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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
  • Nuclear SET Domain-Containing Protein 3 3 4
  • Protein Whistle 3 4
  • WHSC1L1 3 4
  • Wolf-Hirschhorn Syndrome Candidate 1-Like Protein 1 4
  • Histone-Lysine N-Methyltransferase NSD3 3
  • WHSC1-Like Protein 1 4
  • EC 2.1.1.43 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 Leukemia, Acute Myeloid and Wolf-Hirschhorn Syndrome. Among its related pathways are Chromatin organization and PKMTs methylate histone lysines. An important paralog of this gene is NSD2.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for NSD3 Gene

Genomics for NSD3 Gene

GeneHancer (GH) Regulatory Elements for NSD3 Gene

Promoters and enhancers for NSD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J038379 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 683.3 -1.2 -1178 8.1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 ZNF263 SP3 NFYC NSD3 LETM2 ENSG00000272092 DDHD2 RPS20P22 ERLIN2 ASH2L TM2D2 ENSG00000255201 ENSG00000254306
GH08J037889 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 40.5 +484.4 484447 17.5 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 SP3 ZC3H11A RAB11FIP1 ADGRA2 NSD3 ENSG00000255201 ERLIN2 DDHD2 FGFR1 LOC728024 LETM2 ASH2L
GH08J038764 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 31.3 -386.0 -386042 7.5 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A YBX1 ZNF2 IRF4 YY1 ENSG00000255201 DDHD2 ADGRA2 NSD3 TACC1 FGFR1 TM2D2 LETM2 EIF4EBP1 ADAM5
GH08J037693 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 20.2 +684.8 684784 7.9 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF213 ZNF703 ERLIN2 ADGRA2 DDHD2 ENSG00000255201 LOC728024 NSD3 FGFR1 RPS20P22 ENSG00000254306
GH08J037603 Enhancer 1.4 Ensembl ENCODE dbSUPER 29.9 +777.9 777851 1.2 PKNOX1 FOXA2 MLX ARID4B DMAP1 ZNF2 SLC30A9 ZNF207 ZNF548 SP5 DDHD2 RPS20P22 NSD3 ERLIN2 ADGRA2 LOC102723716 FGFR1 ENSG00000255201 ENSG00000260949 ENSG00000254306
- 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

Genomic Locations for NSD3 Gene

Genomic Locations for NSD3 Gene
chr8:38,269,697-38,382,354
(GRCh38/hg38)
Size:
112,658 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; Positions=Several; 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; 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

Post-translational modifications for NSD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NSD3 Gene

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

Suggested Antigen Peptide Sequences for NSD3 Gene

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:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].

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:0005515 protein binding IPI 23455924
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0018024 histone-lysine N-methyltransferase activity TAS --
GO:0046872 metal ion binding IEA --
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
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:0005634 nucleus IC 16682010
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

1 KEGG pathway for NSD3 Gene

Gene Ontology (GO) - Biological Process for NSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016571 histone methylation IDA 16682010
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with NSD3: view

No data available for SIGNOR curated interactions for NSD3 Gene

Drugs & Compounds for NSD3 Gene

(2) Drugs for NSD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Lysine Approved 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

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
ECgene alternative splicing isoforms for
NSD3

Expression for NSD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of NSD3 Gene:

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 34 33
  • 99.79 (n)
OneToOne
dog
(Canis familiaris)
Mammalia WHSC1L1 34 33
  • 94.27 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WHSC1L1 34
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia WHSC1L1 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Whsc1l1 34 33
  • 88.49 (n)
OneToOne
Nsd3 16
cow
(Bos Taurus)
Mammalia WHSC1L1 34 33
  • 87.94 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Whsc1l1 33
  • 87.36 (n)
chicken
(Gallus gallus)
Aves WHSC1L1 34 33
  • 82.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia WHSC1L1 34
  • 84 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii whsc1l1 34 33
  • 63.73 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Mes-4 34
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-12 34
  • 26 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9549 34
  • 51 (a)
OneToMany
Cin.390 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.390 33
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 from dbSNP and Humsavar for NSD3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000034580 -- 38,343,046(-) A/T intron_variant
rs1000048988 -- 38,350,840(-) T/C intron_variant
rs1000085530 -- 38,350,543(-) T/C intron_variant
rs1000102310 -- 38,312,111(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000139731 -- 38,350,332(-) C/T intron_variant

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

(2) MalaCards diseases for NSD3 Gene - From: OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
leukemia, acute myeloid
  • aml
wolf-hirschhorn syndrome
  • whs
- 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 22 58
  2. 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 58
  3. 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 58
  4. 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 58
  5. High-resolution genomic profiles of human lung cancer. (PMID: 15983384) Tonon G … Depinho RA (Proceedings of the National Academy of Sciences of the United States of America 2005) 3 4 58

Products for NSD3 Gene

Sources for NSD3 Gene

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