DHX16 (DEAH-box helicase 16)

Gene

• Entrez ID: 8449
• Gene name: DEAH-box helicase 16
• Gene symbol: DHX16
• Synonyms (NCBI Gene): DBP2, DDX16, NMOAS, PRO2014, PRP8, PRPF2, Prp2
• Chromosome: 6
• Chromosome location: 6p21.33
• Summary: 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 secondary structure such as translation initiation, nuclear and m

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1582931640	C>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1582931908	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1582940678	A>T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1582953009	C>T	Likely-pathogenic, pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, 5 prime UTR variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT032275	hsa-let-7b-5p	Proteomics	18668040
MIRT049188	hsa-miR-92a-3p	CLASH	23622248
MIRT048294	hsa-miR-107	CLASH	23622248
MIRT440820	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT440820	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT935314	hsa-miR-1252	CLIP-seq
MIRT935315	hsa-miR-28-5p	CLIP-seq
MIRT935316	hsa-miR-3139	CLIP-seq
MIRT935317	hsa-miR-3154	CLIP-seq
MIRT935318	hsa-miR-708	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	29360106
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	IMP	20423332, 25296192
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0002376	Process	Immune system process	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IBA
GO:0003724	Function	RNA helicase activity	IEA
GO:0003724	Function	RNA helicase activity	TAS	9547260
GO:0004386	Function	Helicase activity	IBA
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	22365833, 25296192, 28514442, 33961781, 39251607
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	20423332, 25296192, 29360106
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	9547260
GO:0005654	Component	Nucleoplasm	IDA	20423332
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IDA	25296192
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005737	Component	Cytoplasm	IDA	35263596
GO:0005737	Component	Cytoplasm	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0008186	Function	ATP-dependent activity, acting on RNA	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	9547260
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0038187	Function	Pattern recognition receptor activity	IDA	35263596
GO:0043130	Function	Ubiquitin binding	IDA	35263596
GO:0045087	Process	Innate immune response	IEA
GO:0060090	Function	Molecular adaptor activity	IDA	35263596
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	29360106
GO:0140374	Process	Antiviral innate immune response	IDA	28469175, 35263596
GO:0140374	Process	Antiviral innate immune response	IDA	35263596
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 603405
• HGNC: 2739
• e!Ensembl: ENSG00000204560

Protein

• UniProt ID: O60231
• Protein name: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.4.13) (ATP-dependent RNA helicase #3) (DEAH-box protein 16)
• Protein function: Required for pre-mRNA splicing as a component of the spliceosome (PubMed:20423332, PubMed:20841358, PubMed:25296192, PubMed:29360106). Contributes to pre-mRNA splicing after spliceosome formation and prior to the first transesterification reacti
• PDB: 5Z56, 5Z57, 5Z58, 6FF7, 7DVQ, 7QTT, 8CH6, 8I0R, 8I0S, 8I0T, 8I0U, 8I0V
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	402 → 562	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	591 → 730	Helicase conserved C-terminal domain	Family
  PF04408	HA2	792 → 937	Helicase associated domain (HA2)	Domain
  PF07717	OB_NTP_bind	939 → 1015	Oligonucleotide/oligosaccharide-binding (OB)-fold	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the spleen, thyroid and testis. Also expressed in the brain and cerebellum. {ECO:0000269|PubMed:31256877}.
• Sequence:

  MATPAGLERWVQDELHSVLGLSERHVAQFLIGTAQRCTSAEEFVQRLRDTDTLDLSGPAR
  DFALRLWNKVPRKAVVEKPARAAEREARALLEKNRSYRLLEDSEESSEETVSRAGSSLQK
  KRKKRKHLRKKREEEEEEEASEKGKKKTGGSKQQTEKPESEDEWERTERERLQDLEERDA
  FAERVRQRDKDRTRNVLERSDKKAYEEAQKRLKMAEEDRKAMVPELRKKSRREYLAKRER
  EKLEDLEAELADEEFLFGDVELSRHERQELKYKRRVRDLAREYRAAGEQEKLEATNRYHM
  PKETRGQPARAVDLVEEESGAPGEEQRRWEEARLGAASLKFGARDAASQEPKYQLVLEEE
  ETIEFVRATQLQGDEEPSAPPTSTQAQQKESIQAVRRSLPVFPFREELLAAIANHQVLII
  EGETGSGKTTQIPQYLFEEGYTNKGMKIACTQPRRVAAMSVAARVAREMGVKLGNEVGYS
  IRFEDCTSERTVLRYMTDGMLLREFLSEPDLASYSVVMVDEAHERTLHTDILFGLIKDVA
  RFRPELKVLVASATMDTARFSTFFDDAPVFRIPGRRFPVDIFYTKAPEADYLEACVVSVL
  QIHVTQPPGDILVFLTGQEEIEAACEMLQDRCRRLGSKIRELLVLPIYANLPSDMQARIF
  QPTPPGARKVVVATNIAETSLTIEGIIYVLDPGFCKQKSYNPRTGMESLTVTPCSKASAN
  QRAGRAGRVAAGKCFRLYTAWAYQHELEETTVPEIQRTSLGNVVLLLKSLGIHDLMHFDF
  LDPPPYETLLLALEQLYALGALNHLGELTTSGRKMAELPVDPMLSKMILASEKYSCSEEI
  LTVAAMLSVNNSIFYRPKDKVVHADNARVNFFLPGGDHLVLLNVYTQWAESGYSSQWCYE
  NFVQFRSMRRARDVREQLEGLLERVEVGLSSCQGDYIRVRKAITAGYFYHTARLTRSGYR
  TVKQQQTVFIHPNSSLFEQQPRWLLYHELVLTTKEFMRQVLEIESSWLLEVAPHYYKAKE
  LEDPHAKKMPKKIGKTREELG

• Sequence length: 1041

Pathways

KEGG:

Spliceosome

Reactome:

mRNA Splicing - Major Pathway

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
Enlarged kidney	Likely pathogenic; Pathogenic	rs1582931640	RCV000853103	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Pathogenic; Likely pathogenic	rs1582931908, rs1582953009	RCV000853105 RCV000853104	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Multiple renal cysts	Likely pathogenic; Pathogenic	rs1582931640	RCV000853103	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay	Likely pathogenic; Pathogenic	rs2127583475, rs1582931908, rs1582953009	RCV002274334 RCV000853105 RCV000853104	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorders	Likely pathogenic; Pathogenic	rs1582931640, rs1582931908, rs1582940678, rs1582953009	RCV001261675 RCV001261677 RCV001261674 RCV001261676	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuromuscular disease and ocular or auditory anomalies with or without seizures	Likely pathogenic; Pathogenic	rs2534379898, rs1582931640, rs1582931908, rs1582940678, rs1582953009	RCV003156152 RCV000991226 RCV000991228 RCV000991225 RCV000991227	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Reduced renal corticomedullary differentiation	Likely pathogenic; Pathogenic	rs1582931640	RCV000853103	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizure	Pathogenic	rs1582931908	RCV000853105	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DHX16-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIVENTRICULAR HETEROTOPIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	35627223	Associate	★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic lateral sclerosis	Pubtator	36163369	Associate	★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis 4, Juvenile	Amyotrophic lateral sclerosis	BEFREE	15106121		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	9547260	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	GWASDB_DG	23853074		★☆☆☆☆ Found in Text Mining only
Central Nervous System Diseases	Central nervous system disease	Pubtator	31256877	Associate	★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	BEFREE	18721734		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	36701139	Associate	★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	BEFREE	9259430		★☆☆☆☆ Found in Text Mining only
Diastrophic dysplasia	Diastrophic dysplasia	Pubtator	31256877	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Eye Abnormalities	Eye abnormalities	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	36163369	Associate	★☆☆☆☆ Found in Text Mining only
Gastric Antral Vascular Ectasia	Vascular ectasia	BEFREE	9259430		★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	21832969		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	31256877	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Juvenile amyotrophic lateral sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	15106121		★☆☆☆☆ Found in Text Mining only
Kidney Failure, Chronic	Kidney Failure	BEFREE	18721734		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	28304396	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	9259430		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	25965566, 30333215		★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome X	Metabolic Syndrome	BEFREE	28411202, 28640118		★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	36163369	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	17660530		★☆☆☆☆ Found in Text Mining only
Neuromuscular Diseases	Neuromuscular disease	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	34793589	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Peripheral nervous system disease	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	37559353	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	17317632, 17934474, 19098916, 26968627, 27072132		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa 33	Retinitis pigmentosa	Pubtator	27454487	Associate	★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	GWASDB_DG	17804836, 19503088		★☆☆☆☆ Found in Text Mining only
Sarcoma Ewing	Sarcoma	Pubtator	26450900	Associate	★☆☆☆☆ Found in Text Mining only
Spasms Infantile	Infantile spasms	Pubtator	40141454	Associate	★☆☆☆☆ Found in Text Mining only
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 1	Spinocerebellar Ataxia	BEFREE	24814856		★☆☆☆☆ Found in Text Mining only
Spondylocostal dysostosis autosomal recessive	Spondylocostal dysostosis	Pubtator	31256877	Associate	★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	11138345, 9259430		★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	21832969		★☆☆☆☆ Found in Text Mining only
Vitamin D Deficiency	Vitamin d deficiency	Pubtator	36701139	Associate	★☆☆☆☆ Found in Text Mining only
Werner Syndrome	Werner Syndrome	BEFREE	11138345		★☆☆☆☆ Found in Text Mining only
Werner Syndrome	Werner syndrome	Pubtator	20103915	Associate	★☆☆☆☆ Found in Text Mining only