NOP56

NOP56 ribonucleoprotein, the group of U3 small nucleolar ribonucleoprotein|MicroRNA protein coding host genes|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 20:2652593-2658393

Previous symbols: [ "NOL5A" ]

Links

ENSG00000101361 ∙ NCBI:10528 ∙ OMIM:614154 ∙ HGNC:15911 ∙ Uniprot:O00567 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia type 36 (Definitive), mode of inheritance: AD
• spinocerebellar ataxia type 36 (Supportive), mode of inheritance: AD
• spinocerebellar ataxia type 36 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 36	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	21683323; 22744658; 22492559

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NOP56 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP56 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense			40	1	4	45
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	40	7	7

Variants in NOP56

This is a list of pathogenic ClinVar variants found in the NOP56 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-2652657-C-T			Likely benign (Nov 01, 2024)
20-2652843-T-G		Inborn genetic diseases	Uncertain significance (Dec 11, 2024)
20-2652917-C-G		Inborn genetic diseases	Uncertain significance (Mar 08, 2025)
20-2653290-T-C		not specified	Benign (-)
20-2653342-C-T		Inborn genetic diseases	Uncertain significance (Jan 21, 2025)
20-2653358-A-C		Inborn genetic diseases	Uncertain significance (Jan 22, 2025)
20-2653360-G-C		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
20-2654416-G-A		Inborn genetic diseases	Uncertain significance (Feb 26, 2025)
20-2654477-T-C		Inborn genetic diseases	Uncertain significance (Oct 09, 2024)
20-2654511-C-T		NOP56-related disorder	Likely benign (Oct 28, 2019)
20-2654537-A-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2025)
20-2654566-A-G		not specified	Benign (-)
20-2654739-CTCT-C		NOP56-related disorder	Benign (May 01, 2024)
20-2654754-C-T		Inborn genetic diseases	Uncertain significance (May 31, 2023)
20-2654755-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
20-2654781-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2024)
20-2654830-G-C		Mild global developmental delay;Cerebellar ataxia	Uncertain significance (Jan 01, 2017)
20-2654858-T-C		NOP56-related disorder	Benign (Apr 08, 2019)
20-2654919-G-A		Inborn genetic diseases	Uncertain significance (Jul 21, 2021)
20-2654941-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
20-2655320-T-C		not specified	Likely benign (May 27, 2025)
20-2655361-G-T		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
20-2655369-A-G			Benign (Aug 01, 2024)
20-2655370-C-T			Likely benign (Oct 01, 2024)
20-2655390-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP56	protein_coding	protein_coding	ENST00000329276	12	6249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.621	0.379	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.605	299	330	0.906	0.0000192	3875
Missense in Polyphen		59	94.528	0.62416		1075
Synonymous	-0.995	142	128	1.11	0.00000716	1158
Loss of Function	3.99	6	29.3	0.205	0.00000197	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000121
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs. {ECO:0000269|PubMed:12777385, ECO:0000269|PubMed:15574333}.
• Disease: DISEASE: Spinocerebellar ataxia 36 (SCA36) [MIM:614153]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA36 is characterized by complicated clinical features, with ataxia as the first symptom, followed by characteristic late-onset involvement of the motor neuron system. Ataxic symptoms, such as gait and truncal instability, ataxic dysarthria, and uncoordinated limbs, start in late forties to fifties. Characteristically, affected individuals exhibit tongue atrophy with fasciculation. Progression of motor neuron involvement is typically limited to the tongue and main proximal skeletal muscles in both upper and lower extremities. {ECO:0000269|PubMed:21683323}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by large hexanucleotide CGCCTG repeat expansions within intron 1. These expansions induce RNA foci and sequester the RNA-binding protein SRSF2. In addition, the transcription of MIR1292, a microRNA gene located just 19 bp 3' of the GGCCTG repeat, is significantly decreased.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of proteins;Metabolism of RNA;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Protein folding;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.377

Intolerance Scores

• loftool: 0.285
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.990
• hipred: Y
• hipred_score: 0.831
• ghis: 0.625

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nop56

Zebrafish Information Network

• Gene name: nop56
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: rRNA processing
• Cellular component: fibrillar center;nucleoplasm;nucleolus;small nucleolar ribonucleoprotein complex;cytoplasm;membrane;box C/D snoRNP complex;small-subunit processome;pre-snoRNP complex
• Molecular function: RNA binding;protein binding;snoRNA binding;cadherin binding;histone methyltransferase binding