DDX59 (DEAD-box helicase 59)

Gene

• Entrez ID: 83479
• Gene name: DEAD-box helicase 59
• Gene symbol: DDX59
• Synonyms (NCBI Gene): OFD5, ZNHIT5
• Chromosome: 1
• Chromosome location: 1q32.1

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587777067	A>C,T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, intron variant
rs773114666	A>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs886037652	C>T	Pathogenic	Non coding transcript variant, intron variant, coding sequence variant, missense variant
rs1571603072	ATT>-	Likely-pathogenic	Inframe deletion, coding sequence variant, non coding transcript variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2211140	hsa-miR-4729	CLIP-seq
MIRT2211141	hsa-miR-587	CLIP-seq
MIRT2448138	hsa-miR-1297	CLIP-seq
MIRT2448139	hsa-miR-26a	CLIP-seq
MIRT2448140	hsa-miR-26b	CLIP-seq
MIRT2448141	hsa-miR-4272	CLIP-seq
MIRT2448142	hsa-miR-4465	CLIP-seq
MIRT2448138	hsa-miR-1297	CLIP-seq
MIRT2448139	hsa-miR-26a	CLIP-seq
MIRT2448140	hsa-miR-26b	CLIP-seq
MIRT2448141	hsa-miR-4272	CLIP-seq
MIRT2448142	hsa-miR-4465	CLIP-seq
MIRT2448138	hsa-miR-1297	CLIP-seq
MIRT2448139	hsa-miR-26a	CLIP-seq
MIRT2448140	hsa-miR-26b	CLIP-seq
MIRT2448141	hsa-miR-4272	CLIP-seq
MIRT2448142	hsa-miR-4465	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:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IBA
GO:0003724	Function	RNA helicase activity	IEA
GO:0003729	Function	MRNA binding	IBA
GO:0004386	Function	Helicase activity	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 615464
• HGNC: 25360
• e!Ensembl: ENSG00000118197

Protein

• UniProt ID: Q5T1V6
• Protein name: Probable ATP-dependent RNA helicase DDX59 (EC 3.6.4.13) (DEAD box protein 59) (Zinc finger HIT domain-containing protein 5)
• PDB: 2YQP
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04438	zf-HIT	104 → 133	HIT zinc finger	Domain
  PF00270	DEAD	227 → 394	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	428 → 540	Helicase conserved C-terminal domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in fibroblasts (at protein level). {ECO:0000269|PubMed:23972372}.
• Sequence:

  MFVPRSLKIKRNANDDGKSCVAKIIKPDPEDLQLDKSRDVPVDAVATEAATIDRHISESC
  PFPSPGGQLAEVHSVSPEQGAKDSHPSEEPVKSFSKTQRWAEPGEPICVVCGRYGEYICD
  KTDEDVCSLECKAKHLLQVKEKEEKSKLSNPQKADSEPESPLNASYVYKEHPFILNLQED
  QIENLKQQLGILVQGQEVTRPIIDFEHCSLPEVLNHNLKKSGYEVPTPIQMQMIPVGLLG
  RDILASADTGSGKTAAFLLPVIMRALFESKTPSALILTPTRELAIQIERQAKELMSGLPR
  MKTVLLVGGLPLPPQLYRLQQHVKVIIATPGRLLDIIKQSSVELCGVKIVVVDEADTMLK
  MGFQQQVLDILENIPNDCQTILVSATIPTSIEQLASQLLHNPVRIITGEKNLPCANVRQI
  ILWVEDPAKKKKLFEILNDKKLFKPPVLVFVDCKLGADLLSEAVQKITGLKSISIHSEKS
  QIERKNILKGLLEGDYEVVVSTGVLGRGLDLISVRLVVNFDMPSSMDEYVHQIGRVGRLG
  QNGTAITFINNNSKRLFWDIAKRVKPTGSILPPQLLNSPYLHDQKRKEQQKDKQTQNDLV
  TGANLMDIIRKHDKSNSQK

• Sequence length: 619

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
Orofaciodigital syndrome V	Likely pathogenic; Pathogenic	rs546799731, rs769198531, rs1571603072, rs773114666, rs587777067	RCV001729972 RCV001807552 RCV000985116 RCV000986499 RCV000074347	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
DDX59-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME 5	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME TYPE 5	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	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
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	29133145		★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	29133145		★☆☆☆☆ Found in Text Mining only
Cleft Soft Palate	Cleft Soft Palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dental Enamel Hypoplasia	Dental Enamel Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ectopic accessory finger-like appendage	Ectopic accessory finger-like appendage	HPO_DG			★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	31111544		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	35113786	Associate	★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypodontia	Hypodontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy	Leukoencephalopathy	BEFREE	29127725		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	29133145		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	29127725		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Orofaciodigital syndrome 5	Orofaciodigital syndrome	GENOMICS_ENGLAND_DG	23972372, 28711741, 29127725, 30914295		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 5	Orofaciodigital syndrome	UNIPROT_DG	23972372		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 5	Orofaciodigital syndrome	ORPHANET_DG	23972372		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 5	Orofaciodigital syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 5	Orofaciodigital syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital Syndrome I	Orofaciodigital Syndrome	BEFREE	28711741		★☆☆☆☆ Found in Text Mining only
Orofaciodigital syndrome type 5	Orofaciodigital Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital Syndromes	Orofaciodigital syndrome	BEFREE	23972372, 28711741		★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	GENOMICS_ENGLAND_DG	23972372		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	23972372		★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, POSTAXIAL	Polydactyly	BEFREE	28711741		★☆☆☆☆ Found in Text Mining only
Postaxial foot polydactyly	Foot Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of Fallot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Uranostaphyloschisis	Uranostaphyloschisis	BEFREE	28711741		★☆☆☆☆ Found in Text Mining only