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NOP53 (ribosome biogenesis factor)

Written2008-10Tomohiko Maehama
Department of Biochemistry, Cell Biology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan

(Note : for Links provided by Atlas : click)

Identity

Other aliasGLTSCR2 (glioma tumor suppressor candidate region gene 2)
PICT-1
PICT1
p60
HGNC (Hugo) NOP53
LocusID (NCBI) 29997
Atlas_Id 40723
Location 19q13.33  [Link to chromosome band 19q13]
Location_base_pair Starts at 47745536 and ends at 47757066 bp from pter ( according to hg19-Feb_2009)  [Mapping NOP53.png]
Local_order Between D19S1160 and D19S1156
Fusion genes
(updated 2016)
DGAT1 (8q24.3) / GLTSCR2 (19q13.33)FAM120B (6q27) / GLTSCR2 (19q13.33)GLTSCR2 (19q13.33) / GLTSCR2 (19q13.33)
GLTSCR2 (19q13.33) / NACA (12q13.3)GLTSCR2 (19q13.33) / TMEM63A (1q42.12)TAF15 (17q12) / GLTSCR2 (19q13.33)

DNA/RNA

Description The GLTSCR2 gene comprises 13 exons resulting in a transcript of 1567 bases. The start codon is in the 1st exon; the stop codon is in the 13th exon. Northern blot analysis shows a 1.5-kb transcript.
Transcription mRNA: ubiquitously
Pseudogene Not known

Protein

Description 478 amino acids. GLTSCR2 protein contains a putative PEST sequence (PEST score: +7.23, aa: 279-332) and a potential nuclear localization signal (aa: 378-386).
Localisation Nucleolus
Function GLTSCR2 protein binds to PTEN tumor suppressor and regulates its stability in cells. Recent reports show the implication of GLTSCR2 in cell proliferation and apoptosis.
Homology GLTSCR2 orthologs can be found in metazoans. In addition, GLTSCR2 protein shares homology with yeast Nop53p which is involved in ribosome biogenesis.

Mutations

Note There are several synonymous and nonsynonymous SNPs reported for GLTSCR2 (S16R, Q169E, C325F, A383V, Q389R).

Implicated in

Note
  
Entity Cancer
Note A number of groups have proven that the 19q13.32 locus where GLTSCR2 gene locates is frequently altered in glioma and neuroblastoma; however, a tumor suppressor gene(s) specifically encoded in this region has yet to be identified and the implication of GLTSCR2 gene in these tumors remains controversial. Recent studies show aberrations in GLTSCR2 expression in glioblastoma and neuroblastoma.
  

Bibliography

Transcript map of the 3.7-Mb D19S112-D19S246 candidate tumor suppressor region on the long arm of chromosome 19.
Hartmann C, Johnk L, Kitange G, Wu Y, Ashworth LK, Jenkins RB, Louis DN.
Cancer Res. 2002 Jul 15;62(14):4100-8.
PMID 12124348
 
A screen of shRNAs targeting tumor suppressor genes to identify factors involved in A549 paclitaxel sensitivity.
Ji D, Deeds SL, Weinstein EJ.
Oncol Rep. 2007 Dec;18(6):1499-505.
PMID 17982636
 
Suppression of putative tumour suppressor gene GLTSCR2 expression in human glioblastomas.
Kim YJ, Cho YE, Kim YW, Kim JY, Lee S, Park JH.
J Pathol. 2008 Oct;216(2):218-24.
PMID 18729076
 
The tumour suppressor PTEN: involvement of a tumour suppressor candidate protein in PTEN turnover.
Maehama T, Okahara F, Kanaho Y.
Biochem Soc Trans. 2004 Apr;32(Pt 2):343-7. (Review)
PMID 15046605
 
Loss of heterozygosity at 19q13.3 is associated with locally aggressive neuroblastoma.
Mora J, Cheung NK, Chen L, Qin J, Gerald W.
Clin Cancer Res. 2001 May;7(5):1358-61.
PMID 11350906
 
Critical role of PICT-1, a tumor suppressor candidate, in phosphatidylinositol 3,4,5-trisphosphate signals and tumorigenic transformation.
Okahara F, Itoh K, Nakagawara A, Murakami M, Kanaho Y, Maehama T.
Mol Biol Cell. 2006 Nov;17(11):4888-95. Epub 2006 Sep 13.
PMID 16971513
 
A transcript map of the chromosome 19q-arm glioma tumor suppressor region.
Smith JS, Tachibana I, Pohl U, Lee HK, Thanarajasingam U, Portier BP, Ueki K, Ramaswamy S, Billings SJ, Mohrenweiser HW, Louis DN, Jenkins RB.
Genomics. 2000 Feb 15;64(1):44-50.
PMID 10708517
 
The putative tumor suppressor gene GLTSCR2 induces PTEN-modulated cell death.
Yim JH, Kim YJ, Ko JH, Cho YE, Kim SM, Kim JY, Lee S, Park JH.
Cell Death Differ. 2007 Nov;14(11):1872-9. Epub 2007 Jul 27.
PMID 17657248
 

Citation

This paper should be referenced as such :
Maehama, T
GLTSCR2 (glioma tumor suppressor candidate region gene 2)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(9):624-625.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/GLTSCR2ID40723ch19q13.html


External links

Nomenclature
HGNC (Hugo)NOP53   4333
Cards
AtlasGLTSCR2ID40723ch19q13
Entrez_Gene (NCBI)NOP53  29997  NOP53 ribosome biogenesis factor
AliasesGLTSCR2; PICT-1; PICT1
GeneCards (Weizmann)NOP53
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]  chr19:47745536-47757066 [Contig_View]  NOP53 [Vega]
TCGA cBioPortalNOP53
AceView (NCBI)NOP53
Genatlas (Paris)NOP53
WikiGenes29997
SOURCE (Princeton)NOP53
Genetics Home Reference (NIH)NOP53
Genomic and cartography
GoldenPath hg38 (UCSC)NOP53  -     chr19:47745536-47757066 +  19q13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NOP53  -     19q13.33   [Description]    (hg19-Feb_2009)
EnsemblNOP53 - 19q13.33 [CytoView hg19]  NOP53 - 19q13.33 [CytoView hg38]
Mapping of homologs : NCBINOP53 [Mapview hg19]  NOP53 [Mapview hg38]
OMIM605691   
Gene and transcription
Genbank (Entrez)AF161389 AF182076 AF296124 AI540063 AK024486
RefSeq transcript (Entrez)NM_015710
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NOP53
Cluster EST : UnigeneHs.421907 [ NCBI ]
CGAP (NCI)Hs.421907
Gene ExpressionNOP53 [ NCBI-GEO ]   NOP53 [ EBI - ARRAY_EXPRESS ]   NOP53 [ SEEK ]   NOP53 [ MEM ]
Gene Expression Viewer (FireBrowse)NOP53 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)29997
GTEX Portal (Tissue expression)NOP53
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NZM5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NZM5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NZM5
Splice isoforms : SwissVarQ9NZM5
PhosPhoSitePlusQ9NZM5
Domains : Interpro (EBI)Nop53/GLTSCR2   
Domain families : Pfam (Sanger)Nop53 (PF07767)   
Domain families : Pfam (NCBI)pfam07767   
Conserved Domain (NCBI)NOP53
DMDM Disease mutations29997
Blocks (Seattle)NOP53
SuperfamilyQ9NZM5
Peptide AtlasQ9NZM5
IPIIPI00024567   IPI00909733   IPI00908500   IPI00412788   IPI00386308   IPI00383200   
Protein Interaction databases
DIP (DOE-UCLA)Q9NZM5
IntAct (EBI)Q9NZM5
BioGRIDNOP53
STRING (EMBL)NOP53
ZODIACNOP53
Ontologies - Pathways
QuickGOQ9NZM5
Ontology : AmiGOribosomal large subunit assembly  RNA binding  intracellular  nucleolus  5S rRNA binding  biological_process  intracellular membrane-bounded organelle  
Ontology : EGO-EBIribosomal large subunit assembly  RNA binding  intracellular  nucleolus  5S rRNA binding  biological_process  intracellular membrane-bounded organelle  
Pathways : KEGGHerpes simplex infection   
NDEx NetworkNOP53
Atlas of Cancer Signalling NetworkNOP53
Wikipedia pathwaysNOP53
Orthology - Evolution
OrthoDB29997
Phylogenetic Trees/Animal Genes : TreeFamNOP53
HOVERGENQ9NZM5
HOGENOMQ9NZM5
Homologs : HomoloGeneNOP53
Homology/Alignments : Family Browser (UCSC)NOP53
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNOP53 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NOP53
dbVarNOP53
ClinVarNOP53
1000_GenomesNOP53 
Exome Variant ServerNOP53
ExAC (Exome Aggregation Consortium)NOP53 (select the gene name)
Genetic variants : HAPMAP29997
Genomic Variants (DGV)NOP53 [DGVbeta]
DECIPHERNOP53 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNOP53 
Mutations
ICGC Data PortalNOP53 
TCGA Data PortalNOP53 
Broad Tumor PortalNOP53
OASIS PortalNOP53 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDNOP53
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch NOP53
DgiDB (Drug Gene Interaction Database)NOP53
DoCM (Curated mutations)NOP53 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NOP53 (select a term)
intoGenNOP53
NCG5 (London)NOP53
Cancer3DNOP53(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605691   
Orphanet
MedgenNOP53
Genetic Testing Registry NOP53
NextProtQ9NZM5 [Medical]
TSGene29997
GENETestsNOP53
Target ValidationNOP53
Huge Navigator NOP53 [HugePedia]
snp3D : Map Gene to Disease29997
BioCentury BCIQNOP53
ClinGenNOP53
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD29997
Chemical/Pharm GKB GenePA28736
Clinical trialNOP53
Miscellaneous
canSAR (ICR)NOP53 (select the gene name)
Probes
Litterature
PubMed59 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNOP53
EVEXNOP53
GoPubMedNOP53
iHOPNOP53
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 1 17:27:15 CEST 2017

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