NSD2 (nuclear receptor binding SET domain protein 2)

Gene
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
7468
Gene name Gene Name - the full gene name approved by the HGNC.
Nuclear receptor binding SET domain protein 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
NSD2
Synonyms (NCBI Gene) Gene synonyms aliases
KMT3F, KMT3G, MMSET, RAUST, REIIBP, TRX5, WHS, WHSC1
Chromosome Chromosome number
4
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
4p16.3
Summary Summary of gene provided in NCBI Entrez 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 mal
SNPs SNP information provided by dbSNP.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(9)
SNP ID Visualize variation Clinical significance Consequence
rs748707745 C>T Pathogenic Genic upstream transcript variant, coding sequence variant, stop gained
rs1553873247 GAGA>- Pathogenic Coding sequence variant, splice acceptor variant, genic upstream transcript variant, intron variant, upstream transcript variant
rs1560602800 G>A Pathogenic Stop gained, coding sequence variant, genic upstream transcript variant
rs1560635105 C>T Pathogenic Stop gained, coding sequence variant, genic upstream transcript variant
rs1560696317 ->G Pathogenic Frameshift variant, coding sequence variant, genic upstream transcript variant
miRNA miRNA information provided by mirtarbase database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(51)
miRTarBase ID miRNA Experiments Reference
MIRT237889 hsa-miR-5582-5p PAR-CLIP 20371350
MIRT563361 hsa-miR-3622a-5p PAR-CLIP 20371350
MIRT237891 hsa-miR-6826-5p PAR-CLIP 20371350
MIRT563360 hsa-miR-4775 PAR-CLIP 20371350
MIRT237888 hsa-miR-4423-3p PAR-CLIP 20371350
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(39)
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000785 Component Chromatin IBA
GO:0003149 Process Membranous septum morphogenesis IEA
GO:0003289 Process Atrial septum primum morphogenesis IEA
GO:0003290 Process Atrial septum secundum morphogenesis IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
602952 12766 ENSG00000109685
Protein
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID O96028
Protein name Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) (Multiple myeloma SET domain-containing protein) (MMSET) (Nuclear SET domain-containing protein 2) (Protein trithorax-5) (Wolf-Hirschhorn syndrome candidate 1 protein)
Protein function Histone methyltransferase which specifically dimethylates nucleosomal histone H3 at 'Lys-36' (H3K36me2) (PubMed:19808676, PubMed:22099308, PubMed:27571355, PubMed:29728617, PubMed:33941880). Also monomethylates nucleosomal histone H3 at 'Lys-36'
PDB 5LSU , 5VC8 , 6UE6 , 6XCG , 7CRO , 7E8D , 7LMT , 7MDN , 7VLN , 9EXW , 9EXX , 9EXY , 9GBF
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00855 PWWP 220 → 334 PWWP domain Domain
PF00505 HMG_box 455 → 508 HMG (high mobility group) box Domain
PF00855 PWWP 878 → 970 PWWP domain Domain
PF17907 AWS 1022 → 1060 AWS domain Domain
PF00856 SET 1074 → 1180 SET domain Family
PF17982 C5HCH 1282 → 1330 NSD Cys-His rich domain Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed (PubMed:18172012, PubMed:9618163). Predominantly expressed in thymus and testis (PubMed:18172012, PubMed:9787135). {ECO:0000269|PubMed:18172012, ECO:0000269|PubMed:9618163, ECO:0000269|PubMed:9787135}.
Sequence 
MEFSIKQSPLSVQSVVKCIKMKQAPEILGSANGKTPSCEVNRECSVFLSKAQLSSSLQEG
VMQKFNGHDALPFIPADKLKDLTSRVFNGEPGAHDAKLRFESQEMKGIGTPPNTTPIKNG
SPEIKLKITKTYMNGKPLFESSICGDSAADVSQSEENGQKPENKARRNRKRSIKYDSLLE
QGLVEAALVSKISSPSDKKIPAKKESCPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMV
SADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQ
APTKAEKIKLLKPISGKLRAQWEMGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVA
KEAGIAAESLGEMAESSGVSEEAAENPKSVREECIPMKRRRRAKLCSSAETLESHPDIGK
STPQKTAEADPRRGVGSPPGRKKTTVSMPRSRKGDAASQFLVFCQKHRDEVVAEHPDASG
EEIEELLRSQWSLLSEKQRARYNTKFALVAPVQAEEDSGNVNGKKRNHTKRIQDPTEDAE
AEDTPRKRLRTDKHSLRKRDTITDKTARTSSYKAMEAASSLKSQAATKNLSDACKPLKKR
NRASTAASSALGFSKSSSPSASLTENEVSDSPGDEPSESPYESADETQTEVSVSSKKSER
GVTAKKEYVCQLCEKPGSLLLCEGPCCGAFHLACLGLSRRPEGRFTCSECASGIHSCFVC
KESKTDVKRCVVTQCGKFYHEACVKKYPLTVFESRGFRCPLHSCVSCHASNPSNPRPSKG
KMMRCVRCPVAYHSGDACLAAGCSVIASNSIICTAHFTARKGKRHHAHVNVSWCFVCSKG
GSLLCCESCPAAFHPDCLNIEMPDGSWFCNDCRAGKKLHFQDIIWVKLGNYRWWPAEVCH
PKNVPPNIQKMKHEIGEFPVFFFGSKDYYWTHQARVFPYMEGDRGSRYQGVRGIGRVFKN
ALQEAEARFREIKLQREARETQESERKPPPYKHIKVNKPYGKVQIYTADISEIPKCNCKP
TDENPCGFDSECLNRMLMFECHPQVCPAGEFCQNQCFTKRQYPETKIIKTDGKGWGLVAK
RDIRKGEFVNEYVGELIDEEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFM
NHSCQPNCETLKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTVCRCGASNCSG
FLGDRPKTSTTLSSEEKGKKTKKKTRRRRAKGEGKRQSEDECFRCGDGGQLVLCDRKFCT
KAYHLSCLGLGKRPFGKWECPWHHCDVCGKPSTSFCHLCPNSFCKEHQDGTAFSCTPDGR
SYCCEHDLGAASVRSTKTEKPPPEPGKPKGKRRRRRGWRRVTEGK
Sequence length 1365
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG   Reactome
  Lysine degradation
Metabolic pathways
Transcriptional misregulation in cancer 		  PKMTs methylate histone lysines
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
Nonhomologous End-Joining (NHEJ)
Processing of DNA double-strand break ends
G2/M DNA damage checkpoint
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (3)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
4p partial monosomy syndrome 4p partial monosomy syndrome rs1560696317, rs1553873247, rs1560602800, rs1560635105 N/A
Developmental Delay global developmental delay rs1553873247 N/A
Wolf-Hirschhorn Syndrome Wolf-Hirschhorn like syndrome rs1560696317, rs1560602800, rs1560635105 N/A
Show/Hide Unknown Diseases (3)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Lymphoma lymphoma N/A N/A ClinVar
Mental retardation syndromic intellectual disability N/A N/A GenCC
Neurodevelopmental Disorders neurodevelopmental disorder N/A N/A GenCC
Show/Hide Text Mining Associations (70)
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Bone Diseases Associate 33420361
Bone Marrow Neoplasms Associate 32826945
Breast Neoplasms Associate 36805183, 39395300, 39667501
Capillary Malformation Arteriovenous Malformation Inhibit 19121287
Carcinogenesis Associate 18172012, 22028615, 37756162
Carcinoma Basal Cell Stimulate 30215205
Carcinoma Hepatocellular Associate 28426876
Carcinoma Non Small Cell Lung Stimulate 33658396
Carcinoma Non Small Cell Lung Associate 34313353
Carcinoma Renal Cell Associate 31692936