DDX56 (DEAD-box helicase 56)

Gene

• Entrez ID: 54606
• Gene name: DEAD-box helicase 56
• Gene symbol: DDX56
• Synonyms (NCBI Gene): DDX21, DDX26, NOH61
• Chromosome: 7
• Chromosome location: 7p13
• 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT025272	hsa-miR-34a-5p	Proteomics	21566225
MIRT025272	hsa-miR-34a-5p	Proteomics	21566225
MIRT049377	hsa-miR-92a-3p	CLASH	23622248
MIRT043777	hsa-miR-328-3p	CLASH	23622248
MIRT043450	hsa-miR-331-3p	CLASH	23622248
MIRT042629	hsa-miR-423-3p	CLASH	23622248
MIRT1975610	hsa-miR-1914	CLIP-seq
MIRT2211093	hsa-miR-1202	CLIP-seq
MIRT2211094	hsa-miR-1267	CLIP-seq
MIRT2211095	hsa-miR-28-5p	CLIP-seq
MIRT2211096	hsa-miR-31	CLIP-seq
MIRT2211097	hsa-miR-3139	CLIP-seq
MIRT2211098	hsa-miR-3194-5p	CLIP-seq
MIRT2211099	hsa-miR-3972	CLIP-seq
MIRT2211100	hsa-miR-4453	CLIP-seq
MIRT2211101	hsa-miR-4480	CLIP-seq
MIRT2211102	hsa-miR-4509	CLIP-seq
MIRT2211103	hsa-miR-4538	CLIP-seq
MIRT2211104	hsa-miR-4633-3p	CLIP-seq
MIRT2211105	hsa-miR-4652-3p	CLIP-seq
MIRT2211106	hsa-miR-4688	CLIP-seq
MIRT2211107	hsa-miR-4778-5p	CLIP-seq
MIRT2211108	hsa-miR-610	CLIP-seq
MIRT2211109	hsa-miR-708	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0002753	Process	Cytoplasmic pattern recognition receptor signaling pathway	IDA	8524823, 31340999
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674
GO:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IEA
GO:0003724	Function	RNA helicase activity	TAS	10749921
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	31340999
GO:0005634	Component	Nucleus	IEA
GO:0005730	Component	Nucleolus	IBA
GO:0005730	Component	Nucleolus	IDA	33109765
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	10749921
GO:0005829	Component	Cytosol	IDA	33109765
GO:0006364	Process	RRNA processing	IEA
GO:0006606	Process	Protein import into nucleus	IDA	31340999
GO:0010976	Process	Positive regulation of neuron projection development	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0032480	Process	Negative regulation of type I interferon production	IDA	31340999
GO:0035613	Function	RNA stem-loop binding	IDA	33109765
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0044830	Process	Host-mediated perturbation of viral RNA genome replication	IMP	33109765
GO:0051607	Process	Defense response to virus	IDA	33109765
GO:0140311	Function	Protein sequestering activity	IDA	31340999

Other IDs

• MIM: 608023
• HGNC: 18193
• e!Ensembl: ENSG00000136271

Protein

• UniProt ID: Q9NY93
• Protein name: Probable ATP-dependent RNA helicase DDX56 (EC 3.6.4.13) (ATP-dependent 61 kDa nucleolar RNA helicase) (DEAD box protein 21) (DEAD box protein 56)
• Protein function: Nucleolar RNA helicase that plays a role in various biological processes including innate immunity, ribosome biogenesis or nucleolus organization (PubMed:31340999, PubMed:33789112). Plays an essential role in maintaining nucleolar integrity in p
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	31 → 207	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	243 → 380	Helicase conserved C-terminal domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Detected in heart, brain, liver, pancreas, placenta and lung.
• Sequence:

  MEDSEALGFEHMGLDPRLLQAVTDLGWSRPTLIQEKAIPLALEGKDLLARARTGSGKTAA
  YAIPMLQLLLHRKATGPVVEQAVRGLVLVPTKELARQAQSMIQQLATYCARDVRVANVSA
  AEDSVSQRAVLMEKPDVVVGTPSRILSHLQQDSLKLRDSLELLVVDEADLLFSFGFEEEL
  KSLLCHLPRIYQAFLMSATFNEDVQALKELILHNPVTLKLQESQLPGPDQLQQFQVVCET
  EEDKFLLLYALLKLSLIRGKSLLFVNTLERSYRLRLFLEQFSIPTCVLNGELPLRSRCHI
  ISQFNQGFYDCVIATDAEVLGAPVKGKRRGRGPKGDKASDPEAGVARGIDFHHVSAVLNF
  DLPPTPEAYIHRAGRTARANNPGIVLTFVLPTEQFHLGKIEELLSGENRGPILLPYQFRM
  EEIEGFRYRCRDAMRSVTKQAIREARLKEIKEELLHSEKLKTYFEDNPRDLQLLRHDLPL
  HPAVVKPHLGHVPDYLVPPALRGLVRPHKKRKKLSSSCRKAKRAKSQNPLRSFKHKGKKF
  RPTAKPS

• Sequence length: 547

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CARDIOVASCULAR DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERLIPIDEMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anemia, Diamond-Blackfan	Anemia	BEFREE	29364875		★☆☆☆☆ Found in Text Mining only
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	29314290		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	29745862	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	25260534, 28790157, 30165191, 30417346		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	28790157, 38102665	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28842590	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	39866844	Associate	★☆☆☆☆ Found in Text Mining only
Colonic Diseases	Colonic disease	Pubtator	38102665	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	26311743, 31390121		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	26311743, 33328538, 37029300, 37904456, 37988222	Associate	★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	BEFREE	11074253		★☆☆☆☆ Found in Text Mining only
Gastric Antral Vascular Ectasia	Vascular ectasia	BEFREE	11074253		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	LHGDN	11593297		★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	25791297	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	16301996		★☆☆☆☆ Found in Text Mining only
Lung Diseases	Lung disease	Pubtator	38102665	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25260534, 28790157, 30165191, 30417346		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	18482004, 18829551, 23349811		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	30322617		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23353573, 25745998, 28757063, 29844128, 30165191, 30322617, 31351877		★☆☆☆☆ Found in Text Mining only
Mandibulofacial Dysostosis	Mandibulofacial Dysostosis	BEFREE	29364875		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	39713879	Stimulate	★☆☆☆☆ Found in Text Mining only
Muscular Atrophy Spinal	Spinal muscular atrophy	Pubtator	35440492	Associate	★☆☆☆☆ Found in Text Mining only
Myelodysplastic Syndromes	Myelodysplastic syndrome	Pubtator	31855738	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16818630, 25260534, 31390121		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	27198888		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	33754909	Associate	★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	18482004, 18829551, 23349811		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	23349811	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Arterial Hypertension	Pulmonary arterial hypertension	Pubtator	36072642	Associate	★☆☆☆☆ Found in Text Mining only
Scleroderma Systemic	Systemic sclerosis	Pubtator	37988222	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	27835882		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	27835882	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	30322617		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37072811	Associate	★☆☆☆☆ Found in Text Mining only
Testicular Neoplasms	Testicular Neoplasms	BEFREE	29869821		★☆☆☆☆ Found in Text Mining only