This gene is related to the Wolf-Hirschhorn syndrome candidate-1 gene and encodes a protein with PWWP (proline-tryptophan-tryptophan-proline) domains. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. Two alternatively spliced variants have been described. [provided by RefSeq, May 2015] See more...

Aliases for NSD3 Gene

Aliases for NSD3 Gene

  • Nuclear Receptor Binding SET Domain Protein 3 2 3 5
  • WHSC1-Like 1 Isoform 9 With Methyltransferase Activity To Lysine 3 4
  • Wolf-Hirschhorn Syndrome Candidate 1-Like 1 2 3
  • Histone-Lysine N-Methyltransferase NSD3 3 4
  • Nuclear SET Domain-Containing Protein 3 3 4
  • Protein Whistle 3 4
  • WHSC1L1 3 4
  • Wolf-Hirschhorn Syndrome Candidate 1-Like Protein 1 4
  • WHSC1-Like Protein 1 4
  • EC 2.1.1.43 52
  • EC 2.1.1.- 4
  • WHISTLE 3
  • Pp14328 3
  • KMT3F 3
  • KMT3G 3

External Ids for NSD3 Gene

Previous HGNC Symbols for NSD3 Gene

  • WHSC1L1

Summaries for NSD3 Gene

Entrez Gene Summary for NSD3 Gene

  • This gene is related to the Wolf-Hirschhorn syndrome candidate-1 gene and encodes a protein with PWWP (proline-tryptophan-tryptophan-proline) domains. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. Two alternatively spliced variants have been described. [provided by RefSeq, May 2015]

GeneCards Summary for NSD3 Gene

NSD3 (Nuclear Receptor Binding SET Domain Protein 3) is a Protein Coding gene. Diseases associated with NSD3 include Wolf-Hirschhorn Syndrome and Nut Midline Carcinoma. Among its related pathways are PKMTs methylate histone lysines and Chromatin organization. An important paralog of this gene is NSD2.

UniProtKB/Swiss-Prot Summary for NSD3 Gene

  • Histone methyltransferase. Preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, while 'Lys-27' is a mark for transcriptional repression.

Gene Wiki entry for NSD3 Gene

Additional gene information for NSD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NSD3 Gene

Genomics for NSD3 Gene

GeneHancer (GH) Regulatory Elements for NSD3 Gene

Promoters and enhancers for NSD3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NSD3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NSD3

Genomic Locations for NSD3 Gene

Genomic Locations for NSD3 Gene
chr8:38,269,699-38,382,354
(GRCh38/hg38)
Size:
112,656 bases
Orientation:
Minus strand
chr8:38,127,215-38,239,790
(GRCh37/hg19)
Size:
112,576 bases
Orientation:
Minus strand

Genomic View for NSD3 Gene

Genes around NSD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSD3 Gene

Proteins for NSD3 Gene

  • Protein details for NSD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BZ95-NSD3_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase NSD3
    Protein Accession:
    Q9BZ95
    Secondary Accessions:
    • B7ZL11
    • D3DSX1
    • Q1RMD3
    • Q3B796
    • Q6ZSA5
    • Q9BYU8
    • Q9BYU9
    • Q9H2M8
    • Q9H9W9
    • Q9NXA6

    Protein attributes for NSD3 Gene

    Size:
    1437 amino acids
    Molecular mass:
    161613 Da
    Quaternary structure:
    • Interacts with BRD4.
    SequenceCaution:
    • Sequence=AAG44637.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAI07735.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA91110.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NSD3 Gene

    Alternative splice isoforms for NSD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NSD3 Gene

Selected DME Specific Peptides for NSD3 Gene

Q9BZ95:
  • WWPAEIC
  • KGEFVNEYVGELIDEEEC
  • RCPVAYH
  • CGKFYHE
  • RFMNHSC
  • ELTFNYN
  • GKWECPWH
  • NHSCNPN
  • IIDAGPKGN

Post-translational modifications for NSD3 Gene

  • Ubiquitination at Lys1065
  • Modification sites at PhosphoSitePlus

Domains & Families for NSD3 Gene

Gene Families for NSD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for NSD3 Gene

Blocks:
  • Zn-finger-like, PHD finger
  • Zn-finger, RING
  • Nuclear protein SET
  • SET-related region
  • PWWP domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NSD3 Gene

GenScript: Design optimal peptide antigens:
  • WHSC1L1 protein (B7ZL11_HUMAN)
  • Wolf-Hirschhorn syndrome candidate 1-like protein 1 (NSD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BZ95

UniProtKB/Swiss-Prot:

NSD3_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.
genes like me logo Genes that share domains with NSD3: view

Function for NSD3 Gene

Molecular function for NSD3 Gene

UniProtKB/Swiss-Prot Function:
Histone methyltransferase. Preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, while 'Lys-27' is a mark for transcriptional repression.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence=. ;.

Enzyme Numbers (IUBMB) for NSD3 Gene

Phenotypes From GWAS Catalog for NSD3 Gene

Gene Ontology (GO) - Molecular Function for NSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IMP 21555454
GO:0005515 protein binding IPI 21555454
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0018024 histone-lysine N-methyltransferase activity IDA 16682010
genes like me logo Genes that share ontologies with NSD3: view
genes like me logo Genes that share phenotypes with NSD3: view

Animal Models for NSD3 Gene

MGI Knock Outs for NSD3:
  • Nsd3 Nsd3<tm1b(EUCOMM)Hmgu>

Animal Model Products

Clone Products

  • Addgene plasmids for NSD3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NSD3 Gene

Localization for NSD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSD3 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NSD3 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA 21873635
GO:0005634 nucleus IMP,IBA 21555454
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with NSD3: view

Pathways & Interactions for NSD3 Gene

genes like me logo Genes that share pathways with NSD3: view

Pathways by source for NSD3 Gene

SIGNOR curated interactions for NSD3 Gene

Activates:

Gene Ontology (GO) - Biological Process for NSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0010452 histone H3-K36 methylation IEA --
GO:0016571 histone methylation IDA 16682010
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with NSD3: view

Drugs & Compounds for NSD3 Gene

(2) Drugs for NSD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
D-Lysine Approved, Experimental Nutra Full agonist, Agonist 0
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for NSD3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with NSD3: view

Transcripts for NSD3 Gene

mRNA/cDNA for NSD3 Gene

2 REFSEQ mRNAs :
25 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

  • Addgene plasmids for NSD3

Alternative Splicing Database (ASD) splice patterns (SP) for NSD3 Gene

No ASD Table

Relevant External Links for NSD3 Gene

GeneLoc Exon Structure for
NSD3

Expression for NSD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NSD3

mRNA Expression by UniProt/SwissProt for NSD3 Gene:

Q9BZ95-NSD3_HUMAN
Tissue specificity: Highly expressed in brain, heart and skeletal muscle. Expressed at lower level in liver and lung.

Evidence on tissue expression from TISSUES for NSD3 Gene

  • Nervous system(4.6)
  • Lymph node(4.3)
  • Spleen(4.3)
  • Blood(4.2)
  • Lung(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NSD3 Gene

Germ Layers:
  • mesoderm
Systems:
  • immune
  • lymphatic
Regions:
General:
  • blood
  • bone marrow
  • white blood cell

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for NSD3 Gene

Orthologs for NSD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NSD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WHSC1L1 31 30
  • 99.79 (n)
OneToOne
dog
(Canis familiaris)
Mammalia WHSC1L1 31 30
  • 94.27 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WHSC1L1 31
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia WHSC1L1 31
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Whsc1l1 31 30
  • 88.49 (n)
OneToOne
Nsd3 17
cow
(Bos Taurus)
Mammalia WHSC1L1 31 30
  • 87.94 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Whsc1l1 30
  • 87.36 (n)
chicken
(Gallus gallus)
Aves WHSC1L1 31 30
  • 82.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia WHSC1L1 31
  • 84 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii whsc1l1 31 30
  • 63.73 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Mes-4 31
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-12 31
  • 26 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9549 31
  • 51 (a)
OneToMany
Cin.390 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.390 30
Species where no ortholog for NSD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for NSD3 Gene

ENSEMBL:
Gene Tree for NSD3 (if available)
TreeFam:
Gene Tree for NSD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NSD3: view image

Paralogs for NSD3 Gene

Pseudogenes.org Pseudogenes for NSD3 Gene

genes like me logo Genes that share paralogs with NSD3: view

Variants for NSD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NSD3 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
713975 Benign: not provided 38,290,632(-) G/A SYNONYMOUS_VARIANT
716914 Benign: not provided 38,329,811(-) C/G MISSENSE_VARIANT
733352 Benign: not provided 38,304,635(-) T/C MISSENSE_VARIANT
743861 Likely Benign: not provided 38,326,771(-) G/A MISSENSE_VARIANT
752924 Likely Benign: not provided 38,337,455(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NSD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NSD3 Gene

Variant ID Type Subtype PubMed ID
dgv2065e212 CNV loss 25503493
dgv7164n100 CNV gain 25217958
esv1006743 CNV loss 20482838
esv2665656 CNV deletion 23128226
esv2675588 CNV deletion 23128226
esv3616921 CNV loss 21293372
esv3616922 CNV loss 21293372
esv3616923 CNV loss 21293372
nsv1124336 CNV deletion 24896259
nsv477158 CNV novel sequence insertion 20440878
nsv528419 CNV loss 19592680
nsv824602 CNV loss 20364138

Variation tolerance for NSD3 Gene

Residual Variation Intolerance Score: 4.62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NSD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NSD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSD3 Gene

Disorders for NSD3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for NSD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • whs
nut midline carcinoma
  • nuclear protein in testis midline carcinoma
sotos syndrome 1
  • sotos1
weaver syndrome
  • wvs
- elite association - COSMIC cancer census association via MalaCards
Search NSD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NSD3_HUMAN
  • Note=Defects in NSD3 may be involved in non small cell lung carcinomas (NSCLC). Amplified or overexpressed in NSCLC. {ECO:0000269 PubMed:15983384}.
  • Note=A chromosomal aberration involving NSD3 is found in childhood acute myeloid leukemia. Translocation t(8;11)(p11.2;p15) with NUP98. {ECO:0000269 PubMed:11986249}.

Additional Disease Information for NSD3

genes like me logo Genes that share disorders with NSD3: view

No data available for Genatlas for NSD3 Gene

Publications for NSD3 Gene

  1. WHSC1L1, on human chromosome 8p11.2, closely resembles WHSC1 and maps to a duplicated region shared with 4p16.3. (PMID: 11549311) Stec I … den Dunnen JT (Genomics 2001) 3 4 23 54
  2. Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4. (PMID: 29176719) Konuma T … Zeng L (Scientific reports 2017) 3 4 54
  3. The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition. (PMID: 23269674) He C … Shi Y (The Journal of biological chemistry 2013) 2 3 54
  4. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. (PMID: 21555454) Rahman S … Howley PM (Molecular and cellular biology 2011) 3 4 54
  5. Characterization of a novel WHSC1-associated SET domain protein with H3K4 and H3K27 methyltransferase activity. (PMID: 16682010) Kim SM … Seo SB (Biochemical and biophysical research communications 2006) 3 4 54

Products for NSD3 Gene