Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	9416
Gene name	DEAD-box helicase 23
Gene symbol	DDX23
Synonyms (NCBI Gene)	PRPF28SNRNP100U5-100KU5-100KDprp28
Chromosome	12
Chromosome location	12q13.12
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

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miRTarBase ID	miRNA	Experiments	Reference
MIRT050352	hsa-miR-25-3p	CLASH	23622248
MIRT048936	hsa-miR-92a-3p	CLASH	23622248
MIRT045430	hsa-miR-149-5p	CLASH	23622248
MIRT044348	hsa-miR-106b-5p	CLASH	23622248
MIRT044059	hsa-miR-361-5p	CLASH	23622248
MIRT039941	hsa-miR-615-3p	CLASH	23622248
MIRT037450	hsa-miR-744-5p	CLASH	23622248
MIRT036357	hsa-miR-1229-3p	CLASH	23622248
MIRT736412	hsa-miR-21-3p	Luciferase reporter assayNorthern blotting	33311703
MIRT930271	hsa-miR-103b	CLIP-seq
MIRT930272	hsa-miR-1227	CLIP-seq
MIRT930273	hsa-miR-1301	CLIP-seq
MIRT930274	hsa-miR-1322	CLIP-seq
MIRT930275	hsa-miR-1913	CLIP-seq
MIRT930276	hsa-miR-217	CLIP-seq
MIRT930277	hsa-miR-2278	CLIP-seq
MIRT930278	hsa-miR-3064-5p	CLIP-seq
MIRT930279	hsa-miR-3065-3p	CLIP-seq
MIRT930280	hsa-miR-3120-3p	CLIP-seq
MIRT930281	hsa-miR-3135	CLIP-seq
MIRT930282	hsa-miR-3150a-3p	CLIP-seq
MIRT930283	hsa-miR-3160-3p	CLIP-seq
MIRT930284	hsa-miR-3175	CLIP-seq
MIRT930285	hsa-miR-324-3p	CLIP-seq
MIRT930286	hsa-miR-3622b-5p	CLIP-seq
MIRT930287	hsa-miR-3908	CLIP-seq
MIRT930288	hsa-miR-3941	CLIP-seq
MIRT930289	hsa-miR-4293	CLIP-seq
MIRT930290	hsa-miR-4313	CLIP-seq
MIRT930291	hsa-miR-4323	CLIP-seq
MIRT930292	hsa-miR-4418	CLIP-seq
MIRT930293	hsa-miR-4436b-3p	CLIP-seq
MIRT930294	hsa-miR-4487	CLIP-seq
MIRT930295	hsa-miR-450b-5p	CLIP-seq
MIRT930296	hsa-miR-4650-5p	CLIP-seq
MIRT930297	hsa-miR-4652-3p	CLIP-seq
MIRT930298	hsa-miR-466	CLIP-seq
MIRT930299	hsa-miR-4667-5p	CLIP-seq
MIRT930300	hsa-miR-4672	CLIP-seq
MIRT930301	hsa-miR-4700-5p	CLIP-seq
MIRT930302	hsa-miR-4720-5p	CLIP-seq
MIRT930303	hsa-miR-4758-3p	CLIP-seq
MIRT930304	hsa-miR-4761-3p	CLIP-seq
MIRT930305	hsa-miR-4799-3p	CLIP-seq
MIRT930306	hsa-miR-491-3p	CLIP-seq
MIRT930307	hsa-miR-5047	CLIP-seq
MIRT930308	hsa-miR-507	CLIP-seq
MIRT930309	hsa-miR-509-3-5p	CLIP-seq
MIRT930310	hsa-miR-509-5p	CLIP-seq
MIRT930311	hsa-miR-512-3p	CLIP-seq
MIRT930312	hsa-miR-556-5p	CLIP-seq
MIRT930313	hsa-miR-557	CLIP-seq
MIRT930314	hsa-miR-558	CLIP-seq
MIRT930315	hsa-miR-596	CLIP-seq
MIRT930316	hsa-miR-604	CLIP-seq
MIRT930317	hsa-miR-622	CLIP-seq
MIRT930318	hsa-miR-637	CLIP-seq
MIRT930319	hsa-miR-647	CLIP-seq
MIRT930320	hsa-miR-892b	CLIP-seq
MIRT930321	hsa-miR-935	CLIP-seq
MIRT930322	hsa-miR-939	CLIP-seq
MIRT1975371	hsa-miR-1294	CLIP-seq
MIRT1975372	hsa-miR-2277-3p	CLIP-seq
MIRT1975373	hsa-miR-3120-5p	CLIP-seq
MIRT1975374	hsa-miR-3123	CLIP-seq
MIRT1975375	hsa-miR-3607-3p	CLIP-seq
MIRT1975376	hsa-miR-3657	CLIP-seq
MIRT1975377	hsa-miR-3686	CLIP-seq
MIRT930287	hsa-miR-3908	CLIP-seq
MIRT1975378	hsa-miR-3919	CLIP-seq
MIRT1975379	hsa-miR-3978	CLIP-seq
MIRT1975380	hsa-miR-4276	CLIP-seq
MIRT1975381	hsa-miR-4287	CLIP-seq
MIRT1975382	hsa-miR-4316	CLIP-seq
MIRT1975383	hsa-miR-4330	CLIP-seq
MIRT1975384	hsa-miR-4426	CLIP-seq
MIRT1975385	hsa-miR-4436b-5p	CLIP-seq
MIRT1975386	hsa-miR-4469	CLIP-seq
MIRT1975387	hsa-miR-4504	CLIP-seq
MIRT1975388	hsa-miR-4645-3p	CLIP-seq
MIRT1975389	hsa-miR-4647	CLIP-seq
MIRT1975390	hsa-miR-4662b	CLIP-seq
MIRT1975391	hsa-miR-4676-5p	CLIP-seq
MIRT1975392	hsa-miR-4685-3p	CLIP-seq
MIRT1975393	hsa-miR-4755-3p	CLIP-seq
MIRT1975394	hsa-miR-4756-3p	CLIP-seq
MIRT1975395	hsa-miR-4764-5p	CLIP-seq
MIRT1975396	hsa-miR-500a	CLIP-seq
MIRT1975397	hsa-miR-570	CLIP-seq
MIRT1975398	hsa-miR-575	CLIP-seq
MIRT1975399	hsa-miR-583	CLIP-seq
MIRT1975400	hsa-miR-619	CLIP-seq
MIRT1975401	hsa-miR-875-3p	CLIP-seq
MIRT1975402	hsa-miR-942	CLIP-seq
MIRT1975374	hsa-miR-3123	CLIP-seq
MIRT930287	hsa-miR-3908	CLIP-seq
MIRT1975378	hsa-miR-3919	CLIP-seq
MIRT1975380	hsa-miR-4276	CLIP-seq
MIRT1975383	hsa-miR-4330	CLIP-seq
MIRT1975384	hsa-miR-4426	CLIP-seq
MIRT1975389	hsa-miR-4647	CLIP-seq
MIRT1975390	hsa-miR-4662b	CLIP-seq
MIRT1975391	hsa-miR-4676-5p	CLIP-seq
MIRT1975394	hsa-miR-4756-3p	CLIP-seq
MIRT1975397	hsa-miR-570	CLIP-seq
MIRT1975398	hsa-miR-575	CLIP-seq
MIRT1975402	hsa-miR-942	CLIP-seq
MIRT1975373	hsa-miR-3120-5p	CLIP-seq
MIRT1975375	hsa-miR-3607-3p	CLIP-seq
MIRT1975377	hsa-miR-3686	CLIP-seq
MIRT1975385	hsa-miR-4436b-5p	CLIP-seq
MIRT1975388	hsa-miR-4645-3p	CLIP-seq
MIRT1975396	hsa-miR-500a	CLIP-seq
MIRT2679150	hsa-miR-1343	CLIP-seq
MIRT2679151	hsa-miR-1976	CLIP-seq
MIRT1975373	hsa-miR-3120-5p	CLIP-seq
MIRT1975375	hsa-miR-3607-3p	CLIP-seq
MIRT1975377	hsa-miR-3686	CLIP-seq
MIRT1975385	hsa-miR-4436b-5p	CLIP-seq
MIRT1975388	hsa-miR-4645-3p	CLIP-seq
MIRT1975393	hsa-miR-4755-3p	CLIP-seq
MIRT2679152	hsa-miR-486-3p	CLIP-seq
MIRT1975396	hsa-miR-500a	CLIP-seq

Show/Hide all (38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000354	Process	Cis assembly of pre-catalytic spliceosome	IC	9539711
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	9409622
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0000785	Component	Chromatin	IDA	28076779
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003724	Function	RNA helicase activity	TAS	9409622
GO:0003729	Function	MRNA binding	IBA
GO:0004386	Function	Helicase activity	IDA	9539711
GO:0005515	Function	Protein binding	IPI	9774689, 17332742, 20858735, 21044950, 26030138, 28514442, 33961781, 35271311
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	28076779
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005634	Component	Nucleus	TAS	9409622
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0005682	Component	U5 snRNP	IDA	9539711
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	9409622
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	9409622
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0062176	Process	R-loop processing	IDA	28076779
GO:0070062	Component	Extracellular exosome	HDA	19199708
GO:0071013	Component	Catalytic step 2 spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638

MIM	HGNC	e!Ensembl
612172	17347	ENSG00000174243

Q9BUQ8

Protein name

Probable ATP-dependent RNA helicase DDX23 (EC 3.6.4.13) (100 kDa U5 snRNP-specific protein) (DEAD box protein 23) (PRP28 homolog) (U5-100kD)

Protein function

Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation (PubMed:18425142). Independently of its spliceosome formation function, required for the suppression of incorrect R-loops forme

PDB

3JCR , 4NHO , 6AH0 , 6QW6 , 6QX9 , 8H6E , 8H6J , 8Q7W , 8Q7X , 8Q91 , 8QOZ , 8QP8 , 8QP9 , 8QPA , 8QPB , 8QPK , 8QXD , 8R08 , 8R09 , 8R0A , 8R0B , 8RC0 , 8RM5 , 8Y6O

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00270	DEAD	415 → 616	DEAD/DEAH box helicase	Domain
PF00271	Helicase_C	650 → 759	Helicase conserved C-terminal domain	Family

Sequence

MAGELADKKDRDASPSKEERKRSRTPDRERDRDRDRKSSPSKDRKRHRSRDRRRGGSRSR
SRSRSKSAERERRHKERERDKERDRNKKDRDRDKDGHRRDKDRKRSSLSPGRGKDFKSRK
DRDSKKDEEDEHGDKKPKAQPLSLEELLAKKKAEEEAEAKPKFLSKAEREAEALKRRQQE
VEERQRMLEEERKKRKQFQDLGRKMLEDPQERERRERRERMERETNGNEDEEGRQKIREE
KDKSKELHAIKERYLGGIKKRRRTRHLNDRKFVFEWDASEDTSIDYNPLYKERHQVQLLG
RGFIAGIDLKQQKREQSRFYGDLMEKRRTLEEKEQEEARLRKLRKKEAKQRWDDRHWSQK
KLDEMTDRDWRIFREDYSITTKGGKIPNPIRSWKDSSLPPHILEVIDKCGYKEPTPIQRQ
AIPIGLQNRDIIGVAETGSGKTAAFLIPLLVWITTLPKIDRIEESDQGPYAIILAPTREL
AQQIEEETIKFGKPLGIRTVAVIGGISREDQGFRLRMGCEIVIATPGRLIDVLENRYLVL
SRCTYVVLDEADRMIDMGFEPDVQKILEHMPVSNQKPDTDEAEDPEKMLANFESGKHKYR
QTVMFTATMPPAVERLARSYLRRPAVVYIGSAGKPHERVEQKVFLMSESEKRKKLLAILE
QGFDPPIIIFVNQKKGCDVLAKSLEKMGYNACTLHGGKGQEQREFALSNLKAGAKDILVA
TDVAGRGIDIQDVSMVVNYDMAKNIEDYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELK
QAILESPVSSCPPELANHPDAQHKPGTILTKKRREETIFA

Sequence length

820

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway mRNA Splicing - Minor Pathway

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)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Congenital bilateral perisylvian syndrome	Likely pathogenic	rs2498746301	RCV003445287	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic	rs2137480864	RCV002273289	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Abnormal facial shape	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOVASCULAR DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DDX23-related disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DDX23-related Neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Failure to thrive	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fetal growth restriction	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Motor delay	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER WITH VISUAL DEFECTS AND BRAIN ANOMALIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERISYLVIAN SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (10)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenoid Cystic Carcinoma	Adenocarcinoma	BEFREE	28076779		★★★★★ ★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	BEFREE	28076779		★★★★★ ★☆☆☆☆ Found in Text Mining only
Aplasia Cutis Congenita	Aplasia Cutis Congenita	BEFREE	28076779		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Adenoid Cystic	Adenoid cystic carcinoma	Pubtator	28076779	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	20121140	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	GWASCAT_DG	30595370		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	26121981		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myelodysplastic Syndromes	Myelodysplastic syndrome	Pubtator	31855738	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	28473661		★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor B-cell lymphoblastic leukemia	Lymphoblastic Leukemia	BEFREE	30315277		★★★★★ ★☆☆☆☆ Found in Text Mining only

DDX23 (DEAD-box helicase 23)