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GLTSCR2 (glioma tumor suppressor candidate region gene 2)

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

Alias_symbol (synonym)PICT-1
Other aliasPICT1
p60
HGNC (Hugo) GLTSCR2
LocusID (NCBI) 29997
Atlas_Id 40723
Location 19q13.33  [Link to chromosome band 19q13]
Location_base_pair Starts at 48248793 and ends at 48260323 bp from pter ( according to hg19-Feb_2009)  [Mapping GLTSCR2.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)GLTSCR2   4333
Cards
AtlasGLTSCR2ID40723ch19q13
Entrez_Gene (NCBI)GLTSCR2  29997  glioma tumor suppressor candidate region gene 2
AliasesPICT-1; PICT1
GeneCards (Weizmann)GLTSCR2
Ensembl hg19 (Hinxton)ENSG00000105373 [Gene_View]  chr19:48248793-48260323 [Contig_View]  GLTSCR2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000105373 [Gene_View]  chr19:48248793-48260323 [Contig_View]  GLTSCR2 [Vega]
ICGC DataPortalENSG00000105373
TCGA cBioPortalGLTSCR2
AceView (NCBI)GLTSCR2
Genatlas (Paris)GLTSCR2
WikiGenes29997
SOURCE (Princeton)GLTSCR2
Genetics Home Reference (NIH)GLTSCR2
Genomic and cartography
GoldenPath hg19 (UCSC)GLTSCR2  -     chr19:48248793-48260323 +  19q13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)GLTSCR2  -     19q13.3   [Description]    (hg38-Dec_2013)
EnsemblGLTSCR2 - 19q13.3 [CytoView hg19]  GLTSCR2 - 19q13.3 [CytoView hg38]
Mapping of homologs : NCBIGLTSCR2 [Mapview hg19]  GLTSCR2 [Mapview hg38]
OMIM605691   
Gene and transcription
Genbank (Entrez)AF161389 AF182076 AF296124 AI540063 AK024486
RefSeq transcript (Entrez)NM_015710
RefSeq genomic (Entrez)NC_000019 NC_018930 NT_011109 NW_004929415
Consensus coding sequences : CCDS (NCBI)GLTSCR2
Cluster EST : UnigeneHs.421907 [ NCBI ]
CGAP (NCI)Hs.421907
Alternative Splicing GalleryENSG00000105373
Gene ExpressionGLTSCR2 [ NCBI-GEO ]   GLTSCR2 [ EBI - ARRAY_EXPRESS ]   GLTSCR2 [ SEEK ]   GLTSCR2 [ MEM ]
Gene Expression Viewer (FireBrowse)GLTSCR2 [ 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)GLTSCR2
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)GLTSCR2
DMDM Disease mutations29997
Blocks (Seattle)GLTSCR2
SuperfamilyQ9NZM5
Human Protein AtlasENSG00000105373
Peptide AtlasQ9NZM5
HPRD16142
IPIIPI00024567   IPI00909733   IPI00908500   IPI00412788   IPI00386308   IPI00383200   
Protein Interaction databases
DIP (DOE-UCLA)Q9NZM5
IntAct (EBI)Q9NZM5
FunCoupENSG00000105373
BioGRIDGLTSCR2
STRING (EMBL)GLTSCR2
ZODIACGLTSCR2
Ontologies - Pathways
QuickGOQ9NZM5
Ontology : AmiGOintracellular  nucleolus  biological_process  intracellular membrane-bounded organelle  poly(A) RNA binding  
Ontology : EGO-EBIintracellular  nucleolus  biological_process  intracellular membrane-bounded organelle  poly(A) RNA binding  
Pathways : KEGGHerpes simplex infection   
NDEx NetworkGLTSCR2
Atlas of Cancer Signalling NetworkGLTSCR2
Wikipedia pathwaysGLTSCR2
Orthology - Evolution
OrthoDB29997
GeneTree (enSembl)ENSG00000105373
Phylogenetic Trees/Animal Genes : TreeFamGLTSCR2
HOVERGENQ9NZM5
HOGENOMQ9NZM5
Homologs : HomoloGeneGLTSCR2
Homology/Alignments : Family Browser (UCSC)GLTSCR2
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerGLTSCR2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GLTSCR2
dbVarGLTSCR2
ClinVarGLTSCR2
1000_GenomesGLTSCR2 
Exome Variant ServerGLTSCR2
ExAC (Exome Aggregation Consortium)GLTSCR2 (select the gene name)
Genetic variants : HAPMAP29997
Genomic Variants (DGV)GLTSCR2 [DGVbeta]
DECIPHER (Syndromes)19:48248793-48260323  ENSG00000105373
CONAN: Copy Number AnalysisGLTSCR2 
Mutations
ICGC Data PortalGLTSCR2 
TCGA Data PortalGLTSCR2 
Broad Tumor PortalGLTSCR2
OASIS PortalGLTSCR2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGLTSCR2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDGLTSCR2
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 GLTSCR2
DgiDB (Drug Gene Interaction Database)GLTSCR2
DoCM (Curated mutations)GLTSCR2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GLTSCR2 (select a term)
intoGenGLTSCR2
NCG5 (London)GLTSCR2
Cancer3DGLTSCR2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605691   
Orphanet
MedgenGLTSCR2
Genetic Testing Registry GLTSCR2
NextProtQ9NZM5 [Medical]
TSGene29997
GENETestsGLTSCR2
Huge Navigator GLTSCR2 [HugePedia]
snp3D : Map Gene to Disease29997
BioCentury BCIQGLTSCR2
ClinGenGLTSCR2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD29997
Chemical/Pharm GKB GenePA28736
Clinical trialGLTSCR2
Miscellaneous
canSAR (ICR)GLTSCR2 (select the gene name)
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGLTSCR2
EVEXGLTSCR2
GoPubMedGLTSCR2
iHOPGLTSCR2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:41:32 CET 2017

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