Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7468
Gene name	Nuclear receptor binding SET domain protein 2
Gene symbol	NSD2
Synonyms (NCBI Gene)	KMT3FKMT3GMMSETRAUSTREIIBPTRX5WHSWHSC1
Chromosome	4
Chromosome location	4p16.3
Summary	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

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
rs1577434780	G>T	Likely-pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs1577484648	->A	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1577532139	GT>-	Pathogenic	Genic upstream transcript variant, 5 prime UTR variant, frameshift variant, upstream transcript variant, genic downstream transcript variant, coding sequence variant
rs1577584497	->A	Pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant

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
MIRT563358	hsa-miR-4256	PAR-CLIP	20371350
MIRT563359	hsa-miR-4762-3p	PAR-CLIP	20371350
MIRT463973	hsa-miR-142-3p	PAR-CLIP	21572407
MIRT237884	hsa-miR-548at-5p	PAR-CLIP	21572407
MIRT237875	hsa-miR-181a-5p	PAR-CLIP	21572407
MIRT237876	hsa-miR-181b-5p	PAR-CLIP	21572407
MIRT237877	hsa-miR-181c-5p	PAR-CLIP	21572407
MIRT237878	hsa-miR-181d-5p	PAR-CLIP	21572407
MIRT237879	hsa-miR-4262	PAR-CLIP	21572407
MIRT463972	hsa-miR-4255	PAR-CLIP	21572407
MIRT237882	hsa-miR-3973	PAR-CLIP	21572407
MIRT164670	hsa-miR-520g-3p	PAR-CLIP	21572407
MIRT164672	hsa-miR-520h	PAR-CLIP	21572407
MIRT309831	hsa-miR-503-3p	PAR-CLIP	21572407
MIRT237885	hsa-miR-5681b	PAR-CLIP	21572407
MIRT237886	hsa-miR-6832-5p	PAR-CLIP	21572407
MIRT463971	hsa-miR-4732-5p	PAR-CLIP	21572407
MIRT463970	hsa-miR-95-3p	PAR-CLIP	21572407
MIRT237883	hsa-miR-3591-5p	PAR-CLIP	21572407
MIRT237880	hsa-miR-3674	PAR-CLIP	21572407
MIRT463973	hsa-miR-142-3p	PAR-CLIP	23592263
MIRT237884	hsa-miR-548at-5p	PAR-CLIP	23592263
MIRT237875	hsa-miR-181a-5p	PAR-CLIP	23592263
MIRT237876	hsa-miR-181b-5p	PAR-CLIP	23592263
MIRT237877	hsa-miR-181c-5p	PAR-CLIP	23592263
MIRT237878	hsa-miR-181d-5p	PAR-CLIP	23592263
MIRT237879	hsa-miR-4262	PAR-CLIP	23592263
MIRT463972	hsa-miR-4255	PAR-CLIP	23592263
MIRT237882	hsa-miR-3973	PAR-CLIP	23592263
MIRT164670	hsa-miR-520g-3p	PAR-CLIP	23592263
MIRT164672	hsa-miR-520h	PAR-CLIP	23592263
MIRT309831	hsa-miR-503-3p	PAR-CLIP	23592263
MIRT237885	hsa-miR-5681b	PAR-CLIP	23592263
MIRT237886	hsa-miR-6832-5p	PAR-CLIP	23592263
MIRT463971	hsa-miR-4732-5p	PAR-CLIP	23592263
MIRT463970	hsa-miR-95-3p	PAR-CLIP	23592263
MIRT237883	hsa-miR-3591-5p	PAR-CLIP	23592263
MIRT237880	hsa-miR-3674	PAR-CLIP	23592263
MIRT164664	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT164659	hsa-miR-20a-5p	HITS-CLIP	22473208
MIRT164664	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT164658	hsa-miR-17-5p	HITS-CLIP	22473208
MIRT164665	hsa-miR-20b-5p	HITS-CLIP	22473208
MIRT164660	hsa-miR-93-5p	HITS-CLIP	22473208
MIRT164669	hsa-miR-519d-3p	HITS-CLIP	22473208
MIRT164659	hsa-miR-20a-5p	HITS-CLIP	22473208

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
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	19481544, 21293379, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0006302	Process	Double-strand break repair	TAS
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IBA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0042799	Function	Histone H4K20 methyltransferase activity	TAS
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0046975	Function	Histone H3K36 methyltransferase activity	IBA
GO:0046975	Function	Histone H3K36 methyltransferase activity	IEA
GO:0046975	Function	Histone H3K36 methyltransferase activity	IMP	24595546, 33941880
GO:0048298	Process	Positive regulation of isotype switching to IgA isotypes	IEA
GO:0060348	Process	Bone development	IEA
GO:0070201	Process	Regulation of establishment of protein localization	IEA
GO:0140938	Function	Histone H3 methyltransferase activity	TAS
GO:0140954	Function	Histone H3K36 dimethyltransferase activity	IEA
GO:0140955	Function	Histone H3K36 trimethyltransferase activity	IEA
GO:2001032	Process	Regulation of double-strand break repair via nonhomologous end joining	IEA

MIM	HGNC	e!Ensembl
602952	12766	ENSG00000109685

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

	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

136

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
4p partial monosomy syndrome	Pathogenic; Likely pathogenic	rs1725000714, rs2108971782, rs2474331632, rs1553873247, rs1560602800, rs1560635105, rs1560696317	RCV001330272 RCV001754558 RCV002288414 RCV000660609 RCV001249663 RCV001249665 RCV001249664
atypical Wolf-Hirschhorn syndrome	Pathogenic	rs1717589360	RCV001254026
Global developmental delay	Pathogenic	rs1553873247	RCV001779037
Neurodevelopmental delay	Pathogenic	rs1553873247	RCV002274084
NSD2-associated disorder	Pathogenic	rs1717589360	RCV001254026
NSD2-related disorder	Likely pathogenic; Pathogenic	rs2109020378, rs2474219766, rs2474340489, rs1553873247, rs1577434780	RCV004728828 RCV004545864 RCV003410483 RCV004735729 RCV000791294
Rauch-Steindl syndrome	Pathogenic; Likely pathogenic	rs1726909627, rs2108959336, rs2108877068, rs752037034, rs2109020378, rs2108971327, rs2108805626, rs2108976771, rs2108950399, rs2108940433, rs2474340960, rs2474621918, rs2474621465, rs1717034691, rs2474762078 View all (9 more)	RCV001807861 RCV001807862 RCV001807863 RCV001807864 RCV001807865 RCV001807866 RCV001814607 RCV003227533 RCV002251158 RCV002267700 RCV002289510 RCV005416044 RCV003135498 RCV003224971 RCV003236700 RCV003239299 RCV003326225 RCV003333382 RCV003335889 RCV003494513 RCV003988693 RCV004006236 RCV004584296 RCV001809736 RCV004768630 RCV003492199
Syndromic intellectual disability	Pathogenic; Likely pathogenic	rs2108805708, rs1553872623	RCV001786514 RCV004549039
Wolf-Hirschhorn like syndrome	Likely pathogenic; Pathogenic	rs2108958731, rs1560602800, rs1560635105, rs1560696317	RCV001420667 RCV000736076 RCV000736077 RCV000736075

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	-; Benign	rs73202837, rs886059317	RCV005950708 RCV005897801
Cervical cancer	Benign; -	rs199564032, rs10019502, rs886059317	RCV005929974 RCV005950593 RCV005897802
Cholangiocarcinoma	Likely benign	rs768855129	RCV005934711
Clear cell carcinoma of kidney	Likely benign	rs200130380	RCV005929975
Gastric cancer	Benign	rs886059317	RCV005897803
Lymphoma	Conflicting classifications of pathogenicity	rs772470710	RCV000790856
Medulloblastoma WNT activated	Conflicting classifications of pathogenicity	rs772470710	RCV006254160
Microcephaly	Uncertain significance	rs1724772708	RCV001290429
Neurodevelopmental disorder	Uncertain significance	rs200415868	RCV002273308
NSD2-related neurodevelopmental disorder	Uncertain significance	rs2108971216	RCV002260569
Precursor B-cell acute lymphoblastic leukemia	Conflicting classifications of pathogenicity	rs772470710	RCV006254159
Sarcoma	Benign; -; Likely benign	rs57276793, rs73202837, rs768855129	RCV005929973 RCV005950709 RCV005934710
Thymoma	-	rs73202837	RCV005950710
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs886059317, rs768855129	RCV005897804 RCV005934712
WHSC1-related disorder	Uncertain significance	rs1577537810	RCV004549863

Show/Hide Text Mining Associations (70)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
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
Chondroblastoma	Associate	27229140
Chromosome 14 trisomy	Associate	22972034
Colonic Neoplasms	Associate	36180906
Colorectal Neoplasms	Associate	28338204
Constipation	Associate	31171569
Crohn Disease	Associate	37331566
Developmental Disabilities	Associate	31171569, 33941880
DNA Virus Infections	Associate	21788515
Emanuel syndrome	Associate	15198734, 34893510, 35166240, 35984902, 38598835
Encephalitis Herpes Simplex	Associate	33361816
Endometriosis	Associate	20935158
Erythema Ab Igne	Associate	23241889
Failure to Thrive	Associate	31171569
Fatty Liver Alcoholic	Associate	28426876
Feeding and Eating Disorders	Associate	23963300
Fetal Growth Retardation	Associate	31171569
Genetic Diseases Inborn	Associate	32416892
Glioblastoma	Associate	19121287
Growth Disorders	Associate	23963300, 29892088, 31171569, 33276791, 33941880
Heart Defects Congenital	Associate	32341405, 34324492
Hereditary leiomyomatosis and renal cell cancer	Associate	32191807
Hypoxia	Associate	33420361
Infertility	Associate	20935158
Intellectual Disability	Associate	33001864, 33276791
Kidney Neoplasms	Associate	31692936
Language Development Disorders	Associate	23963300
Laryngeal Neoplasms	Associate	29176703
Learning Disabilities	Associate	32341405
Leukemia	Stimulate	18172012
Leukemia	Associate	32826945, 34597466, 37150325
Leukemia Myeloid	Associate	32826945
Lung Neoplasms	Associate	22028615
Lymphatic Metastasis	Stimulate	39395300
Lymphoma Mantle Cell	Associate	24682267, 30175400, 34882582, 35266562
Multiple Myeloma	Associate	11337357, 11418483, 11529856, 12139740, 12433679, 14531906, 15198734, 15677557, 16115125, 16197452, 16728703, 17303695, 17914559, 18172012, 19059936 View all (27 more)
Muscle Hypotonia	Associate	31171569
Muscular Dystrophy Emery Dreifuss	Associate	36657019
Neoplasm Metastasis	Associate	28338204
Neoplasms	Associate	18172012, 18381641, 20511669, 22028615, 22797064, 22972034, 24710217, 25748235, 26771714, 26847058, 27183271, 28338204, 28426876, 30171150, 30171259 View all (9 more)
Neoplasms	Stimulate	19121287
Oncogene Addiction	Associate	37150325
Orofacial Cleft 1	Associate	26561393
Osteosarcoma	Associate	28338204
Otofaciocervical Syndrome	Associate	26561393
Ovarian Neoplasms	Associate	28537669, 31092221
Pathological Conditions Anatomical	Associate	33001864
Personality Disorders	Stimulate	26771714
Platypnea Orthodeoxia Syndrome	Associate	15677557
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	30171259, 31248990, 37016431
Prostatic Hyperplasia	Associate	38062230
Prostatic Intraepithelial Neoplasia	Stimulate	38062230
Prostatic Neoplasms	Associate	22797064, 33976366, 38062230
Prostatic Neoplasms Castration Resistant	Associate	38062230
Prostatitis	Associate	19481544, 38062230
Squamous Cell Carcinoma of Head and Neck	Associate	32497898, 34546854
Stomach Neoplasms	Associate	24809779
Testicular Germ Cell Tumor	Associate	25748235
Wilms Tumor	Associate	35184066
Wolf Hirschhorn Syndrome	Inhibit	19121287, 21788515
Wolf Hirschhorn Syndrome	Associate	20974671, 22028615, 23241889, 23963300, 26960370, 29892088, 31171569, 31382906, 32416892, 33276791, 33941880

NSD2 (nuclear receptor binding SET domain protein 2)