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NSD1 (Nuclear receptor-binding, su (var), enhancer-of-zeste and trithorax domain-containing protein 1

Written2002-03Lyndal Kearney
Leukaemia Research Fund Centre, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK

(Note : for Links provided by Atlas : click)

Identity

HGNC (Hugo) NSD1
LocusID (NCBI) 64324
Atlas_Id 356
Location 5q35.2  [Link to chromosome band 5q35]
Location_base_pair Starts at 176560833 and ends at 176727214 bp from pter ( according to hg19-Feb_2009)  [Mapping NSD1.png]
Fusion genes
(updated 2016)
ARMCX4 (Xq22.1) / NSD1 (5q35.2)B4GALT7 (5q35.3) / NSD1 (5q35.2)CDH23 (10q22.1) / NSD1 (5q35.2)
EEF2 (19p13.3) / NSD1 (5q35.2)HNRNPA2B1 (7p15.2) / NSD1 (5q35.2)NSD1 (5q35.2) / ANKRD28 (3p25.1)
NSD1 (5q35.2) / CDH23 (10q22.1)NSD1 (5q35.2) / FAT2 (5q33.1)NSD1 (5q35.2) / NSD1 (5q35.2)
NSD1 (5q35.2) / NUP98 (11p15.4)NSD1 (5q35.2) / TBC1D1 (4p14)NSD1 (5q35.2) / UNC5A (5q35.2)
NSD1 (5q35.2) / ZNF346 (5q35.2)NUP98 (11p15.4) / NSD1 (5q35.2)STIM1 (11p15.4) / NSD1 (5q35.2)
UIMC1 (5q35.2) / NSD1 (5q35.2)

DNA/RNA

Description At least 23 exons. cDNA is 8552 bp, 8088 bp open reading frame
Transcription Two transcripts: 9.0 and 10 kb

Protein

 
Description 2696 amino acids. Murine Nsd1 is a nuclear protein containing SET, proline-tryptophan-tryptophan-proline (PWWP) and plant homedomain protein (PHD) finger domains. The protein has two distinct nuclear receptor (NR)-interaction domains (NID-L, NID+L). Human NSD1 shows 86% identity to the murine Nsd1 at the nucleotide level and 83% at the amino acid level, retaining the nuclear interaction domains (NID) as well as the SET/SAC and PHD finger domains.
Expression Widely expressed
Function Features of a basic transcription factor, also of a bifunctional transcriptional regulator, (similar to murine Nsd1)
Homology NSD2: (Wolf-Hirschhorn syndrome critical region on 4p); NSD3: expressed in tumour cell lines

Implicated in

Note
Entity t(5;11)(q35;p15.5)/ acute non lymphoblastic leukemia (AML)
Disease De novo childhood AML
Prognosis Only 5 cases reported. All had poor response to treatment/short survival
Cytogenetics Cryptic: associated with del(5q) (sole cytogenetic abnormality) or a normal karyotype
Hybrid/Mutated Gene 5' NUP98- 3' NSD1 ; NSD1-NUP98 also present in all cases tested
Abnormal Protein NH2 NUP98- COOH NSD1: Fuses the FXFG portion of NUP98 to the SET, SAC and PHD finger domains of NSD1. NSD1-NUP98: Fuses the RNA-binding domain of NSD1 to the NID domain NUP98
  

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
 
A cryptic t(5;11)(q35;p15.5) in 2 children with acute myeloid leukemia with apparently normal karyotypes, identified by a multiplex fluorescence in situ hybridization telomere assay.
Brown J, Jawad M, Twigg SR, Saracoglu K, Sauerbrey A, Thomas AE, Eils R, Harbott J, Kearney L
Blood. 2002 ; 99 (7) : 2526-2531.
PMID 11895789
 
Two distinct nuclear receptor interaction domains in NSD1, a novel SET protein that exhibits characteristics of both corepressors and coactivators.
Huang N, vom Baur E, Garnier JM, Lerouge T, Vonesch JL, Lutz Y, Chambon P, Losson R
The EMBO journal. 1998 ; 17 (12) : 3398-3412.
PMID 9628876
 
A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia.
Jaju RJ, Fidler C, Haas OA, Strickson AJ, Watkins F, Clark K, Cross NC, Cheng JF, Aplan PD, Kearney L, Boultwood J, Wainscoat JS
Blood. 2001 ; 98 (4) : 1264-1267.
PMID 11493482
 
A new recurrent translocation, t(5;11)(q35;p15.5), associated with del(5q) in childhood acute myeloid leukemia. The UK Cancer Cytogenetics Group (UKCCG)
Jaju RJ, Haas OA, Neat M, Harbott J, Saha V, Boultwood J, Brown JM, Pirc-Danoewinata H, Krings BW, Müller U, Morris SW, Wainscoat JS, Kearney L
Blood. 1999 ; 94 (2) : 773-780.
PMID 10397745
 
Molecular characterization of NSD1, a human homologue of the mouse Nsd1 gene.
Kurotaki N, Harada N, Yoshiura K, Sugano S, Niikawa N, Matsumoto N
Gene. 2001 ; 279 (2) : 197-204.
PMID 11733144
 
NUP98 gene fusions in hematologic malignancies.
Lam DH, Aplan PD
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2001 ; 15 (11) : 1689-1695.
PMID 11681408
 
WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma.
Stec I, Wright TJ, van Ommen GJ, de Boer PA, van Haeringen A, Moorman AF, Altherr MR, den Dunnen JT
Human molecular genetics. 1998 ; 7 (7) : 1071-1082.
PMID 9618163
 

Citation

This paper should be referenced as such :
Kearney, L
NSD1 (nuclear receptor-binding, su(var), enhancer-of-zeste, trithorax domain-containing protein 1
Atlas Genet Cytogenet Oncol Haematol. 2002;6(3):191-192.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/NSD1ID356.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(3;11)(p25;p15) ANKRD28/NUP98
t(5;11)(q35;p15.5) NUP98/NSD1
t(5;11)(q35;q12) NSD1/FEN1

Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 2 ]
  Beckwith-Wiedemann syndrome Sotos syndrome (SOS)

External links

Nomenclature
HGNC (Hugo)NSD1   14234
Cards
AtlasNSD1ID356
Entrez_Gene (NCBI)NSD1  64324  nuclear receptor binding SET domain protein 1
AliasesARA267; KMT3B; SOTOS; SOTOS1; 
STO
GeneCards (Weizmann)NSD1
Ensembl hg19 (Hinxton)ENSG00000165671 [Gene_View]  chr5:176560833-176727214 [Contig_View]  NSD1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000165671 [Gene_View]  chr5:176560833-176727214 [Contig_View]  NSD1 [Vega]
ICGC DataPortalENSG00000165671
TCGA cBioPortalNSD1
AceView (NCBI)NSD1
Genatlas (Paris)NSD1
WikiGenes64324
SOURCE (Princeton)NSD1
Genomic and cartography
GoldenPath hg19 (UCSC)NSD1  -     chr5:176560833-176727214 +  5q35   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)NSD1  -     5q35   [Description]    (hg38-Dec_2013)
EnsemblNSD1 - 5q35 [CytoView hg19]  NSD1 - 5q35 [CytoView hg38]
Mapping of homologs : NCBINSD1 [Mapview hg19]  NSD1 [Mapview hg38]
OMIM117550   130650   606681   
Gene and transcription
Genbank (Entrez)AF085858 AF322907 AF380302 AF395588 AK001546
RefSeq transcript (Entrez)NM_022455 NM_172349
RefSeq genomic (Entrez)NC_000005 NC_018916 NG_009821 NT_023133 NW_004929325
Consensus coding sequences : CCDS (NCBI)NSD1
Cluster EST : UnigeneHs.106861 [ NCBI ]
CGAP (NCI)Hs.106861
Alternative Splicing GalleryENSG00000165671
Gene ExpressionNSD1 [ NCBI-GEO ]   NSD1 [ EBI - ARRAY_EXPRESS ]   NSD1 [ SEEK ]   NSD1 [ MEM ]
Gene Expression Viewer (FireBrowse)NSD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)64324
GTEX Portal (Tissue expression)NSD1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96L73 (Uniprot)
NextProtQ96L73  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96L73
Splice isoforms : SwissVarQ96L73 (Swissvar)
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 ]   
PhosPhoSitePlusQ96L73
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)  
DMDM Disease mutations64324
Blocks (Seattle)NSD1
PDB (SRS)3OOI   
PDB (PDBSum)3OOI   
PDB (IMB)3OOI   
PDB (RSDB)3OOI   
Structural Biology KnowledgeBase3OOI   
SCOP (Structural Classification of Proteins)3OOI   
CATH (Classification of proteins structures)3OOI   
SuperfamilyQ96L73
Human Protein AtlasENSG00000165671
Peptide AtlasQ96L73
HPRD09455
IPIIPI00102107   IPI00173901   IPI00332367   IPI00448893   IPI00963897   IPI00964246   IPI00964665   IPI00915453   IPI00967710   IPI00965678   IPI00966692   IPI00967441   IPI00964779   
Protein Interaction databases
DIP (DOE-UCLA)Q96L73
IntAct (EBI)Q96L73
FunCoupENSG00000165671
BioGRIDNSD1
STRING (EMBL)NSD1
ZODIACNSD1
Ontologies - Pathways
QuickGOQ96L73
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  regulation of histone H3-K36 methylation  RNA polymerase II core promoter sequence-specific DNA binding  chromatin binding  transcription cofactor activity  transcription corepressor activity  nucleoplasm  chromosome  transcription, DNA-templated  zinc ion binding  histone H3-K36 methylation  histone H3-K36 methylation  histone methylation  histone-lysine N-methyltransferase activity  estrogen receptor binding  regulation of peptidyl-serine phosphorylation  histone H4-K20 methylation  histone lysine methylation  histone methyltransferase activity (H4-K20 specific)  retinoic acid receptor binding  positive regulation of transcription, DNA-templated  retinoid X receptor binding  thyroid hormone receptor binding  histone methyltransferase activity (H3-K36 specific)  histone methyltransferase activity (H3-K36 specific)  androgen receptor binding  regulation of RNA polymerase II regulatory region sequence-specific DNA binding  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  regulation of histone H3-K36 methylation  RNA polymerase II core promoter sequence-specific DNA binding  chromatin binding  transcription cofactor activity  transcription corepressor activity  nucleoplasm  chromosome  transcription, DNA-templated  zinc ion binding  histone H3-K36 methylation  histone H3-K36 methylation  histone methylation  histone-lysine N-methyltransferase activity  estrogen receptor binding  regulation of peptidyl-serine phosphorylation  histone H4-K20 methylation  histone lysine methylation  histone methyltransferase activity (H4-K20 specific)  retinoic acid receptor binding  positive regulation of transcription, DNA-templated  retinoid X receptor binding  thyroid hormone receptor binding  histone methyltransferase activity (H3-K36 specific)  histone methyltransferase activity (H3-K36 specific)  androgen receptor binding  regulation of RNA polymerase II regulatory region sequence-specific DNA binding  
Pathways : KEGGLysine degradation   
REACTOMEQ96L73 [protein]
REACTOME PathwaysR-HSA-3214841 PKMTs methylate histone lysines [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkNSD1
Wikipedia pathwaysNSD1
Orthology - Evolution
OrthoDB64324
GeneTree (enSembl)ENSG00000165671
Phylogenetic Trees/Animal Genes : TreeFamNSD1
Homologs : HomoloGeneNSD1
Homology/Alignments : Family Browser (UCSC)NSD1
Gene fusions - Rearrangements
Fusion : MitelmanB4GALT7/NSD1 [5q35.3/5q35.2]  [t(5;5)(q35;q35)]  
Fusion : MitelmanCDH23/NSD1 [10q22.1/5q35.2]  [t(5;10)(q35;q22)]  
Fusion : MitelmanNSD1/CDH23 [5q35.2/10q22.1]  [t(5;10)(q35;q22)]  
Fusion : MitelmanNSD1/FAT2 [5q35.2/5q33.1]  [t(5;5)(q33;q35)]  
Fusion : MitelmanNSD1/NUP98 [5q35.2/11p15.4]  [t(5;11)(q35;p15)]  
Fusion : MitelmanNSD1/UNC5A [5q35.2/5q35.2]  [t(5;5)(q35;q35)]  
Fusion : MitelmanNSD1/ZNF346 [5q35.2/5q35.2]  [t(5;5)(q35;q35)]  
Fusion : MitelmanNUP98/NSD1 [11p15.4/5q35.2]  [ins(5;11)(q35;p15p13)]  [t(5;11)(q35;p15)]  
[t(5;11;12)(q35;p15;q24)]  
Fusion : MitelmanSTIM1/NSD1 [11p15.4/5q35.2]  [t(5;11)(q35;p15)]  
Fusion: TCGAB4GALT7 5q35.3 NSD1 5q35.2 BRCA
Fusion: TCGACDH23 10q22.1 NSD1 5q35.2 BRCA
Fusion: TCGANSD1 5q35.2 CDH23 10q22.1 BRCA
Fusion: TCGANSD1 5q35.2 FAT2 5q33.1 BLCA
Fusion: TCGANSD1 5q35.2 NUP98 11p15.4 LAML
Fusion: TCGANSD1 5q35.2 UNC5A 5q35.2 LUAD
Fusion: TCGANSD1 5q35.2 ZNF346 5q35.2 BRCA OV
Fusion: TCGANUP98 11p15.4 NSD1 5q35.2 LAML
Fusion : TICdbNSD1 [5q35.2]  -  ANKRD28 [3p25.1]
Fusion : TICdbNUP98 [11p15.4]  -  NSD1 [5q35.2]
Fusion Cancer (Beijing)EEF2 [19p13.3]  -  NSD1 [5q35.2]  [FUSC002228]
Polymorphisms : SNP, variants
NCBI Variation ViewerNSD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NSD1
dbVarNSD1
ClinVarNSD1
1000_GenomesNSD1 
Exome Variant ServerNSD1
ExAC (Exome Aggregation Consortium)NSD1 (select the gene name)
Genetic variants : HAPMAP64324
Genomic Variants (DGV)NSD1 [DGVbeta]
Mutations
ICGC Data PortalNSD1 
TCGA Data PortalNSD1 
Broad Tumor PortalNSD1
OASIS PortalNSD1 [ Somatic mutations - Copy number]
Cancer Gene: CensusNSD1 
Somatic Mutations in Cancer : COSMICNSD1 
intOGen PortalNSD1
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
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch NSD1
DgiDB (Drug Gene Interaction Database)NSD1
DoCM (Curated mutations)NSD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NSD1 (select a term)
intoGenNSD1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)5:176560833-176727214  ENSG00000165671
CONAN: Copy Number AnalysisNSD1 
Mutations and Diseases : HGMDNSD1
OMIM117550    130650    606681   
MedgenNSD1
Genetic Testing Registry NSD1
NextProtQ96L73 [Medical]
TSGene64324
GENETestsNSD1
Huge Navigator NSD1 [HugePedia]
snp3D : Map Gene to Disease64324
BioCentury BCIQNSD1
ClinGenNSD1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD64324
Chemical/Pharm GKB GenePA31790
Clinical trialNSD1
Miscellaneous
canSAR (ICR)NSD1 (select the gene name)
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=NSD1
Probes
ProbeHSP2301A4
Litterature
PubMed66 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNSD1
EVEXNSD1
GoPubMedNSD1
iHOPNSD1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Aug 10 18:56:25 CEST 2016

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