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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)


HGNC (Hugo) NSD3
HGNC Alias symbFLJ20353
HGNC Previous nameWHSC1L1
HGNC Previous nameWolf-Hirschhorn syndrome candidate 1-like 1
LocusID (NCBI) 54904
Atlas_Id 42810
Location 8p11.23  [Link to chromosome band 8p11]
Location_base_pair Starts at 38269705 and ends at 38382271 bp from pter ( according to GRCh38/hg38-Dec_2013)  [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)


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).


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 .


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 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


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


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 ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  8p11 myeloproliferative syndrome (FGFR1)
t(8;11)(p11;p15) NUP98::WHSC1L1
t(8;11)(p12;p15) NUP98::NSD3

External links

HGNC (Hugo)NSD3   12767
Atlas Explorer : (Salamanque)NSD3
Entrez_Gene (NCBI)NSD3    nuclear receptor binding SET domain protein 3
GeneCards (Weizmann)NSD3
Ensembl hg19 (Hinxton)ENSG00000147548 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000147548 [Gene_View]  ENSG00000147548 [Sequence]  chr8:38269705-38382271 [Contig_View]  NSD3 [Vega]
ICGC DataPortalENSG00000147548
TCGA cBioPortalNSD3
AceView (NCBI)NSD3
Genatlas (Paris)NSD3
SOURCE (Princeton)NSD3
Genetics Home Reference (NIH)NSD3
Genomic and cartography
GoldenPath hg38 (UCSC)NSD3  -     chr8:38269705-38382271 -  8p11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NSD3  -     8p11.23   [Description]    (hg19-Feb_2009)
GoldenPathNSD3 - 8p11.23 [CytoView hg19]  NSD3 - 8p11.23 [CytoView hg38]
Genome Data Viewer NCBINSD3 [Mapview hg19]  
Gene and transcription
Genbank (Entrez)AF255649 AF318339 AF332468 AF332469 AJ295990
RefSeq transcript (Entrez)NM_017778 NM_023034
Consensus coding sequences : CCDS (NCBI)NSD3
Gene ExpressionNSD3 [ NCBI-GEO ]   NSD3 [ EBI - ARRAY_EXPRESS ]   NSD3 [ SEEK ]   NSD3 [ MEM ]
Gene Expression Viewer (FireBrowse)NSD3 [ Firebrowse - Broad ]
GenevisibleExpression of NSD3 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54904
GTEX Portal (Tissue expression)NSD3
Human Protein AtlasENSG00000147548-NSD3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)NSD3
Human Protein Atlas [tissue]ENSG00000147548-NSD3 [tissue]
Protein Interaction databases
Ontologies - Pathways
PubMed55 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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