:T	donor_loss	1.0000
17:37621395:TACC:T	donor_loss	1.0000
17:37621396:ACCT:A	donor_loss	1.0000
17:37621397:CCT:C	donor_loss	1.0000
17:37621519:CC:C	acceptor_gain	1.0000
17:37621520:CC:C	acceptor_gain	1.0000
17:37624340:ATACC:A	donor_loss	1.0000
17:37624341:TAC:T	donor_loss	1.0000
17:37624342:A:AT	donor_loss	1.0000
17:37624430:AATTC:A	acceptor_gain	1.0000
17:37624431:ATTC:A	acceptor_gain	1.0000
17:37624432:TTC:T	acceptor_gain	1.0000
17:37624432:TTCC:T	acceptor_loss	1.0000
17:37624433:TC:T	acceptor_gain	1.0000
17:37624433:TCCT:T	acceptor_loss	1.0000
17:37624434:CC:C	acceptor_gain	1.0000
17:37624434:CCT:C	acceptor_loss	1.0000
17:37624435:C:CA	acceptor_loss	1.0000
17:37624435:C:CC	acceptor_gain	1.0000
17:37625890:AATAC:A	donor_loss	1.0000
17:37625891:ATACC:A	donor_loss	1.0000
17:37625892:TA:T	donor_loss	1.0000
17:37625893:A:AT	donor_loss	1.0000
17:37625894:C:CA	donor_loss	1.0000
17:37626094:CAACA:C	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000086910 (17:37641364 T>C,G), RS1000091160 (17:37625727 T>C), RS1000139010 (17:37641610 A>T), RS1000290684 (17:37635733 C>G), RS1000343168 (17:37612047 A>C), RS1000385285 (17:37637030 T>C), RS1000477412 (17:37630474 C>T), RS1000544868 (17:37622814 C>G), RS1000673338 (17:37616432 G>C), RS1000684177 (17:37624064 G>A), RS1000734011 (17:37636736 A>G), RS1000745303 (17:37636071 T>C), RS1000752669 (17:37616848 C>T), RS1000805122 (17:37617148 C>G), RS1000830804 (17:37610030 C>G)

Disease associations

OMIM: gene MIM:612500 | disease phenotypes: MIM:614527

GenCC curated gene-disease

Mondo (1): chromosome 17q12 deletion syndrome (MONDO:0013797)

Orphanet (1): 17q12 microdeletion syndrome (Orphanet:261265)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001941_16	Ovarian cancer	8.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
bisphenol A	decreases methylation, increases expression, affects cotreatment, affects expression, increases abundance	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
ginger extract	affects cotreatment, affects expression, increases abundance	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases stability	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
ICG 001	decreases expression	1
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Arsenic	affects methylation	1
Benzene	increases expression	1
Dinitrochlorobenzene	affects binding	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Oils, Volatile	increases abundance, affects cotreatment, affects expression	1
Oxygen	decreases expression	1
Quercetin	decreases expression	1
Ribonucleotides	affects binding	1
Silicon Dioxide	increases expression	1
T-2 Toxin	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight