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Aliases for NSD2 Gene

Aliases for NSD2 Gene

  • Nuclear Receptor Binding SET Domain Protein 2 2 3 5
  • Nuclear SET Domain-Containing Protein 2 3 4
  • Wolf-Hirschhorn Syndrome Candidate 1 2 3
  • EC 2.1.1.43 4 61
  • WHSC1 3 4
  • MMSET 3 4
  • TRX5 3 4
  • Multiple Myeloma SET Domain Containing Protein Type III 3
  • Probable Histone-Lysine N-Methyltransferase NSD2 3
  • Multiple Myeloma SET Domain Containing Protein 2
  • Multiple Myeloma SET Domain-Containing Protein 4
  • Wolf-Hirschhorn Syndrome Candidate 1 Protein 4
  • IL5 Promoter REII Region-Binding Protein 3
  • Histone-Lysine N-Methyltransferase NSD2 3
  • Trithorax/Ash1-Related Protein 5 3
  • Protein Trithorax-5 4
  • KIAA1090 4
  • REIIBP 3
  • KMT3F 3
  • KMT3G 3
  • WHS 3

External Ids for NSD2 Gene

Previous HGNC Symbols for NSD2 Gene

  • WHSC1

Summaries for NSD2 Gene

Entrez Gene Summary for NSD2 Gene

  • This gene encodes a protein that contains four domains present in other developmental proteins: a PWWP domain, an HMG box, a SET domain, and a PHD-type zinc finger. It is expressed ubiquitously in early development. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene maps to the 165 kb WHS critical region and has also been involved in the chromosomal translocation t(4;14)(p16.3;q32.3) in multiple myelomas. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. Some transcript variants are nonsense-mediated mRNA (NMD) decay candidates, hence not represented as reference sequences. [provided by RefSeq, Jul 2008]

GeneCards Summary for NSD2 Gene

NSD2 (Nuclear Receptor Binding SET Domain Protein 2) is a Protein Coding gene. Diseases associated with NSD2 include Wolf-Hirschhorn Syndrome and Multiple Myeloma. Among its related pathways are DNA Double-Strand Break Repair and Lysine degradation. An important paralog of this gene is NSD1.

UniProtKB/Swiss-Prot for NSD2 Gene

  • Histone methyltransferase with histone H3 Lys-27 (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.

Gene Wiki entry for NSD2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NSD2 Gene

Genomics for NSD2 Gene

Regulatory Elements for NSD2 Gene

Enhancers for NSD2 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
GH04G002007 1.2 ENCODE 12 +137.8 137811 3.2 CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 ZFP41 SSRP1 ZNF610 NELFA SCARNA22 C4orf48 NSD2 MXD4 ENSG00000251148 ZFYVE28 ENSG00000250623 CRIPAK HAUS3
GH04G001907 0.8 ENCODE dbSUPER 12 +36.5 36533 0.2 FOSL1 ESRRA KLF9 KDM1A FOS KLF4 NSD2 LETM1 GC04P001890 PIR46454
GH04G002011 0.6 Ensembl 11.7 +140.4 140394 0.5 CEBPA HLF CEBPB ZBTB33 ZNF384 CEBPG C4orf48 NELFA SCARNA22 NSD2 MXD4 ENSG00000250623 ENSG00000251148 ZFYVE28 HAUS3 POLN
GH04G001905 0.5 dbSUPER 12.6 +34.3 34264 0.9 CTCF ESRRA SCRT2 KLF9 FOS NSD2 LETM1 GC04P001890 PIR46454
GH04G001867 1.8 FANTOM5 ENCODE dbSUPER 2.9 -0.2 -207 7.0 HDGF PKNOX1 CREB3L1 AGO1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 NELFA CRIPAK HAUS3 NSD2 GC04M001869
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NSD2 on UCSC Golden Path with GeneCards custom track

Promoters for NSD2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000164889 104 2601 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for NSD2 Gene

Chromosome:
4
Start:
1,871,396 bp from pter
End:
1,982,207 bp from pter
Size:
110,812 bases
Orientation:
Plus strand

Genomic View for NSD2 Gene

Genes around NSD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSD2 Gene

Proteins for NSD2 Gene

  • Protein details for NSD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O96028-NSD2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase NSD2
    Protein Accession:
    O96028
    Secondary Accessions:
    • A2A2T2
    • A2A2T3
    • A2A2T4
    • A7MCZ1
    • D3DVQ2
    • O96031
    • Q4VBY8
    • Q672J1
    • Q6IS00
    • Q86V01
    • Q9BZB4
    • Q9UI92
    • Q9UPR2

    Protein attributes for NSD2 Gene

    Size:
    1365 amino acids
    Molecular mass:
    152258 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA83042.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NSD2 Gene

    Alternative splice isoforms for NSD2 Gene

neXtProt entry for NSD2 Gene

Selected DME Specific Peptides for NSD2 Gene

O96028:
  • RFMNHSC
  • ELTFNYN
  • GKWECPWH
  • KGEFVNEYVGELIDEEEC
  • RCPVAYH
  • CGKFYHE
  • IIDAGPKGN

Post-translational modifications for NSD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for NSD2 Gene

Graphical View of Domain Structure for InterPro Entry

O96028

UniProtKB/Swiss-Prot:

NSD2_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 NSD2: view

Function for NSD2 Gene

Molecular function for NSD2 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 with histone H3 Lys-27 (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.

Enzyme Numbers (IUBMB) for NSD2 Gene

Gene Ontology (GO) - Molecular Function for NSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 19481544
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with NSD2: view
genes like me logo Genes that share phenotypes with NSD2: view

Human Phenotype Ontology for NSD2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NSD2 Gene

MGI Knock Outs for NSD2:

Animal Model Products

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for NSD2 Gene

Localization for NSD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSD2 Gene

Nucleus. Chromosome.
Isoform 4: Cytoplasm.

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 NSD2 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for NSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NSD2: view

Pathways & Interactions for NSD2 Gene

genes like me logo Genes that share pathways with NSD2: view

SIGNOR curated interactions for NSD2 Gene

Activates:

Gene Ontology (GO) - Biological Process for NSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0003149 membranous septum morphogenesis IEA --
GO:0003289 atrial septum primum morphogenesis IEA --
GO:0003290 atrial septum secundum morphogenesis IEA --
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
genes like me logo Genes that share ontologies with NSD2: view

Drugs & Compounds for NSD2 Gene

(3) Drugs for NSD2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Lysine Approved Nutra Full agonist, Agonist 0
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with NSD2: view

Transcripts for NSD2 Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NSD2 Gene

No ASD Table

Relevant External Links for NSD2 Gene

GeneLoc Exon Structure for
NSD2
ECgene alternative splicing isoforms for
NSD2

Expression for NSD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of NSD2 Gene:

NSD2

mRNA Expression by UniProt/SwissProt for NSD2 Gene:

O96028-NSD2_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for NSD2 Gene

  • Nervous system(4.8)
  • Spleen(4.2)
  • Bone marrow(2.8)
  • Blood(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NSD2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • urethra
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with NSD2: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for NSD2 Gene

Orthologs for NSD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NSD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WHSC1 34 35
  • 99.71 (n)
dog
(Canis familiaris)
Mammalia WHSC1 34 35
  • 88.39 (n)
mouse
(Mus musculus)
Mammalia Whsc1 34 35
  • 87.39 (n)
Nsd2 16
rat
(Rattus norvegicus)
Mammalia Whsc1 34
  • 86.85 (n)
oppossum
(Monodelphis domestica)
Mammalia WHSC1 35
  • 83 (a)
OneToOne
cow
(Bos Taurus)
Mammalia WHSC1 34 35
  • 82.91 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia WHSC1 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves WHSC1 34 35
  • 76.93 (n)
lizard
(Anolis carolinensis)
Reptilia WHSC1 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia whsc1 34
  • 68.29 (n)
zebrafish
(Danio rerio)
Actinopterygii whsc1 34 35
  • 67.56 (n)
wufc12c04 34
fruit fly
(Drosophila melanogaster)
Insecta Mes-4 35
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-23 35
  • 33 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9549 35
  • 53 (a)
OneToMany
Species where no ortholog for NSD2 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)
  • wheat (Triticum aestivum)

Evolution for NSD2 Gene

ENSEMBL:
Gene Tree for NSD2 (if available)
TreeFam:
Gene Tree for NSD2 (if available)

Paralogs for NSD2 Gene

Pseudogenes.org Pseudogenes for NSD2 Gene

genes like me logo Genes that share paralogs with NSD2: view

Variants for NSD2 Gene

Sequence variations from dbSNP and Humsavar for NSD2 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs548600548 Pathogenic 1,957,986(+) AAGCC(A/C/T)GAGAA reference, synonymous-codon
rs111668967 Likely benign 1,979,994(+) CCCAG(A/T)GTGGC utr-variant-3-prime
rs112014939 Likely benign 1,918,543(+) AGAAG(A/G)CCACA reference, missense
rs112146288 Likely benign 1,979,433(+) TGGCT(A/G)TATCA utr-variant-3-prime
rs112691599 Likely benign 1,981,543(+) GCCCA(C/T)AGGGG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for NSD2 Gene

Variant ID Type Subtype PubMed ID
dgv8903n54 CNV gain 21841781
dgv8904n54 CNV gain+loss 21841781
dgv8905n54 CNV gain+loss 21841781
dgv8906n54 CNV loss 21841781
esv27096 CNV loss 19812545
esv2726833 CNV deletion 23290073
esv2726834 CNV deletion 23290073
nsv1073290 CNV deletion 25765185
nsv1144066 CNV deletion 24896259
nsv478611 CNV novel sequence insertion 20440878
nsv593340 CNV gain 21841781
nsv593346 CNV loss 21841781
nsv593347 CNV gain 21841781
nsv593348 CNV gain 21841781
nsv593349 CNV gain+loss 21841781
nsv593361 CNV gain 21841781
nsv593364 CNV gain+loss 21841781
nsv819354 CNV gain 19587683
nsv829836 CNV loss 17160897

Variation tolerance for NSD2 Gene

Residual Variation Intolerance Score: 1.99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.70; 32.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NSD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NSD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSD2 Gene

Disorders for NSD2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NSD2 Gene - From: OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • 4p deletion syndrome
multiple myeloma
  • myeloma, multiple amyloidosis, systemic, included
chromosomal deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search NSD2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NSD2_HUMAN
  • Note=A chromosomal aberration involving NSD2 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH.
  • Note=NSD2 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. NSD2 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.

Relevant External Links for NSD2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NSD2
genes like me logo Genes that share disorders with NSD2: view

No data available for Genatlas for NSD2 Gene

Publications for NSD2 Gene

  1. 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. (PMID: 9618163) Stec I. … den Dunnen J.T. (Hum. Mol. Genet. 1998) 2 3 4 22 64
  2. The t(4;14) translocation in myeloma dysregulates both FGFR3 and a novel gene, MMSET, resulting in IgH/MMSET hybrid transcripts. (PMID: 9787135) Chesi M. … Bergsagel P.L. (Blood 1998) 2 3 4 22 64
  3. Multiple-myeloma-related WHSC1/MMSET isoform RE-IIBP is a histone methyltransferase with transcriptional repression activity. (PMID: 18172012) Kim J.Y. … Seo S.B. (Mol. Cell. Biol. 2008) 3 4 22 64
  4. Overexpression of transcripts originating from the MMSET locus characterizes all t(4;14)(p16;q32)-positive multiple myeloma patients. (PMID: 15677557) Keats J.J. … Pilarski L.M. (Blood 2005) 3 4 22 64
  5. The etiology of Wolf-Hirschhorn syndrome. (PMID: 15734578) Bergemann A.D. … Hirschhorn K. (Trends Genet. 2005) 3 4 22 64

Products for NSD2 Gene

  • Addgene plasmids for NSD2

Sources for NSD2 Gene

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