NOP56 (NOP56 ribonucleoprotein)

Gene

• Entrez ID: 10528
• Gene name: NOP56 ribonucleoprotein
• Gene symbol: NOP56
• Synonyms (NCBI Gene): NOL5A, SCA36
• Chromosome: 20
• Chromosome location: 20p13
• Summary: Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is simi

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT030362	hsa-miR-24-3p	Microarray	19748357
MIRT049889	hsa-miR-31-5p	CLASH	23622248
MIRT1189335	hsa-miR-1257	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT1189337	hsa-miR-2110	CLIP-seq
MIRT1189338	hsa-miR-3150a-3p	CLIP-seq
MIRT1189339	hsa-miR-3153	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT1189341	hsa-miR-3611	CLIP-seq
MIRT1189342	hsa-miR-4271	CLIP-seq
MIRT1189343	hsa-miR-4668-5p	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT1189345	hsa-miR-4725-3p	CLIP-seq
MIRT1189346	hsa-miR-581	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq
MIRT2283857	hsa-miR-1224-3p	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT2283858	hsa-miR-3123	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT2283859	hsa-miR-3189-5p	CLIP-seq
MIRT2283860	hsa-miR-3919	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT2283861	hsa-miR-4758-3p	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq
MIRT2283857	hsa-miR-1224-3p	CLIP-seq
MIRT1189336	hsa-miR-1587	CLIP-seq
MIRT2283858	hsa-miR-3123	CLIP-seq
MIRT1189340	hsa-miR-3189-3p	CLIP-seq
MIRT2283859	hsa-miR-3189-5p	CLIP-seq
MIRT2283860	hsa-miR-3919	CLIP-seq
MIRT1189344	hsa-miR-4674	CLIP-seq
MIRT2283861	hsa-miR-4758-3p	CLIP-seq
MIRT1189347	hsa-miR-635	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001650	Component	Fibrillar center	IDA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	TAS	9372940
GO:0005515	Function	Protein binding	IPI	17636026, 30021884, 32296183, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	9372940
GO:0005732	Component	Sno(s)RNA-containing ribonucleoprotein complex	IDA	17636026
GO:0005737	Component	Cytoplasm	IEA
GO:0006364	Process	RRNA processing	TAS	9372940
GO:0016020	Component	Membrane	HDA	19946888
GO:0030515	Function	SnoRNA binding	IBA
GO:0030515	Function	SnoRNA binding	IDA	17636026
GO:0030515	Function	SnoRNA binding	IEA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IBA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IDA	39570315
GO:0031428	Component	Box C/D methylation guide snoRNP complex	IEA
GO:0031428	Component	Box C/D methylation guide snoRNP complex	NAS	17636026
GO:0032040	Component	Small-subunit processome	IBA
GO:0032040	Component	Small-subunit processome	IDA	34516797
GO:0032040	Component	Small-subunit processome	IEA
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042274	Process	Ribosomal small subunit biogenesis	IDA	34516797
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0070761	Component	Pre-snoRNP complex	IDA	17636026
GO:1990226	Function	Histone methyltransferase binding	IPI	17636026
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 614154
• HGNC: 15911
• e!Ensembl: ENSG00000101361

Protein

• UniProt ID: O00567
• Protein name: Nucleolar protein 56 (Nucleolar protein 5A)
• Protein function: Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs (PubMed:12777385, PubMed:15574333). Part of the small subunit (SSU) processome, first precurso
• PDB: 7MQ8, 7MQ9, 7MQA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08156	NOP5NT	5 → 70	NOP5NT (NUC127) domain	Domain
  PF01798	Nop	174 → 407	snoRNA binding domain, fibrillarin	Family

• Sequence:

  MVLLHVLFEHAVGYALLALKEVEEISLLQPQVEESVLNLGKFHSIVRLVAFCPFASSQVA
  LENANAVSEGVVHEDLRLLLETHLPSKKKKVLLGVGDPKIGAAIQEELGYNCQTGGVIAE
  ILRGVRLHFHNLVKGLTDLSACKAQLGLGHSYSRAKVKFNVNRVDNMIIQSISLLDQLDK
  DINTFSMRVREWYGYHFPELVKIINDNATYCRLAQFIGNRRELNEDKLEKLEELTMDGAK
  AKAILDASRSSMGMDISAIDLINIESFSSRVVSLSEYRQSLHTYLRSKMSQVAPSLSALI
  GEAVGARLIAHAGSLTNLAKYPASTVQILGAEKALFRALKTRGNTPKYGLIFHSTFIGRA
  AAKNKGRISRYLANKCSIASRIDCFSEVPTSVFGEKLREQVEERLSFYETGEIPRKNLDV
  MKEAMVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALALASSENSSSTPEECEEMSEKPK
  KKKKQKPQEVPQENGMEDPSISFSKPKKKKSFSKEELMSSDLEETAGSTSIPKRKKSTPK
  EETVNDPEEAGHRSGSKKKRKFSKEEPVSSGPEEAVGKSSSKKKKKFHKASQED

• Sequence length: 594

Pathways

KEGG:

Ribosome biogenesis in eukaryotes
Spinocerebellar ataxia

Reactome:

Major pathway of rRNA processing in the nucleolus and cytosol

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
Spinocerebellar ataxia type 36	Likely pathogenic; Pathogenic	rs1295942947, rs1555779353	RCV001849220 RCV000024102	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATAXIA, SPINOCEREBELLAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cerebellar ataxia	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Mild global developmental delay	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NOP56-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 36	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIAS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STOMACH NEOPLASMS	—	CTD	★★☆☆☆ 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	CTD_human_DG	27602772		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	30946360		★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	23146615, 26661328		★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	22492559	Associate	★☆☆☆☆ Found in Text Mining only
Ataxia, Spinocerebellar	Spinocerebellar Ataxia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atherosclerosis	Atherosclerosis	Pubtator	29685964	Associate	★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Burkitt Lymphoma	Burkitt`s Lymphoma	BEFREE	24013231		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33750838, 34257558	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	29099775	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Cerebellar Diseases	BEFREE	27862279, 28918022		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	20473941		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	20473941	Associate	★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fecal Incontinence	Bowel incontinence	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hereditary Diffuse Gastric Cancer	Gastric Cancer	CTD_human_DG	21364753		★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	30946360	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	CTD_human_DG	21364753		★☆☆☆☆ Found in Text Mining only
Mandibulofacial Dysostosis	Mandibulofacial dysostosis	Pubtator	12777385	Associate	★☆☆☆☆ Found in Text Mining only
Migraine Disorders	Migraine	HPO_DG			★☆☆☆☆ Found in Text Mining only
Motor neuron atrophy	Motor neuron atrophy	BEFREE	28918022		★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor Neuron Disease	BEFREE	23146615		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24013231		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	25476002		★☆☆☆☆ Found in Text Mining only
Neuromuscular Diseases	Neuromuscular disease	Pubtator	24269018	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	27862279		★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	BEFREE	26661328		★☆☆☆☆ Found in Text Mining only
Spinocerebellar ataxia 36	Spinocerebellar Ataxia	BEFREE	21683323, 22492559, 22744658, 24985895, 25476002, 25593102, 26661328, 28918022, 30610877		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar ataxia 36	Spinocerebellar Ataxia	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar ataxia 36	Spinocerebellar Ataxia	ORPHANET_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar ataxia 36	Spinocerebellar Ataxia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar Ataxia Type 1	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 2	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar ataxia type 36	Spinocerebellar Ataxia	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar Ataxia Type 4	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 5	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 6 (disorder)	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 7	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxias	Spinocerebellar ataxia	Pubtator	21683323, 40004498	Stimulate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar Ataxias	Spinocerebellar ataxia	Pubtator	22492559	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Stomach Neoplasms	Stomach Neoplasms	CTD_human_DG	21364753		★★☆☆☆ Found in Text Mining + Unknown/Other Associations