NOP56 NOP56 ribonucleoprotein [Homo sapiens (human)] - Gene

Summary

Official Symbol: NOP56provided by HGNC
Official Full Name: NOP56 ribonucleoproteinprovided by HGNC
Primary source: HGNC:HGNC:15911
See related: Ensembl:ENSG00000101361 MIM:614154; AllianceGenome:HGNC:15911
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NOL5A; SCA36
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]
Expression: Ubiquitous expression in lymph node (RPKM 34.3), appendix (RPKM 31.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p13

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (2652632..2658393)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (2683093..2688860)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (2633278..2639039)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hexanucleotide repeat expansion in SCA36 reduces the expression of genes involved in ribosome biosynthesis and protein translation.
Title: Hexanucleotide repeat expansion in SCA36 reduces the expression of genes involved in ribosome biosynthesis and protein translation.
Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
Title: Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
The roles of NOP56 in cancer and SCA36.
Title: The roles of NOP56 in cancer and SCA36.
A PRC2-independent function for EZH2 in regulating rRNA 2'-O methylation and IRES-dependent translation.
Title: A PRC2-independent function for EZH2 in regulating rRNA 2'-O methylation and IRES-dependent translation.
Hexanucleotide Repeat Expansions in c9FTD/ALS and SCA36 Confer Selective Patterns of Neurodegeneration In Vivo.
Title: Hexanucleotide Repeat Expansions in c9FTD/ALS and SCA36 Confer Selective Patterns of Neurodegeneration In Vivo.
[Effect of piRNA NU13 in regulating biological behaviors of human Wilms tumor cells in vitro].
Title: [Effect of piRNA NU13 in regulating biological behaviors of human Wilms tumor cells in vitro].
This is the first report on the clinical aspect of ribosome biogenesis in pediatric BCP-ALL [B-cell precursor acute lymphoblastic leukemia ], and it shows that overexpression of CMYC and C/D box nucleoproteins FBL and NOP56 is an antecedent event in patients who subsequently relapse
Title: Analysis of the rRNA methylation complex components in pediatric B-cell precursor acute lymphoblastic leukemia: A pilot study.
Excess snoRNP core proteins prevent further production of NOP56 and instead trigger the generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway.
Title: Box C/D snoRNP Autoregulation by a cis-Acting snoRNA in the NOP56 Pre-mRNA.
Genetic and clinical analysis of spinocerebellar ataxia type 36 in Mainland China, with its causative mutation as a hexanucleotide GGCCTG repeat expansion in intron 1 of the NOP56 gene, has been described.
Title: Genetic and clinical analysis of spinocerebellar ataxia type 36 in Mainland China.
Studies indicate that the causative mutation for spinocerebellar ataxias SCA36, namely intronic hexanucleotide GGCCTG expansion in NOP56 gene, has been identified.
Title: [Recent advances in clinical and genetic research of spinocerebellar ataxia type 36].

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spinocerebellar ataxia type 36 MedGen: C3472711 OMIM: 614153 GeneReviews: Hereditary Ataxia Overview, Spinocerebellar Ataxia Type 36	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G07287 (e-PCR)
- UniSTS:80654

D20S559E (e-PCR)
- UniSTS:59939

WI-16193 (e-PCR)
- UniSTS:9520

G54023 (e-PCR)
- UniSTS:109405

MARC_6809-6810:992007497:1 (e-PCR)
- UniSTS:231277

WI-18557 (e-PCR)
- UniSTS:24962

RH74 (e-PCR)
- UniSTS:19965

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables histone methyltransferase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables snoRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables snoRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in rRNA processing	TAS Traceable Author Statement more info	PubMed
involved_in ribosomal small subunit biogenesis	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of box C/D methylation guide snoRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of box C/D methylation guide snoRNP complex	NAS Non-traceable Author Statement more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in nucleolus	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of pre-snoRNP complex	IDA Inferred from Direct Assay more info	PubMed
part_of small-subunit processome	IBA Inferred from Biological aspect of Ancestor more info
part_of small-subunit processome	IDA Inferred from Direct Assay more info	PubMed
part_of sno(s)RNA-containing ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleolar protein 56

Names: NOP56 ribonucleoprotein homolog; nucleolar protein 5A (56kDa with KKE/D repeat)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_032136.1 RefSeqGene

Range

5101..10862

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006392.4 → NP_006383.2 nucleolar protein 56

See identical proteins and their annotated locations for NP_006383.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the protein-coding transcript.

Source sequence(s)

BC035369, BC104793, DA805367

Consensus CDS

CCDS13030.1

UniProtKB/Swiss-Prot

O00567, Q2M3T6, Q9NQ05

UniProtKB/TrEMBL

A8K9K6

Related

ENSP00000370589.3, ENST00000329276.10

Conserved Domains (2) summary

COG1498
Location:48 → 412

SIK1; RNA processing factor Prp31, contains Nop domain [Translation, ribosomal structure and biogenesis]

pfam08156
Location:5 → 70

NOP5NT; NOP5NT (NUC127) domain

RNA

NR_027700.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The extra sequence introduces an in-frame stop codon that makes this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK292721, BC004937, BC104791, CV338938
NR_145428.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate internal exon compared to variant 1. The extra sequence introduces an in-frame stop codon that makes this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC035369, BC104793, CN371696, DA805367