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

Identity

Other namesNSD3 (Nuclear receptor-binding, su(var), enhancer-of-zeste and trithorax domain-containing protein 3).
HGNC (Hugo) WHSC1L1
Location 8p11.2
Location_base_pair Starts at 38293092 and ends at 38358947 bp from pter ( according to hg18-Mar_2006)  [Mapping]
Local_order WHSC1L1/NSD3 is 30 kb more telomeric than FGFR1 .

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

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

External links

Nomenclature
HGNC (Hugo)WHSC1L1   12767
Entrez_Gene (NCBI)WHSC1L1  54904  Wolf-Hirschhorn syndrome candidate 1-like 1
Cards
AtlasWHSC1L1NSD3ID42810ch8p11
GeneCards (Weizmann)WHSC1L1
Ensembl (Hinxton)ENSG00000147548 [Gene_View]  WHSC1L1 [Vega]
AceView (NCBI)WHSC1L1
Genatlas (Paris)WHSC1L1
euGene (Indiana)54904
SOURCE (Stanford)NM_017778 NM_023034
Gene Expression (Array Express) ENSG00000147548
Genomic and cartography
GoldenPath (UCSC)WHSC1L1  -  8p11.2   chr8:38293092-38358947 -  8p11.2   [Description]    (hg18-Mar_2006)
EnsemblWHSC1L1 - 8p11.2 [CytoView]
Mapping of homologs : NCBIWHSC1L1 [Mapview]
OMIM601626   607083   
Gene and transcription
Gene : Genbank (Entrez)AF255649 AF318339 AF332468 AF332469 AJ295990
Reference sequence (RefSeq transcript) :SRSNM_017778 NM_023034
Reference transcript : EntrezNM_017778 NM_023034
RefSeq genomic : SRSAC_000051 AC_000140 NC_000008 NT_167187 NW_001839128 NW_923907
RefSeq genomic : EntrezAC_000051 AC_000140 NC_000008 NT_167187 NW_001839128 NW_923907
Consensus coding sequences : CCDS NCBIWHSC1L1
Cluster EST : UnigeneHs.608111 [ SRS ] Hs.608111 [ NCBI ]
Alternative Splicing : Fast-db (Paris)3902
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtQ9BZ95 (SRS) Q9BZ95 (Expasy) Q9BZ95 (Uniprot)
With graphics : InterProQ9BZ95
Splice isoforms : VarSplice FASTAQ9BZ95(VarSplice FASTA)
Domaine pattern : Prosite (SRS)AWS (PS51215)    POST_SET (PS50868)    PWWP (PS50812)    SET (PS50280)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domain pattern : Prosite (Expaxy)AWS (PS51215)    POST_SET (PS50868)    PWWP (PS50812)    SET (PS50280)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (SRS)AWS    Post-SET_dom    PWWP    SET_dom    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING   
Domains : Interpro (EBI)AWS    Post-SET_dom    PWWP    SET_dom    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING   
Related proteins : CluSTrQ9BZ95
Domain families : Pfam SRSPWWP (PF00855)    SET (PF00856)   
Domain families : Pfam SangerPWWP (PF00855)    SET (PF00856)   
Domain families : Pfam NCBIpfam00855    pfam00856   
Domain families : Smart EMBLAWS (SM00570)  PHD (SM00249)  PostSET (SM00508)  PWWP (SM00293)  RING (SM00184)  SET (SM00317)  
Blocks (Seattle)Q9BZ95
Crystal structure of protein : PDB SRS2DAQ   
Crystal structure of protein : PDBSum2DAQ   
Crystal structure of protein : IMB2DAQ   
Crystal structure of protein : PDB RSDB2DAQ   
HPRD06155
Protein Interaction databases
DIP (DOE-UCLA)Q9BZ95
IntAct (EBI)Q9BZ95
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBIWHSC1L1
SNP : GeneSNP UtahWHSC1L1
SNP : HGBaseWHSC1L1
Genetic variants : HAPMAPWHSC1L1
Cancer Gene: CensusWHSC1L1 
Somatic Mutations in Cancer : COSMICWHSC1L1 
Translocation Breakpoints in Cancer : TICdbWHSC1L1 
Mutations and Diseases : HGMDWHSC1L1
Hereditary diseases : OMIM601626    607083   
Hereditary diseases : GENETests601626    607083   
Diseases : Genetic AssociationWHSC1L1
General knowledge
Homologs : HomoloGeneWHSC1L1
Homology/Alignments : Family Browser UCSCWHSC1L1
Phylogenetic Trees/Animal Genes : TreeFamWHSC1L1
Catalytic activity : Enzyme2.1.1.43 [ Enzyme-Expasy ]   2.1.1.43 [ Enzyme-SRS ]   2.1.1.43 [ IntEnz-EBI ]   2.1.1.43 [ BRENDA ]   2.1.1.43 [ KEGG ]   
Chemical/Protein Interactions : CTD54904
Keywords Ontology : AmiGOprotein binding  nucleus  nucleus  nucleus  nucleolus  mitochondrion  methyltransferase activity  zinc ion binding  cell growth  chromatin modification  histone methylation  transferase activity  histone-lysine N-methyltransferase activity  cell differentiation  regulation of transcription  metal ion binding  
Keywords Ontology : EGO-EBIprotein binding  nucleus  nucleus  nucleus  nucleolus  mitochondrion  methyltransferase activity  zinc ion binding  cell growth  chromatin modification  histone methylation  transferase activity  histone-lysine N-methyltransferase activity  cell differentiation  regulation of transcription  metal ion binding  
Pathways : BIOCARTA
Pathways : KEGG
Other databases
Probes
Probes : ImagenesWHSC1L1 Related clones (RZPD - Berlin)
Literature
PubMed10 Pubmed reference(s) in Entrez
PubGeneWHSC1L1

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
 
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
 
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
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written03-2005Jean Loup Huret

Citation

This paper should be referenced as such :
Huret JL . WHSC1L1 (Wolf-Hirschhorn syndrome candidate 1 like gene 1). Atlas Genet Cytogenet Oncol Haematol. March 2005 .
URL : http://AtlasGeneticsOncology.org/Genes/WHSC1L1NSD3ID42810ch8p11.html

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indexed on : Sat Feb 27 10:54:52 CET 2010

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