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WHSC1L1 (Wolf-Hirschhorn syndrome candidate 1 like gene 1)

Written2005-03Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers; CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)FLJ20353
NSD3
WHISTLE
Other aliasNSD3 (Nuclear receptor-binding, su(var), enhancer-of-zeste and trithorax domain-containing protein 3).
HGNC (Hugo) WHSC1L1
LocusID (NCBI) 54904
Atlas_Id 42810
Location 8p11.23  [Link to chromosome band 8p11]
Location_base_pair Starts at 38173935 and ends at 38239790 bp from pter ( according to hg19-Feb_2009)  [Mapping WHSC1L1.png]
Local_order WHSC1L1/NSD3 is 30 kb more telomeric than FGFR1 .
Fusion genes
(updated 2016)
CAPN15 (16p13.3) / WHSC1L1 (8p11.23)CHD7 (8q12.2) / WHSC1L1 (8p11.23)LSM1 (8p11.23) / WHSC1L1 (8p11.23)
MTSS1 (8q24.13) / WHSC1L1 (8p11.23)NUP98 (11p15.4) / WHSC1L1 (8p11.23)PROSC (8p11.23) / WHSC1L1 (8p11.23)
WHSC1L1 (8p11.23) / ADAM18 (8p11.22)WHSC1L1 (8p11.23) / ADAM32 (8p11.22)WHSC1L1 (8p11.23) / ANK1 (8p11.21)
WHSC1L1 (8p11.23) / COX4I1 (16q24.1)WHSC1L1 (8p11.23) / CSMD1 (8p23.2)WHSC1L1 (8p11.23) / DUSP26 (8p12)
WHSC1L1 (8p11.23) / FGFR1 (8p11.23)WHSC1L1 (8p11.23) / GAB2 (11q14.1)WHSC1L1 (8p11.23) / MUCL1 (12q13.2)
WHSC1L1 (8p11.23) / NEGR1 (1p31.1)WHSC1L1 (8p11.23) / NUP98 (11p15.4)WHSC1L1 (8p11.23) / NUTM1 (15q14)
WHSC1L1 (8p11.23) / PLEKHA2 (8p11.22)WHSC1L1 (8p11.23) / PSD3 (8p22)WHSC1L1 (8p11.23) / SNX20 (16q12.1)
WHSC1L1 (8p11.23) / TTC3 (21q22.13)WHSC1L1 (8p11.23) / WHSC1L1 (8p11.23)WHSC1L1 (8p11.23) / ZMAT4 (8p11.21)

DNA/RNA

Description The gene spans 127 kb on minus strand.
Transcription 2 major transcripts: a short transcript ending after an alternative exon 10b (3995 bp), and a long form from exon 1 to 24 (5428 bp).

Protein

Description The long transcript encodes a 1437 aminonacids protein (162 kDa) containing from N-term to C-term: a PWWP (proline-tryptophan-tryptophan-proline) domain, 4 PHD (plant-home domain)- type zinc finger motifs, a second PWWP domain, a SET associated cystein rich domain (SAC), a SET domain, a fifth PHD,and a Cys-His rich domain. The short transcript encodes a 645 amino acids protein (73 kDa) containing only the N-term t PWWP domain.
Expression wide.
Localisation putative nuclear location.
Function may have a regulatory role.
Homology NSD1, WHSC1/NSD2 .

Mutations

Somatic a hybrid gene involving WHSC1L1/NSD3 was found in a rare leukemia subtype (see below); amplification of a region containing WHSC1L1/NSD3 was found in a subset of breast cancers (but it remains to be determined which gene, within an amplicon, is the critical gene).

Implicated in

Note
  
Entity t(8;11)(p11;p15) Acute non lymphocytic leukemia with WHSC1L1/NSD3 - NUP98 .
Prognosis yet unknown: only 1 case with a proven hybrid gene 5' NUP98 - 3' NSD3; 2 other possible cases, but other genes may also be involved.
  

To be noted

This region in 8p11.2 seems to be derived from a duplication of 4p16.3 with similar genes WHSC1L1, FGFR1, and TACC1 in 8p11 from pter, and TACC3, FGFR3, and WHSC1 in 4p16 from pter

Bibliography

NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines.
Angrand PO, Apiou F, Stewart AF, Dutrillaux B, Losson R, Chambon P
Genomics. 2001 ; 74 (1) : 79-88.
PMID 11374904
 
NUP98 is fused to the NSD3 gene in acute myeloid leukemia associated with t(8;11)(p11.2;p15).
Rosati R, La Starza R, Veronese A, Aventin A, Schwienbacher C, Vallespi T, Negrini M, Martelli MF, Mecucci C
Blood. 2002 ; 99 (10) : 3857-3860.
PMID 11986249
 
WHSC1L1, on human chromosome 8p11.2, closely resembles WHSC1 and maps to a duplicated region shared with 4p16.3.
Stec I, van Ommen GJ, den Dunnen JT
Genomics. 2001 ; 76 (1-3) : 5-8.
PMID 11549311
 

Citation

This paper should be referenced as such :
Huret, JL
WHSC1L1 (Wolf-Hirschhorn syndrome candidate 1 like gene 1)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(2):143-144.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/WHSC1L1NSD3ID42810ch8p11.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  8p11 myeloproliferative syndrome (FGFR1)
t(8;11)(p11;p15) NUP98/WHSC1L1


External links

Nomenclature
HGNC (Hugo)WHSC1L1   12767
Cards
AtlasWHSC1L1NSD3ID42810ch8p11
Entrez_Gene (NCBI)WHSC1L1  54904  Wolf-Hirschhorn syndrome candidate 1-like 1
AliasesNSD3; WHISTLE; pp14328
GeneCards (Weizmann)WHSC1L1
Ensembl hg19 (Hinxton)ENSG00000147548 [Gene_View]  chr8:38173935-38239790 [Contig_View]  WHSC1L1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000147548 [Gene_View]  chr8:38173935-38239790 [Contig_View]  WHSC1L1 [Vega]
ICGC DataPortalENSG00000147548
TCGA cBioPortalWHSC1L1
AceView (NCBI)WHSC1L1
Genatlas (Paris)WHSC1L1
WikiGenes54904
SOURCE (Princeton)WHSC1L1
Genetics Home Reference (NIH)WHSC1L1
Genomic and cartography
GoldenPath hg19 (UCSC)WHSC1L1  -     chr8:38173935-38239790 -  8p11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)WHSC1L1  -     8p11.2   [Description]    (hg38-Dec_2013)
EnsemblWHSC1L1 - 8p11.2 [CytoView hg19]  WHSC1L1 - 8p11.2 [CytoView hg38]
Mapping of homologs : NCBIWHSC1L1 [Mapview hg19]  WHSC1L1 [Mapview hg38]
OMIM607083   
Gene and transcription
Genbank (Entrez)AF255649 AF318339 AF332468 AF332469 AJ295990
RefSeq transcript (Entrez)NM_017778 NM_023034
RefSeq genomic (Entrez)NC_000008 NC_018919 NG_023292 NT_167187 NW_004929337
Consensus coding sequences : CCDS (NCBI)WHSC1L1
Cluster EST : UnigeneHs.655314 [ NCBI ]
CGAP (NCI)Hs.655314
Alternative Splicing GalleryENSG00000147548
Gene ExpressionWHSC1L1 [ NCBI-GEO ]   WHSC1L1 [ EBI - ARRAY_EXPRESS ]   WHSC1L1 [ SEEK ]   WHSC1L1 [ MEM ]
Gene Expression Viewer (FireBrowse)WHSC1L1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54904
GTEX Portal (Tissue expression)WHSC1L1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BZ95   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BZ95  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BZ95
Splice isoforms : SwissVarQ9BZ95
Catalytic activity : Enzyme2.1.1.43 [ Enzyme-Expasy ]   2.1.1.432.1.1.43 [ IntEnz-EBI ]   2.1.1.43 [ BRENDA ]   2.1.1.43 [ KEGG ]   
PhosPhoSitePlusQ9BZ95
Domaine pattern : Prosite (Expaxy)AWS (PS51215)    POST_SET (PS50868)    PWWP (PS50812)    SET (PS50280)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)AWS_dom    Post-SET_dom    PWWP_dom    SET_dom    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)PWWP (PF00855)    SET (PF00856)   
Domain families : Pfam (NCBI)pfam00855    pfam00856   
Domain families : Smart (EMBL)AWS (SM00570)  PHD (SM00249)  PostSET (SM00508)  PWWP (SM00293)  RING (SM00184)  SET (SM00317)  
Conserved Domain (NCBI)WHSC1L1
DMDM Disease mutations54904
Blocks (Seattle)WHSC1L1
PDB (SRS)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (PDBSum)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (IMB)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (RSDB)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
Structural Biology KnowledgeBase2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
SCOP (Structural Classification of Proteins)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
CATH (Classification of proteins structures)2DAQ    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
SuperfamilyQ9BZ95
Human Protein AtlasENSG00000147548
Peptide AtlasQ9BZ95
HPRD06155
IPIIPI00743157   IPI00792713   IPI00307783   IPI00444331   IPI00941089   IPI00383309   IPI00847141   IPI00980085   IPI00979503   IPI00976341   IPI00982878   IPI00978327   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZ95
IntAct (EBI)Q9BZ95
FunCoupENSG00000147548
BioGRIDWHSC1L1
STRING (EMBL)WHSC1L1
ZODIACWHSC1L1
Ontologies - Pathways
QuickGOQ9BZ95
Ontology : AmiGOprotein binding  nucleus  nucleoplasm  chromosome  transcription, DNA-templated  regulation of transcription, DNA-templated  zinc ion binding  histone methylation  histone-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  histone lysine methylation  histone lysine methylation  histone lysine methylation  
Ontology : EGO-EBIprotein binding  nucleus  nucleoplasm  chromosome  transcription, DNA-templated  regulation of transcription, DNA-templated  zinc ion binding  histone methylation  histone-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  histone lysine methylation  histone lysine methylation  histone lysine methylation  
Pathways : KEGGLysine degradation   
NDEx NetworkWHSC1L1
Atlas of Cancer Signalling NetworkWHSC1L1
Wikipedia pathwaysWHSC1L1
Orthology - Evolution
OrthoDB54904
GeneTree (enSembl)ENSG00000147548
Phylogenetic Trees/Animal Genes : TreeFamWHSC1L1
HOVERGENQ9BZ95
HOGENOMQ9BZ95
Homologs : HomoloGeneWHSC1L1
Homology/Alignments : Family Browser (UCSC)WHSC1L1
Gene fusions - Rearrangements
Fusion : MitelmanCAPN15/WHSC1L1 [16p13.3/8p11.23]  [t(8;16)(p12;p13)]  
Fusion : MitelmanCHD7/WHSC1L1 [8q12.1/8p11.23]  [t(8;8)(p12;q12)]  
Fusion : MitelmanLSM1/WHSC1L1 [8p11.23/8p11.23]  [t(8;8)(p11;p12)]  
Fusion : MitelmanMTSS1/WHSC1L1 [8q24.13/8p11.23]  [t(8;8)(p12;q24)]  
Fusion : MitelmanNUP98/WHSC1L1 [11p15.4/8p11.23]  [t(8;11)(p12;p15)]  
Fusion : MitelmanWHSC1L1/ADAM32 [8p11.23/8p11.22]  [t(8;8)(p11;p12)]  
Fusion : MitelmanWHSC1L1/ANK1 [8p11.23/8p11.21]  [t(8;8)(p11;p12)]  
Fusion : MitelmanWHSC1L1/CSMD1 [8p11.23/8p23.2]  [t(8;8)(p12;p23)]  
Fusion : MitelmanWHSC1L1/FGFR1 [8p11.23/8p11.23]  [t(8;8)(p11;p12)]  
Fusion : MitelmanWHSC1L1/GAB2 [8p11.23/11q14.1]  [t(8;11)(p12;q14)]  
Fusion : MitelmanWHSC1L1/MUCL1 [8p11.23/12q13.2]  [t(8;12)(p12;q13)]  
Fusion : MitelmanWHSC1L1/NEGR1 [8p11.23/1p31.1]  [t(1;8)(p31;p12)]  
Fusion : MitelmanWHSC1L1/PLEKHA2 [8p11.23/8p11.22]  [t(8;8)(p11;p12)]  
Fusion : MitelmanWHSC1L1/SNX20 [8p11.23/16q12.1]  [t(8;16)(p12;q12)]  
Fusion : MitelmanWHSC1L1/ZMAT4 [8p11.23/8p11.21]  [t(8;8)(p11;p12)]  
Fusion: TCGACHD7 8q12.1 WHSC1L1 8p11.23 OV
Fusion: TCGALSM1 8p11.23 WHSC1L1 8p11.23 LUSC
Fusion: TCGAMTSS1 8q24.13 WHSC1L1 8p11.23 SKCM
Fusion: TCGASOLH WHSC1L1 8p11.23 LUSC
Fusion: TCGAWHSC1L1 8p11.23 ADAM32 8p11.22 BRCA
Fusion: TCGAWHSC1L1 8p11.23 ANK1 8p11.21 BRCA
Fusion: TCGAWHSC1L1 8p11.23 C15orf55 LUSC
Fusion: TCGAWHSC1L1 8p11.23 CSMD1 8p23.2 BRCA
Fusion: TCGAWHSC1L1 8p11.23 DUSP26 8p12 OV
Fusion: TCGAWHSC1L1 8p11.23 FGFR1 8p11.23 BRCA
Fusion: TCGAWHSC1L1 8p11.23 GAB2 11q14.1 BRCA
Fusion: TCGAWHSC1L1 8p11.23 MUCL1 12q13.2 OV
Fusion: TCGAWHSC1L1 8p11.23 NEGR1 1p31.1 BRCA
Fusion: TCGAWHSC1L1 8p11.23 PLEKHA2 8p11.22 BRCA
Fusion: TCGAWHSC1L1 8p11.23 PSD3 8p22 BRCA
Fusion: TCGAWHSC1L1 8p11.23 SNX20 16q12.1 BRCA
Fusion: TCGAWHSC1L1 8p11.23 ZMAT4 8p11.21 BRCA
Fusion : TICdbNUP98 [11p15.4]  -  WHSC1L1 [8p11.23]
Fusion Cancer (Beijing)W-C1L1 [8p11.23]  -  FGFR1 [8p11.23]  [FUSC001300]  [FUSC001300]  [FUSC001300]  [FUSC001300]  [FUSC001300]  [FUSC001300]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerWHSC1L1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)WHSC1L1
dbVarWHSC1L1
ClinVarWHSC1L1
1000_GenomesWHSC1L1 
Exome Variant ServerWHSC1L1
ExAC (Exome Aggregation Consortium)WHSC1L1 (select the gene name)
Genetic variants : HAPMAP54904
Genomic Variants (DGV)WHSC1L1 [DGVbeta]
DECIPHER (Syndromes)8:38173935-38239790  ENSG00000147548
CONAN: Copy Number AnalysisWHSC1L1 
Mutations
ICGC Data PortalWHSC1L1 
TCGA Data PortalWHSC1L1 
Broad Tumor PortalWHSC1L1
OASIS PortalWHSC1L1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICWHSC1L1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDWHSC1L1
intOGen PortalWHSC1L1
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 WHSC1L1
DgiDB (Drug Gene Interaction Database)WHSC1L1
DoCM (Curated mutations)WHSC1L1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)WHSC1L1 (select a term)
intoGenWHSC1L1
NCG5 (London)WHSC1L1
Cancer3DWHSC1L1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607083   
Orphanet
MedgenWHSC1L1
Genetic Testing Registry WHSC1L1
NextProtQ9BZ95 [Medical]
TSGene54904
GENETestsWHSC1L1
Huge Navigator WHSC1L1 [HugePedia]
snp3D : Map Gene to Disease54904
BioCentury BCIQWHSC1L1
ClinGenWHSC1L1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD54904
Chemical/Pharm GKB GenePA37370
Clinical trialWHSC1L1
Miscellaneous
canSAR (ICR)WHSC1L1 (select the gene name)
Probes
Litterature
PubMed27 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineWHSC1L1
EVEXWHSC1L1
GoPubMedWHSC1L1
iHOPWHSC1L1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Apr 12 11:41:43 CEST 2017

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