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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
HGNC Alias symbARA267
FLJ22263
KMT3B
HGNC Previous nameSTO
HGNC Previous nameSotos syndrome
LocusID (NCBI) 64324
Atlas_Id 356
Location 5q35.2  [Link to chromosome band 5q35]
Location_base_pair Starts at 177133079 and ends at 177300213 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping NSD1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ARMCX4 (Xq22.1)::NSD1 (5q35.2)B4GALT7 (5q35.3)::NSD1 (5q35.2)B4GALT7 (5q35.3)::NSD1 (5q35.3)
CDH23 (10q22.1)::NSD1 (5q35.2)CDH23 (10q22.1)::NSD1 (5q35.3)EEF2 (19p13.3)::NSD1 (5q35.2)
EEF2 (19p13.3)::NSD1 (5q35.3)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)NSD1 (5q35.3)::ANKRD28 (3p25.1)NSD1 (5q35.3)::CDH23 (10q22.1)
NSD1 (5q35.3)::EFNA5 (5q21.3)NSD1 (5q35.3)::FAT2 (5q33.1)NSD1 (5q35.3)::NUP98 (11p15.4)
NSD1 (5q35.3)::UNC5A (5q35.2)NSD1 (5q35.3)::ZNF346 (5q35.2)NUP98 (11p15.4)::NSD1 (5q35.2)
NUP98 (11p15.4)::NSD1 (5q35.3)STIM1 (11p15.4)::NSD1 (5q35.2)STIM1 (11p15.4)::NSD1 (5q35.3)
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 / 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 (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 ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 5 ]
  t(3;11)(p25;p15) ANKRD28::NUP98
t(5;11)(q35;p15.5) NUP98::NSD1
t(5;11)(q35;q12) NSD1::FEN1
t(5;5)(q35;q35) LMAN2::NSD1
t(5;11)(q35;p15) STIM1::NSD1


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
LRG (Locus Reference Genomic)LRG_512
Cards
AtlasNSD1ID356
Entrez_Gene (NCBI)NSD1    nuclear receptor binding SET domain protein 1
AliasesARA267; KMT3B; SOTOS; SOTOS1; 
STO
GeneCards (Weizmann)NSD1
Ensembl hg19 (Hinxton)ENSG00000165671 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000165671 [Gene_View]  ENSG00000165671 [Sequence]  chr5:177133079-177300213 [Contig_View]  NSD1 [Vega]
ICGC DataPortalENSG00000165671
TCGA cBioPortalNSD1
AceView (NCBI)NSD1
Genatlas (Paris)NSD1
SOURCE (Princeton)NSD1
Genetics Home Reference (NIH)NSD1
Genomic and cartography
GoldenPath hg38 (UCSC)NSD1  -     chr5:177133079-177300213 +  5q35.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NSD1  -     5q35.3   [Description]    (hg19-Feb_2009)
GoldenPathNSD1 - 5q35.3 [CytoView hg19]  NSD1 - 5q35.3 [CytoView hg38]
ImmunoBaseENSG00000165671
Genome Data Viewer NCBINSD1 [Mapview hg19]  
OMIM117550   606681   
Gene and transcription
Genbank (Entrez)AF085858 AF322907 AF380302 AF395588 AK001546
RefSeq transcript (Entrez)NM_001365684 NM_022455 NM_172349
Consensus coding sequences : CCDS (NCBI)NSD1
Gene ExpressionNSD1 [ NCBI-GEO ]   NSD1 [ EBI - ARRAY_EXPRESS ]   NSD1 [ SEEK ]   NSD1 [ MEM ]
Gene Expression Viewer (FireBrowse)NSD1 [ Firebrowse - Broad ]
GenevisibleExpression of NSD1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)64324
GTEX Portal (Tissue expression)NSD1
Human Protein AtlasENSG00000165671-NSD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96L73   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96L73  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96L73
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    C5HCH    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)AWS (PF17907)    C5HCH (PF17982)    PWWP (PF00855)    SET (PF00856)   
Domain families : Pfam (NCBI)pfam17907    pfam17982    pfam00855    pfam00856   
Domain families : Smart (EMBL)AWS (SM00570)  PHD (SM00249)  PostSET (SM00508)  PWWP (SM00293)  SET (SM00317)  
Conserved Domain (NCBI)NSD1
PDB (RSDB)3OOI    6KQP    6KQQ   
PDB Europe3OOI    6KQP    6KQQ   
PDB (PDBSum)3OOI    6KQP    6KQQ   
PDB (IMB)3OOI    6KQP    6KQQ   
Structural Biology KnowledgeBase3OOI    6KQP    6KQQ   
SCOP (Structural Classification of Proteins)3OOI    6KQP    6KQQ   
CATH (Classification of proteins structures)3OOI    6KQP    6KQQ   
SuperfamilyQ96L73
AlphaFold pdb e-kbQ96L73   
Human Protein Atlas [tissue]ENSG00000165671-NSD1 [tissue]
HPRD09455
Protein Interaction databases
DIP (DOE-UCLA)Q96L73
IntAct (EBI)Q96L73
BioGRIDNSD1
STRING (EMBL)NSD1
ZODIACNSD1
Ontologies - Pathways
QuickGOQ96L73
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  regulation of histone H3-K36 methylation  chromatin  RNA polymerase II cis-regulatory region sequence-specific DNA binding  chromatin binding  transcription coregulator activity  transcription corepressor activity  protein binding  nucleus  nucleoplasm  regulation of transcription, DNA-templated  zinc ion binding  histone H3-K36 methylation  histone methylation  estrogen receptor binding  regulation of peptidyl-serine phosphorylation  histone H4-K20 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)  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 by RNA polymerase II  regulation of histone H3-K36 methylation  chromatin  RNA polymerase II cis-regulatory region sequence-specific DNA binding  chromatin binding  transcription coregulator activity  transcription corepressor activity  protein binding  nucleus  nucleoplasm  regulation of transcription, DNA-templated  zinc ion binding  histone H3-K36 methylation  histone methylation  estrogen receptor binding  regulation of peptidyl-serine phosphorylation  histone H4-K20 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)  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 [pathway]   
NDEx NetworkNSD1
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]  
Fusion : MitelmanCDH23::NSD1 [10q22.1/5q35.2]  
Fusion : MitelmanNSD1::CDH23 [5q35.2/10q22.1]  
Fusion : MitelmanNSD1::FAT2 [5q35.2/5q33.1]  
Fusion : MitelmanNSD1::NUP98 [5q35.2/11p15.4]  
Fusion : MitelmanNSD1::UNC5A [5q35.2/5q35.2]  
Fusion : MitelmanNSD1::ZNF346 [5q35.2/5q35.2]  
Fusion : MitelmanNUP98::NSD1 [11p15.4/5q35.2]  
Fusion : MitelmanSTIM1::NSD1 [11p15.4/5q35.2]  
Fusion Cancer (Beijing)EEF2 [19p13.3]  -  NSD1 [5q35.2]  [FUSC002228]
Fusion : QuiverNSD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNSD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NSD1
dbVarNSD1
ClinVarNSD1
MonarchNSD1
1000_GenomesNSD1 
Exome Variant ServerNSD1
GNOMAD BrowserENSG00000165671
Varsome BrowserNSD1
ACMGNSD1 variants
VarityQ96L73
Genomic Variants (DGV)NSD1 [DGVbeta]
DECIPHERNSD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNSD1 
Mutations
ICGC Data PortalNSD1 
TCGA Data PortalNSD1 
Broad Tumor PortalNSD1
OASIS PortalNSD1 [ Somatic mutations - Copy number]
Cancer Gene: CensusNSD1 
Somatic Mutations in Cancer : COSMICNSD1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DNSD1
Mutations and Diseases : HGMDNSD1
intOGen PortalNSD1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaNSD1
DgiDB (Drug Gene Interaction Database)NSD1
DoCM (Curated mutations)NSD1
CIViC (Clinical Interpretations of Variants in Cancer)NSD1
OncoKBNSD1
NCG (London)NSD1
Cancer3DNSD1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM117550    606681   
Orphanet588    604    1121    19128    19282   
DisGeNETNSD1
MedgenNSD1
Genetic Testing Registry NSD1
NextProtQ96L73 [Medical]
GENETestsNSD1
Target ValidationNSD1
Huge Navigator NSD1 [HugePedia]
ClinGenNSD1 (curated)
Clinical trials, drugs, therapy
MyCancerGenomeNSD1
Protein Interactions : CTDNSD1
Pharm GKB GenePA31790
PharosQ96L73
Clinical trialNSD1
Miscellaneous
canSAR (ICR)NSD1
HarmonizomeNSD1
DataMed IndexNSD1
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=NSD1
Probes
Litterature
PubMed103 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXNSD1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Oct 8 21:24:04 CEST 2021

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