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NSD3 (nuclear receptor binding SET domain protein 3)

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

Other aliasWHSC1L1
HGNC (Hugo) NSD3
LocusID (NCBI) 54904
Atlas_Id 42810
Location 8p11.23  [Link to chromosome band 8p11]
Location_base_pair Starts at 38316417 and ends at 38382272 bp from pter ( according to hg19-Feb_2009)  [Mapping NSD3.png]
Local_order WHSC1L1/NSD3 is 30 kb more telomeric than FGFR1 .
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CAPN15 (16p13.3) / NSD3 (8p11.23)CHD7 (8q12.2) / NSD3 (8p11.23)CHST11 (12q23.3) / NSD3 (8p11.23)
LSM1 (8p11.23) / NSD3 (8p11.23)MTSS1 (8q24.13) / NSD3 (8p11.23)MUC1 (1q22) / NSD3 (8p11.23)
NSD3 (8p11.23) / ADAM18 (8p11.22)NSD3 (8p11.23) / ADAM32 (8p11.22)NSD3 (8p11.23) / ANK1 (8p11.21)
NSD3 (8p11.23) / COX4I1 (16q24.1)NSD3 (8p11.23) / CSMD1 (8p23.2)NSD3 (8p11.23) / DUSP26 (8p12)
NSD3 (8p11.23) / FGFR1 (8p11.23)NSD3 (8p11.23) / GAB2 (11q14.1)NSD3 (8p11.23) / MUCL1 (12q13.2)
NSD3 (8p11.23) / NEGR1 (1p31.1)NSD3 (8p11.23) / NSD3 (8p11.23)NSD3 (8p11.23) / NUP98 (11p15.4)
NSD3 (8p11.23) / NUTM1 (15q14)NSD3 (8p11.23) / PLEKHA2 (8p11.22)NSD3 (8p11.23) / PSD3 (8p22)
NSD3 (8p11.23) / SNX20 (16q12.1)NSD3 (8p11.23) / TTC3 (21q22.13)NSD3 (8p11.23) / ZMAT4 (8p11.21)
NUP98 (11p15.4) / NSD3 (8p11.23)THAP12 (11q13.5) / NSD3 (8p11.23)

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)NSD3   12767
Cards
AtlasWHSC1L1NSD3ID42810ch8p11
Entrez_Gene (NCBI)NSD3  54904  nuclear receptor binding SET domain protein 3
AliasesKMT3F; KMT3G; WHISTLE; WHSC1L1; 
pp14328
GeneCards (Weizmann)NSD3
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]  chr8:38316417-38382272 [Contig_View]  NSD3 [Vega]
TCGA cBioPortalNSD3
AceView (NCBI)NSD3
Genatlas (Paris)NSD3
WikiGenes54904
SOURCE (Princeton)NSD3
Genetics Home Reference (NIH)NSD3
Genomic and cartography
GoldenPath hg38 (UCSC)NSD3  -     chr8:38316417-38382272 -  8p11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NSD3  -     8p11.23   [Description]    (hg19-Feb_2009)
EnsemblNSD3 - 8p11.23 [CytoView hg19]  NSD3 - 8p11.23 [CytoView hg38]
Mapping of homologs : NCBINSD3 [Mapview hg19]  NSD3 [Mapview hg38]
OMIM607083   
Gene and transcription
Genbank (Entrez)AF255649 AF318339 AF332468 AF332469 AJ295990
RefSeq transcript (Entrez)NM_017778 NM_023034
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NSD3
Cluster EST : UnigeneHs.655314 [ NCBI ]
CGAP (NCI)Hs.655314
Gene ExpressionNSD3 [ NCBI-GEO ]   NSD3 [ EBI - ARRAY_EXPRESS ]   NSD3 [ SEEK ]   NSD3 [ MEM ]
Gene Expression Viewer (FireBrowse)NSD3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54904
GTEX Portal (Tissue expression)NSD3
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/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)  SET (SM00317)  
Conserved Domain (NCBI)NSD3
DMDM Disease mutations54904
Blocks (Seattle)NSD3
PDB (SRS)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (PDBSum)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (IMB)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
PDB (RSDB)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
Structural Biology KnowledgeBase2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
SCOP (Structural Classification of Proteins)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
CATH (Classification of proteins structures)2DAQ    2NCZ    2ND1    4GND    4GNE    4GNF    4GNG    4RXJ    4YZ8   
SuperfamilyQ9BZ95
Peptide AtlasQ9BZ95
IPIIPI00743157   IPI00792713   IPI00307783   IPI00444331   IPI00941089   IPI00383309   IPI00847141   IPI00980085   IPI00979503   IPI00976341   IPI00982878   IPI00978327   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZ95
IntAct (EBI)Q9BZ95
BioGRIDNSD3
STRING (EMBL)NSD3
ZODIACNSD3
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  
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  
Pathways : KEGGLysine degradation   
NDEx NetworkNSD3
Atlas of Cancer Signalling NetworkNSD3
Wikipedia pathwaysNSD3
Orthology - Evolution
OrthoDB54904
Phylogenetic Trees/Animal Genes : TreeFamNSD3
HOVERGENQ9BZ95
HOGENOMQ9BZ95
Homologs : HomoloGeneNSD3
Homology/Alignments : Family Browser (UCSC)NSD3
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: TCGA_MDACCCHD7 8q12.1 WHSC1L1 8p11.23 OV
Fusion: TCGA_MDACCLSM1 8p11.23 WHSC1L1 8p11.23 LUSC
Fusion: TCGA_MDACCMTSS1 8q24.13 WHSC1L1 8p11.23 SKCM
Fusion: TCGA_MDACCSOLH WHSC1L1 8p11.23 LUSC
Fusion: TCGA_MDACCWHSC1L1 8p11.23 ADAM32 8p11.22 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 ANK1 8p11.21 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 C15orf55 LUSC
Fusion: TCGA_MDACCWHSC1L1 8p11.23 CSMD1 8p23.2 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 DUSP26 8p12 OV
Fusion: TCGA_MDACCWHSC1L1 8p11.23 FGFR1 8p11.23 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 GAB2 11q14.1 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 MUCL1 12q13.2 OV
Fusion: TCGA_MDACCWHSC1L1 8p11.23 NEGR1 1p31.1 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 PLEKHA2 8p11.22 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 PSD3 8p22 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 SNX20 16q12.1 BRCA
Fusion: TCGA_MDACCWHSC1L1 8p11.23 ZMAT4 8p11.21 BRCA
Tumor Fusion PortalNSD3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNSD3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NSD3
dbVarNSD3
ClinVarNSD3
1000_GenomesNSD3 
Exome Variant ServerNSD3
ExAC (Exome Aggregation Consortium)
Genetic variants : HAPMAP54904
Genomic Variants (DGV)NSD3 [DGVbeta]
DECIPHERNSD3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNSD3 
Mutations
ICGC Data PortalNSD3 
TCGA Data PortalNSD3 
Broad Tumor PortalNSD3
OASIS PortalNSD3 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDNSD3
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 NSD3
DgiDB (Drug Gene Interaction Database)NSD3
DoCM (Curated mutations)NSD3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NSD3 (select a term)
intoGenNSD3
NCG5 (London)NSD3
Cancer3DNSD3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607083   
Orphanet
DisGeNETNSD3
MedgenNSD3
Genetic Testing Registry NSD3
NextProtQ9BZ95 [Medical]
TSGene54904
GENETestsNSD3
Target ValidationNSD3
Huge Navigator NSD3 [HugePedia]
snp3D : Map Gene to Disease54904
BioCentury BCIQNSD3
ClinGenNSD3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD54904
Chemical/Pharm GKB GenePA37370
Clinical trialNSD3
Miscellaneous
canSAR (ICR)NSD3 (select the gene name)
Probes
Litterature
PubMed29 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNSD3
EVEXNSD3
GoPubMedNSD3
iHOPNSD3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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