DDX54 (DEAD-box helicase 54)

Gene

• Entrez ID: 79039
• Gene name: DEAD-box helicase 54
• Gene symbol: DDX54
• Synonyms (NCBI Gene): DP97
• Chromosome: 12
• Chromosome location: 12q24.13
• Summary: This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA second

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs148961522	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs764707570	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs777276705	C>T	Likely-pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT026599	hsa-miR-192-5p	Sequencing	20371350
MIRT031772	hsa-miR-16-5p	Proteomics	18668040
MIRT047683	hsa-miR-10a-5p	CLASH	23622248
MIRT042275	hsa-miR-484	CLASH	23622248
MIRT038067	hsa-miR-423-5p	CLASH	23622248
MIRT037544	hsa-miR-744-5p	CLASH	23622248
MIRT931166	hsa-miR-1237	CLIP-seq
MIRT931167	hsa-miR-1245b-3p	CLIP-seq
MIRT931168	hsa-miR-125a-3p	CLIP-seq
MIRT931169	hsa-miR-125a-5p	CLIP-seq
MIRT931170	hsa-miR-125b	CLIP-seq
MIRT931171	hsa-miR-1261	CLIP-seq
MIRT931172	hsa-miR-1266	CLIP-seq
MIRT931173	hsa-miR-128	CLIP-seq
MIRT931174	hsa-miR-1292	CLIP-seq
MIRT931175	hsa-miR-130a	CLIP-seq
MIRT931176	hsa-miR-130b	CLIP-seq
MIRT931177	hsa-miR-15a	CLIP-seq
MIRT931178	hsa-miR-15b	CLIP-seq
MIRT931179	hsa-miR-16	CLIP-seq
MIRT931180	hsa-miR-1825	CLIP-seq
MIRT931181	hsa-miR-1827	CLIP-seq
MIRT931182	hsa-miR-1912	CLIP-seq
MIRT931183	hsa-miR-195	CLIP-seq
MIRT931184	hsa-miR-219-1-3p	CLIP-seq
MIRT931185	hsa-miR-2277-3p	CLIP-seq
MIRT931186	hsa-miR-27a	CLIP-seq
MIRT931187	hsa-miR-27b	CLIP-seq
MIRT931188	hsa-miR-2861	CLIP-seq
MIRT931189	hsa-miR-301a	CLIP-seq
MIRT931190	hsa-miR-301b	CLIP-seq
MIRT931191	hsa-miR-3127-5p	CLIP-seq
MIRT931192	hsa-miR-3177-3p	CLIP-seq
MIRT931193	hsa-miR-3182	CLIP-seq
MIRT931194	hsa-miR-3184	CLIP-seq
MIRT931195	hsa-miR-3187-3p	CLIP-seq
MIRT931196	hsa-miR-361-3p	CLIP-seq
MIRT931197	hsa-miR-3665	CLIP-seq
MIRT931198	hsa-miR-3666	CLIP-seq
MIRT931199	hsa-miR-371b-3p	CLIP-seq
MIRT931200	hsa-miR-3918	CLIP-seq
MIRT931201	hsa-miR-3929	CLIP-seq
MIRT931202	hsa-miR-3934	CLIP-seq
MIRT931203	hsa-miR-3944-5p	CLIP-seq
MIRT931204	hsa-miR-424	CLIP-seq
MIRT931205	hsa-miR-4256	CLIP-seq
MIRT931206	hsa-miR-4265	CLIP-seq
MIRT931207	hsa-miR-4268	CLIP-seq
MIRT931208	hsa-miR-4269	CLIP-seq
MIRT931209	hsa-miR-4295	CLIP-seq
MIRT931210	hsa-miR-4296	CLIP-seq
MIRT931211	hsa-miR-4313	CLIP-seq
MIRT931212	hsa-miR-4319	CLIP-seq
MIRT931213	hsa-miR-4322	CLIP-seq
MIRT931214	hsa-miR-4417	CLIP-seq
MIRT931215	hsa-miR-4419b	CLIP-seq
MIRT931216	hsa-miR-4448	CLIP-seq
MIRT931217	hsa-miR-4478	CLIP-seq
MIRT931218	hsa-miR-4518	CLIP-seq
MIRT931219	hsa-miR-451b	CLIP-seq
MIRT931220	hsa-miR-4529-5p	CLIP-seq
MIRT931221	hsa-miR-4539	CLIP-seq
MIRT931222	hsa-miR-454	CLIP-seq
MIRT931223	hsa-miR-4640-5p	CLIP-seq
MIRT931224	hsa-miR-4643	CLIP-seq
MIRT931225	hsa-miR-4645-5p	CLIP-seq
MIRT931226	hsa-miR-4649-3p	CLIP-seq
MIRT931227	hsa-miR-4659a-5p	CLIP-seq
MIRT931228	hsa-miR-4659b-5p	CLIP-seq
MIRT931229	hsa-miR-4671-3p	CLIP-seq
MIRT931230	hsa-miR-4673	CLIP-seq
MIRT931231	hsa-miR-4681	CLIP-seq
MIRT931232	hsa-miR-4682	CLIP-seq
MIRT931233	hsa-miR-4688	CLIP-seq
MIRT931234	hsa-miR-4717-3p	CLIP-seq
MIRT931235	hsa-miR-4722-3p	CLIP-seq
MIRT931236	hsa-miR-4726-5p	CLIP-seq
MIRT931237	hsa-miR-4753-5p	CLIP-seq
MIRT931238	hsa-miR-4755-3p	CLIP-seq
MIRT931239	hsa-miR-4763-5p	CLIP-seq
MIRT931240	hsa-miR-4769-3p	CLIP-seq
MIRT931241	hsa-miR-4802-3p	CLIP-seq
MIRT931242	hsa-miR-497	CLIP-seq
MIRT931243	hsa-miR-5096	CLIP-seq
MIRT931244	hsa-miR-510	CLIP-seq
MIRT931245	hsa-miR-512-3p	CLIP-seq
MIRT931246	hsa-miR-513a-5p	CLIP-seq
MIRT931247	hsa-miR-542-3p	CLIP-seq
MIRT931248	hsa-miR-544b	CLIP-seq
MIRT931249	hsa-miR-571	CLIP-seq
MIRT931250	hsa-miR-646	CLIP-seq
MIRT931251	hsa-miR-657	CLIP-seq
MIRT931252	hsa-miR-663b	CLIP-seq
MIRT931253	hsa-miR-671-5p	CLIP-seq
MIRT931254	hsa-miR-759	CLIP-seq
MIRT931255	hsa-miR-760	CLIP-seq
MIRT931256	hsa-miR-938	CLIP-seq
MIRT931257	hsa-miR-1178	CLIP-seq
MIRT931258	hsa-miR-1208	CLIP-seq
MIRT931167	hsa-miR-1245b-3p	CLIP-seq
MIRT931173	hsa-miR-128	CLIP-seq
MIRT931174	hsa-miR-1292	CLIP-seq
MIRT931259	hsa-miR-1972	CLIP-seq
MIRT931260	hsa-miR-2116	CLIP-seq
MIRT931186	hsa-miR-27a	CLIP-seq
MIRT931187	hsa-miR-27b	CLIP-seq
MIRT931261	hsa-miR-31	CLIP-seq
MIRT931192	hsa-miR-3177-3p	CLIP-seq
MIRT931262	hsa-miR-346	CLIP-seq
MIRT931263	hsa-miR-3611	CLIP-seq
MIRT931264	hsa-miR-3688-5p	CLIP-seq
MIRT931207	hsa-miR-4268	CLIP-seq
MIRT931208	hsa-miR-4269	CLIP-seq
MIRT931265	hsa-miR-4288	CLIP-seq
MIRT931216	hsa-miR-4448	CLIP-seq
MIRT931223	hsa-miR-4640-5p	CLIP-seq
MIRT931225	hsa-miR-4645-5p	CLIP-seq
MIRT931230	hsa-miR-4673	CLIP-seq
MIRT931266	hsa-miR-4677-5p	CLIP-seq
MIRT931231	hsa-miR-4681	CLIP-seq
MIRT931236	hsa-miR-4726-5p	CLIP-seq
MIRT931238	hsa-miR-4755-3p	CLIP-seq
MIRT931267	hsa-miR-493	CLIP-seq
MIRT931268	hsa-miR-503	CLIP-seq
MIRT931243	hsa-miR-5096	CLIP-seq
MIRT931246	hsa-miR-513a-5p	CLIP-seq
MIRT931269	hsa-miR-632	CLIP-seq
MIRT931270	hsa-miR-767-3p	CLIP-seq
MIRT1975557	hsa-miR-1238	CLIP-seq
MIRT931168	hsa-miR-125a-3p	CLIP-seq
MIRT1975558	hsa-miR-1468	CLIP-seq
MIRT931194	hsa-miR-3184	CLIP-seq
MIRT1975559	hsa-miR-4732-3p	CLIP-seq
MIRT1975560	hsa-miR-642b	CLIP-seq
MIRT2211063	hsa-miR-1205	CLIP-seq
MIRT931180	hsa-miR-1825	CLIP-seq
MIRT2211064	hsa-miR-1909	CLIP-seq
MIRT2211065	hsa-miR-3120-5p	CLIP-seq
MIRT2211066	hsa-miR-3689a-3p	CLIP-seq
MIRT2211067	hsa-miR-3689c	CLIP-seq
MIRT931199	hsa-miR-371b-3p	CLIP-seq
MIRT931200	hsa-miR-3918	CLIP-seq
MIRT931201	hsa-miR-3929	CLIP-seq
MIRT931208	hsa-miR-4269	CLIP-seq
MIRT931215	hsa-miR-4419b	CLIP-seq
MIRT2211068	hsa-miR-4426	CLIP-seq
MIRT2211069	hsa-miR-4446-3p	CLIP-seq
MIRT2211070	hsa-miR-4447	CLIP-seq
MIRT2211071	hsa-miR-4472	CLIP-seq
MIRT931217	hsa-miR-4478	CLIP-seq
MIRT2211072	hsa-miR-4492	CLIP-seq
MIRT2211073	hsa-miR-4498	CLIP-seq
MIRT931219	hsa-miR-451b	CLIP-seq
MIRT931223	hsa-miR-4640-5p	CLIP-seq
MIRT931225	hsa-miR-4645-5p	CLIP-seq
MIRT2211074	hsa-miR-4647	CLIP-seq
MIRT2211075	hsa-miR-4662b	CLIP-seq
MIRT931230	hsa-miR-4673	CLIP-seq
MIRT2211076	hsa-miR-4675	CLIP-seq
MIRT2211077	hsa-miR-4721	CLIP-seq
MIRT931236	hsa-miR-4726-5p	CLIP-seq
MIRT2211078	hsa-miR-4728-5p	CLIP-seq
MIRT2211079	hsa-miR-4741	CLIP-seq
MIRT2211080	hsa-miR-4747-5p	CLIP-seq
MIRT931238	hsa-miR-4755-3p	CLIP-seq
MIRT2211081	hsa-miR-550a	CLIP-seq
MIRT2211082	hsa-miR-593	CLIP-seq
MIRT2211083	hsa-miR-762	CLIP-seq
MIRT931168	hsa-miR-125a-3p	CLIP-seq
MIRT2448132	hsa-miR-4522	CLIP-seq
MIRT2448133	hsa-miR-4710	CLIP-seq
MIRT2448134	hsa-miR-4727-5p	CLIP-seq
MIRT931238	hsa-miR-4755-3p	CLIP-seq
MIRT931240	hsa-miR-4769-3p	CLIP-seq
MIRT931166	hsa-miR-1237	CLIP-seq
MIRT931167	hsa-miR-1245b-3p	CLIP-seq
MIRT2514941	hsa-miR-1976	CLIP-seq
MIRT931186	hsa-miR-27a	CLIP-seq
MIRT931187	hsa-miR-27b	CLIP-seq
MIRT931193	hsa-miR-3182	CLIP-seq
MIRT931195	hsa-miR-3187-3p	CLIP-seq
MIRT931207	hsa-miR-4268	CLIP-seq
MIRT931216	hsa-miR-4448	CLIP-seq
MIRT931220	hsa-miR-4529-5p	CLIP-seq
MIRT931243	hsa-miR-5096	CLIP-seq
MIRT931246	hsa-miR-513a-5p	CLIP-seq
MIRT931252	hsa-miR-663b	CLIP-seq
MIRT931256	hsa-miR-938	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003714	Function	Transcription corepressor activity	IDA	12466272
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IDA	12466272
GO:0003724	Function	RNA helicase activity	IEA
GO:0004386	Function	Helicase activity	IEA
GO:0005102	Function	Signaling receptor binding	IDA	12466272
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	12466272
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IBA
GO:0005730	Component	Nucleolus	IDA	12466272
GO:0005730	Component	Nucleolus	IEA
GO:0005794	Component	Golgi apparatus	IDA
GO:0006364	Process	RRNA processing	IBA
GO:0006396	Process	RNA processing	IDA	12466272
GO:0006396	Process	RNA processing	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016070	Process	RNA metabolic process	IDA	12466272
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030331	Function	Nuclear estrogen receptor binding	IDA	12466272
GO:0030520	Process	Estrogen receptor signaling pathway	TAS	12466272
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA

Other IDs

• MIM: 611665
• HGNC: 20084
• e!Ensembl: ENSG00000123064

Protein

• UniProt ID: Q8TDD1
• Protein name: ATP-dependent RNA helicase DDX54 (EC 3.6.4.13) (ATP-dependent RNA helicase DP97) (DEAD box RNA helicase 97 kDa) (DEAD box protein 54)
• Protein function: Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors.
• PDB: 8FKT, 8FKU, 8FKV, 8FKW, 8FKX, 8FKY
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	120 → 288	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	322 → 433	Helicase conserved C-terminal domain	Family
  PF08147	DBP10CT	714 → 774	DBP10CT (NUC160) domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the fallopian tube, cervix and uterus. Also expressed in the brain. {ECO:0000269|PubMed:31256877}.
• Sequence:

  MAADKGPAAGPRSRAAMAQWRKKKGLRKRRGAASQARGSDSEDGEFEIQAEDDARARKLG
  PGRPLPTFPTSECTSDVEPDTREMVRAQNKKKKKSGGFQSMGLSYPVFKGIMKKGYKVPT
  PIQRKTIPVILDGKDVVAMARTGSGKTACFLLPMFERLKTHSAQTGARALILSPTRELAL
  QTLKFTKELGKFTGLKTALILGGDRMEDQFAALHENPDIIIATPGRLVHVAVEMSLKLQS
  VEYVVFDEADRLFEMGFAEQLQEIIARLPGGHQTVLFSATLPKLLVEFARAGLTEPVLIR
  LDVDTKLNEQLKTSFFLVREDTKAAVLLHLLHNVVRPQDQTVVFVATKHHAEYLTELLTT
  QRVSCAHIYSALDPTARKINLAKFTLGKCSTLIVTDLAARGLDIPLLDNVINYSFPAKGK
  LFLHRVGRVARAGRSGTAYSLVAPDEIPYLLDLHLFLGRSLTLARPLKEPSGVAGVDGML
  GRVPQSVVDEEDSGLQSTLEASLELRGLARVADNAQQQYVRSRPAPSPESIKRAKEMDLV
  GLGLHPLFSSRFEEEELQRLRLVDSIKNYRSRATIFEINASSRDLCSQVMRAKRQKDRKA
  IARFQQGQQGRQEQQEGPVGPAPSRPALQEKQPEKEEEEEAGESVEDIFSEVVGRKRQRS
  GPNRGAKRRREEARQRDQEFYIPYRPKDFDSERGLSISGEGGAFEQQAAGAVLDLMGDEA
  QNLTRGRQQLKWDRKKKRFVGQSGQEDKKKIKTESGRYISSSYKRDLYQKWKQKQKIDDR
  DSDEEGASDRRGPERRGGKRDRGQGASRPHAPGTPAGRVRPELKTKQQILKQRRRAQKLH
  FLQRGGLKQLSARNRRRVQELQQGAFGRGARSKKGKMRKRM

• Sequence length: 881

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Intellectual disability	Likely pathogenic	rs777276705, rs764707570, rs774035439	RCV000853109 RCV000853107 RCV000853108	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay	Likely pathogenic	rs777276705, rs764707570, rs774035439	RCV000853109 RCV000853107 RCV000853108	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorders	Likely pathogenic	rs777276705, rs764707570, rs774035439	RCV001261681 RCV001261679 RCV001261680	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizure	Likely pathogenic	rs764707570	RCV000853107	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HYPOPLASIA OF KIDNEY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DDX54-related disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DDX54-related Neurodevelopment Syndrome	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DDX54-related Neurodevelopmental Disorder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple renal cysts	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYCYSTIC OVARY SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Reduced renal corticomedullary differentiation	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Renal hypoplasia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Breast Carcinoma	Breast Carcinoma	BEFREE	12466272		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	CTD_human_DG	19233941		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of breast	Breast Cancer	BEFREE	12466272		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	CTD_human_DG	19233941		★☆☆☆☆ Found in Text Mining only
Polycystic Ovary Syndrome	Polycystic Ovary Syndrome	CTD_human_DG	21411543		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sclerocystic Ovaries	Sclerocystic Ovaries	CTD_human_DG	21411543		★☆☆☆☆ Found in Text Mining only