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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
  • EC 2.1.1.43 4 58
  • WHSC1L1 3 4
  • Wolf-Hirschhorn Syndrome Candidate 1-Like Protein 1 4
  • Histone-Lysine N-Methyltransferase NSD3 3
  • WHSC1-Like Protein 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 Leukemia, Acute Myeloid and Wolf-Hirschhorn Syndrome. Among its related pathways are Chromatin organization and Lysine degradation. 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

Regulatory Elements for NSD3 Gene

Enhancers for NSD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H037889 2.1 FANTOM5 Ensembl ENCODE dbSUPER 48.8 +484.4 484447 17 ZFP64 FEZF1 DMAP1 SP3 ZC3H11A MEF2D GLIS1 NBN NR2C1 KDM1A ENSG00000255201 ADGRA2 NSD3 DDHD2 ERLIN2 FGFR1 LOC728024 RAB11FIP1 RPS20P22 ASH2L
GH08H038764 2 FANTOM5 Ensembl ENCODE dbSUPER 31.3 -386.0 -386043 7 HDGF PKNOX1 FOXA2 SIN3A ARID4B YBX1 ZNF2 YY1 ZNF302 ZNF143 DDHD2 ENSG00000255201 ADGRA2 NSD3 TACC1 FGFR1 RPS20P22 LETM2 EIF4EBP1 ADAM5
GH08H037543 1.5 Ensembl ENCODE dbSUPER 30.4 +837.0 837005 4 PKNOX1 ARNT ZNF133 FEZF1 GLI4 ZNF2 ZNF121 GLIS2 KLF7 ZNF548 ENSG00000255201 ADGRA2 NSD3 ENSG00000254306 LOC105379374 ERLIN2 FGFR1 ENSG00000253414 LINC01605
GH08H037603 1.5 Ensembl ENCODE dbSUPER 29.9 +777.9 777851 1 PKNOX1 FOXA2 ATF1 MLX ZNF493 ZNF133 ARID4B DMAP1 ZNF2 ZNF121 DDHD2 RPS20P22 NSD3 ERLIN2 ADGRA2 LOC102723716 FGFR1 ENSG00000255201 ENSG00000260949 ENSG00000254306
GH08H038379 1.8 FANTOM5 ENCODE dbSUPER 24 -1.2 -1179 8 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC ZNF610 ZNF585B GLIS1 DDHD2 NSD3 ERLIN2 ASH2L RPS20P22 TM2D2 ENSG00000255201 LETM2 ENSG00000254306 ADAM5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NSD3 on UCSC Golden Path with GeneCards custom track

Promoters for NSD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000223660 454 3801 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1

Genomic Location for NSD3 Gene

Chromosome:
8
Start:
38,269,697 bp from pter
End:
38,382,354 bp from pter
Size:
112,658 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

Selected DME Specific Peptides for NSD3 Gene

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

Post-translational modifications for NSD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

Enzyme Numbers (IUBMB) 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 tm1b(EUCOMM)Hmgu

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for NSD3
  • Applied Biological Materials Clones for NSD3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , 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:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification 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
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with NSD3: view

Transcripts for NSD3 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for NSD3
  • Applied Biological Materials Clones for NSD3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
Organs:
General:
  • blood
  • bone marrow
  • white blood cell

Primer Products

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 33 34
  • 94.27 (n)
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 33 34
  • 87.94 (n)
rat
(Rattus norvegicus)
Mammalia Whsc1l1 33
  • 87.36 (n)
chicken
(Gallus gallus)
Aves WHSC1L1 33 34
  • 82.4 (n)
lizard
(Anolis carolinensis)
Reptilia WHSC1L1 34
  • 84 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii whsc1l1 33 34
  • 63.73 (n)
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
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)

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 Sequence Context AA Info Type
rs1000034580 -- 38,343,046(+) AAAAA(A/T)TTAGC intron-variant
rs1000048988 -- 38,350,840(+) ATAAG(C/T)ATCTG intron-variant
rs1000085530 -- 38,350,543(+) TTTCT(C/T)GTAAA intron-variant
rs1000102310 -- 38,312,111(+) CAAGT(A/G)CTTAC intron-variant
rs1000139731 -- 38,350,332(+) CCACA(C/T)CCTCT 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)

Relevant External Links 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, GeneTests, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
leukemia, acute myeloid
  • leukemia, acute myeloid, somatic
wolf-hirschhorn syndrome
  • 4p deletion syndrome
- 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=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}.
  • Note=Defects in NSD3 may be involved in non small cell lung carcinomas (NSCLC). Amplified or overexpressed in NSCLC. {ECO:0000269 PubMed:15983384}.

Relevant External Links for NSD3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 60
  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 60
  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 60
  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 60

Products for NSD3 Gene

  • Addgene plasmids for NSD3

Sources for NSD3 Gene

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