NOP56

protein-coding

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

Gene 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 similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]

Previous symbols:
  • NOL5A

MANE transcript

NM_006392.4

Inheritance

AD

ClinVar variants

P:1U:90B:22

Top phenotype

Spinocerebellar ataxia 36

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr20:2,652,593-2,658,393

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spinocerebellar ataxia type 36DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0013594

Submitter: Ambry Genetics

spinocerebellar ataxia type 36STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013594

Submitter: Labcorp Genetics (formerly Invitae)

spinocerebellar ataxia type 36SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0013594

Submitter: Orphanet

Clinical Genomic Database (CGD)

Spinocerebellar ataxia 36AD

Manifestation: Neurologic

Intervention: General

Rationale: 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

Refs: 21683323; 22744658; 22492559Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NOP56 variants in ClinVar

7 Conditions Cataloged
Inborn genetic diseasesTotal: 79
not providedTotal: 16
NOP56-related disorderTotal: 12
not specifiedTotal: 11
Spinocerebellar ataxia type 36Total: 2
Cerebellar ataxiaTotal: 1
Mild global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006392.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
8
clinvar
4
clinvar
14
missense
87
clinvar
8
clinvar
1
clinvar
96
nonsense
2
clinvar
1
clinvar
3
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total0190175113

Highest pathogenic variant AF is 0.000025402096

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006392.4RefSeqNP_006383.212MANE Select
ENST00000329276.10EnsemblENSP00000370589.312MANE Select
ENST00000415272.2EnsemblENSP00000403199.16Standard
ENST00000445139.1EnsemblENSP00000388497.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
nop56Danio rerio

Structure: anatomical system

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ribosome biogenesis in eukaryotes - Homo sapiens (human)
  • rRNA processing
  • Metabolism of proteins
  • Metabolism of RNA
  • Chaperonin-mediated protein folding

Biological Process

  • rRNA processing

Molecular Function

  • RNA binding
  • protein binding
  • snoRNA binding
  • cadherin binding
  • histone methyltransferase binding

Cellular Component

  • fibrillar center
  • nucleoplasm
  • nucleolus
  • small nucleolar ribonucleoprotein complex
  • cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000329276
Coding exons
12
Length
6249
Individuals with no LoFs
125726
Homozygous LoFs
0
Heterozygous LoFs
22
Defined
125748
p
0.0000875
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6052993300.9060.00001923875
Missense (PolyPhen)5994.5280.624161075
Synonymous-0.9951421281.110.000007161158
Loss of Function3.99629.30.2050.00000197323

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000660.000062rare
Latino/Admixed American0.0000590.000058rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000540.000054rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000120.00012rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.377

Intolerance Scores

LoFtool
0.285
RVIS EVS
-0.44
RVIS percentile EVS
24.53

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.785

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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