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NOL4L (nucleolar protein 4 like)

Written2018-10Jean Loup Huret
jean-loup.huret@atlasgeneticsoncology.org

Abstract Review on NOL4L, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords NOL4L; C20orf112; C20orf113; Acute lymphoblastic leukemia; Acute myeloid leukemia: Breast adenocarcinoma; Skin melanoma; Uterus cancer; Bladder cancer.

(Note : for Links provided by Atlas : click)

Identity

Alias_namesC20orf113
C20orf112
chromosome 20 open reading frame 113
chromosome 20 open reading frame 112
Alias_symbol (synonym)dJ1184F4.2
DKFZP566G1424
dJ1184F4.4
Other aliasLOC140688
HGNC (Hugo) NOL4L
Atlas_Id 51676
Location 20q11.2  [Link to chromosome band 20q11]
Location_base_pair Starts at 32443059 and ends at 32483584 bp from pter ( according to hg19-Feb_2009)  [Mapping NOL4L.png]
Local_order Cen --- PLAGL2, POFUT1, KIF3B, ASXL1, NOL4L, NOL4L-DT, C20orf203, COMMD7, DNMT3B ---Tel
 
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ACTB/NOL4LPAX5/NOL4LMMD/NOL4L
NOL4L/COMMD7NOL4L/EFCAB8PDRG1/NOL4L
RUNX1/NOL4L
Note This gene and protein is very poorly known; a very few data comes from the literature, and other data from databases.

DNA/RNA

Description 11 exons
Transcription 8 potential splice forms coding for potential proteins with 76 amino acids (aa) to 680 aa.

Protein

Note Nothing is known concerning the domains of the protein, nor it's function.
Description Two coding proteins: NOL4L-010, from: 11 exons; transcript length: 6,577 bps translation: 680 amino acids; and NOL4L-001, from: 8 exons; transcript length: 5,991 bps translation: 436 amino acids. A Poly-Asp is found at aa 161 to 169 according to Vega (http://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=OTTHUMG00000032219;r=20:32443059-32585074) and UniProt (https://www.uniprot.org/uniprot/Q96MY1#expression).
Expression Expressed in all tissues; High expression in the testis, and, to a lesser extend, in the small intestine, other digestive organs, brain and bone marrow. NOL4L orthologs are present in most vertebrates and are well conserved. In zebrafish embryos, Znol4lb (the zebrafish nol4l with the highest identity with human NOL4L) mRNA is localized to the intermediate mesoderm. It is expressed in the central nervous system, pronephros, the gut and, at low levels, in the hematopoietic cells (Borah et al. 2016).
Localisation Mainly localized to the nucleoplasm.
Function Acccording to BioGRID (https://thebiogrid.org/12665), interacts with:
CTBP1 (C-terminal binding protein 1), corepressor targeting various transcription regulators.
TEX9 (testis expressed 9).
SRPK1 (SRSF protein kinase 1), involved in the regulation of splicing via phosphorylation of splicing factors.
CTBP2 (C-terminal binding protein 2), corepressor targeting various transcription regulators.
SKA3 (spindle and kinetochore associated complex subunit 3), component of a microtubule-binding complex essential for chromosome segregation.
TRIM25 (tripartite motif containing 25), ubiquitin E3 ligase.
MIR206 (microRNA 206).

Implicated in

Note High expression of NOL4L is an unfavourable prognostic factor in endometrial cancer.
High expression of NOL4L is a favourable prognostic factor in urothelial cancer.
Expression level of NOL4L has no prognostic significance in: Glioma, Thyroid cancer, Lung cancer, Liver cancer, Pancreatic cancer, Head and neck cancer, Stomach cancer, Colorectal cancer, Renal cancer, Prostate cancer, Testis cancer, Breast cancer, Cervical cancer, Ovarian cancer, Melanoma .
Main translocations: (detailed herein below)
- dic(9;20)(p13;q11) PAX5/NOL4L.
- t(20;21)(q11;q22) RUNX1/NOL4L.
Other fusion transcripts: (data extracted from the Atlas http://atlasgeneticsoncology.org//Bands/20q11.html)
- fusion/translocation t(7;20)(p22;q11) ACTB/NOL4L in triple-negative (TN) adenocarcinoma. The triple-negative breast cancer subtype is the most aggressive form of invasive breast adenocarcinoma (Asmann et al. 2012).
- fusion/translocation t(17;20)(q22;q11) MMD/NOL4L in breast adenocarcinoma (Yoshihara et al. 2015).
- fusion 20q11-20q11 NOL4L/ COMMD7 in breast adenocarcinoma (Yoshihara et al. 2015).
- fusion 20q11-20q11 NOL4L/ EFCAB8 in malignant melanoma of the skin (Hu et al., 2018).
- fusion 20q11-20q11 PDRG1/NOL4L in malignant epithelial tumor of the uterus corpus (Hu et al., 2018).
  
Entity Pediatric acute lymphoblastic leukemia (ALL)
Note 5 cases of dic(9;20) (p13;q11) PAX5/NOL4L available to date (Nebral et al., 2007; An et al., 2008; Kawamata et al., 2008; Kawamata et al. 2012).
Hybrid/Mutated Gene In one case, exon 5 of PAX5 was fused to exon 8 of NOL4L, and in four cases, exon 8 of PAX5 was fused to exon 3 of NOL4L, producing two proteins, a short (PAX5/C20ORF112S) and long (PAX5/C20ORF112L) form, localizing in the nucleus, and/or in the cytoplasm and the nucleus (Kawamata et al., 2008).
Oncogenesis Four downstream target genes of PAX5 ( ATP1B1, BLK, SEPT2 and TCF7L2) were down-regulated by induction of PAX5/NOL4L. Loss of the C-terminal end of PAX5 may play role in generation of a dominant negative form of mutated PAX5 (Kawamata et al., 2008).
  
  
Entity Acute myeloid leukemia (AML)
Note A 62-year-old man was diagnosed with AML with maturation (M2- AML), and presented with a t(20;21)(q11.2;q22.1) RUNX1/NOL4L accompanied with monosomy 7 (Guastadisegni et al. 2010).
Hybrid/Mutated Gene RUNX1 exon 6 was fused to NOL4L exon 8.
Oncogenesis Wild-type NOL4L was expressed at low levels in AML and normal bone marrow, whereas the RUNX1/NOL4L was expressed at high levels (Guastadisegni et al. 2010).
  

Bibliography

Variable breakpoints target PAX5 in patients with dicentric chromosomes: a model for the basis of unbalanced translocations in cancer
An Q, Wright SL, Konn ZJ, Matheson E, Minto L, Moorman AV, Parker H, Griffiths M, Ross FM, Davies T, Hall AG, Harrison CJ, Irving JA, Strefford JC
Proc Natl Acad Sci U S A 2008 Nov 4;105(44):17050-4
PMID 18957548
 
Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer
Asmann YW, Necela BM, Kalari KR, Hossain A, Baker TR, Carr JM, Davis C, Getz JE, Hostetter G, Li X, McLaughlin SA, Radisky DC, Schroth GP, Cunliffe HE, Perez EA, Thompson EA
Cancer Res 2012 Apr 15;72(8):1921-8
PMID 22496456
 
Nucleolar protein 4-like has a complex expression pattern in zebrafish embryos
Borah S, Barrodia P, Swain RK
Int J Dev Biol 2016;60(1-3):53-6
PMID 26934290
 
CBFA2T2 and C20orf112: two novel fusion partners of RUNX1 in acute myeloid leukemia
Guastadisegni MC, Lonoce A, Impera L, Di Terlizzi F, Fugazza G, Aliano S, Grasso R, Cluzeau T, Raynaud S, Rocchi M, Storlazzi CT
Leukemia 2010 Aug;24(8):1516-9
PMID 20520637
 
TumorFusions: an integrative resource for cancer-associated transcript fusions
Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang FM, Martinez-Ledesma E, Lee SH, Zheng S, Verhaak RGW
Nucleic Acids Res 2018 Jan 4;46(D1):D1144-D1149
PMID 29099951
 
Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray
Kawamata N, Ogawa S, Zimmermann M, Niebuhr B, Stocking C, Sanada M, Hemminki K, Yamatomo G, Nannya Y, Koehler R, Flohr T, Miller CW, Harbott J, Ludwig WD, Stanulla M, Schrappe M, Bartram CR, Koeffler HP
Proc Natl Acad Sci U S A 2008 Aug 19;105(33):11921-6
PMID 18697940
 
Identification of PML as novel PAX5 fusion partner in childhood acute lymphoblastic leukaemia
Nebral K, König M, Harder L, Siebert R, Haas OA, Strehl S
Br J Haematol 2007 Oct;139(2):269-74
PMID 17897302
 
The landscape and therapeutic relevance of cancer-associated transcript fusions
Yoshihara K, Wang Q, Torres-Garcia W, Zheng S, Vegesna R, Kim H, Verhaak RG
Oncogene 2015 Sep 10;34(37):4845-54
PMID 25500544
 

Citation

This paper should be referenced as such :
Huret JL
NOL4L (nucleolar protein 4 like);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/NOL4LID51676ch20q11.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(20;21)(q11;q22) RUNX1/NOL4L
dic(9;20)(p13;q11) PAX5/NOL4L
dic(9;20)(p13;q11) PAX5/NOL4L


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(7;20)(p22;q11) ACTB/NOL4L
t(17;20)(q22;q11) MMD/NOL4L
NOL4L/COMMD7 (20q11)


External links

Nomenclature
HGNC (Hugo)NOL4L   16106
Cards
AtlasNOL4LID51676ch20q11
Entrez_Gene (NCBI)NOL4L  140688  nucleolar protein 4 like
AliasesC20orf112; C20orf113
GeneCards (Weizmann)NOL4L
Ensembl hg19 (Hinxton)ENSG00000197183 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000197183 [Gene_View]  ENSG00000197183 [Sequence]  chr20:32443059-32483584 [Contig_View]  NOL4L [Vega]
ICGC DataPortalENSG00000197183
TCGA cBioPortalNOL4L
AceView (NCBI)NOL4L
Genatlas (Paris)NOL4L
WikiGenes140688
SOURCE (Princeton)NOL4L
Genetics Home Reference (NIH)NOL4L
Genomic and cartography
GoldenPath hg38 (UCSC)NOL4L  -     chr20:32443059-32483584 -  20q11.21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NOL4L  -     20q11.21   [Description]    (hg19-Feb_2009)
GoldenPathNOL4L - 20q11.21 [CytoView hg19]  NOL4L - 20q11.21 [CytoView hg38]
ImmunoBaseENSG00000197183
Mapping of homologs : NCBINOL4L [Mapview hg19]  NOL4L [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK056286 AK097804 AL122043 AL834520 BC023657
RefSeq transcript (Entrez)NM_001256798 NM_001351680 NM_080616
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NOL4L
Cluster EST : UnigeneHs.729596 [ NCBI ]
CGAP (NCI)Hs.729596
Alternative Splicing GalleryENSG00000197183
Gene ExpressionNOL4L [ NCBI-GEO ]   NOL4L [ EBI - ARRAY_EXPRESS ]   NOL4L [ SEEK ]   NOL4L [ MEM ]
Gene Expression Viewer (FireBrowse)NOL4L [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
GTEX Portal (Tissue expression)NOL4L
Human Protein AtlasENSG00000197183-NOL4L [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96MY1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96MY1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96MY1
Splice isoforms : SwissVarQ96MY1
PhosPhoSitePlusQ96MY1
Domains : Interpro (EBI)NOL4L   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)NOL4L
DMDM Disease mutations140688
Blocks (Seattle)NOL4L
SuperfamilyQ96MY1
Human Protein Atlas [tissue]ENSG00000197183-NOL4L [tissue]
Peptide AtlasQ96MY1
HPRD10728
IPIIPI00289086   IPI00607558   IPI00872049   IPI00644822   IPI00645248   IPI00647935   IPI00552263   IPI00645330   
Protein Interaction databases
DIP (DOE-UCLA)Q96MY1
IntAct (EBI)Q96MY1
FunCoupENSG00000197183
BioGRIDNOL4L
STRING (EMBL)NOL4L
ZODIACNOL4L
Ontologies - Pathways
QuickGOQ96MY1
Ontology : AmiGOprotein binding  nucleoplasm  cytosol  
Ontology : EGO-EBIprotein binding  nucleoplasm  cytosol  
NDEx NetworkNOL4L
Atlas of Cancer Signalling NetworkNOL4L
Wikipedia pathwaysNOL4L
Orthology - Evolution
GeneTree (enSembl)ENSG00000197183
Phylogenetic Trees/Animal Genes : TreeFamNOL4L
HOGENOMQ96MY1
Homologs : HomoloGeneNOL4L
Homology/Alignments : Family Browser (UCSC)NOL4L
Gene fusions - Rearrangements
Fusion : MitelmanACTB/NOL4L [7p22.1/20q11.21]  [t(7;20)(p22;q11)]  
Fusion : MitelmanPAX5/NOL4L [9p13.2/20q11.21]  [dic(9;20)(p13;q11)]  
Fusion : MitelmanRUNX1/NOL4L [21q22.12/20q11.21]  [t(20;21)(q11;q22)]  
Fusion : Fusion_HubASXL1--NOL4L    NOL4L--COMMD7    NOL4L--PAX5    NOL4L--RUNX1   
Fusion : QuiverNOL4L
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNOL4L [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NOL4L
dbVarNOL4L
ClinVarNOL4L
1000_GenomesNOL4L 
Exome Variant ServerNOL4L
ExAC (Exome Aggregation Consortium)ENSG00000197183
GNOMAD BrowserENSG00000197183
Varsome BrowserNOL4L
Genetic variants : HAPMAP140688
Genomic Variants (DGV)NOL4L [DGVbeta]
DECIPHERNOL4L [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNOL4L 
Mutations
ICGC Data PortalNOL4L 
TCGA Data PortalNOL4L 
Broad Tumor PortalNOL4L
OASIS PortalNOL4L [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDNOL4L
BioMutasearch NOL4L
DgiDB (Drug Gene Interaction Database)NOL4L
DoCM (Curated mutations)NOL4L (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NOL4L (select a term)
intoGenNOL4L
NCG5 (London)NOL4L
Cancer3DNOL4L(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETNOL4L
MedgenNOL4L
Genetic Testing Registry NOL4L
NextProtQ96MY1 [Medical]
GENETestsNOL4L
Target ValidationNOL4L
Huge Navigator NOL4L [HugePedia]
snp3D : Map Gene to Disease
BioCentury BCIQNOL4L
ClinGenNOL4L
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD140688
Chemical/Pharm GKB GenePA25652
Clinical trialNOL4L
Miscellaneous
canSAR (ICR)NOL4L (select the gene name)
DataMed IndexNOL4L
Probes
Litterature
PubMed18 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNOL4L
EVEXNOL4L
GoPubMedNOL4L
iHOPNOL4L
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Jul 8 15:17:31 CEST 2019

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