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Aliases for NSD1 Gene

Aliases for NSD1 Gene

  • Nuclear Receptor Binding SET Domain Protein 1 2 3 5
  • Nuclear Receptor-Binding SET Domain-Containing Protein 1 3 4
  • Androgen Receptor-Associated Protein Of 267 KDa 3 4
  • Androgen Receptor Coactivator 267 KDa Protein 3 4
  • NR-Binding SET Domain-Containing Protein 3 4
  • Lysine N-Methyltransferase 3B 3 4
  • H3-K36-HMTase 3 4
  • H4-K20-HMTase 3 4
  • EC 4 61
  • ARA267 3 4
  • KMT3B 3 4
  • Histone-Lysine N-Methyltransferase, H3 Lysine-36 And H4 Lysine-20 Specific 3
  • Androgen Receptor-Associated Coregulator 267 3
  • Sotos Syndrome 2
  • SOTOS1 3
  • SOTOS 3
  • STO 3

External Ids for NSD1 Gene

Previous HGNC Symbols for NSD1 Gene

  • STO

Previous GeneCards Identifiers for NSD1 Gene

  • GC05P176935
  • GC05P177404
  • GC05P176496
  • GC05P176541
  • GC05P176493
  • GC05P176560
  • GC05P171481

Summaries for NSD1 Gene

Entrez Gene Summary for NSD1 Gene

  • This gene encodes a protein containing a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The encoded protein enhances androgen receptor (AR) transactivation, and this enhancement can be increased further in the presence of other androgen receptor associated coregulators. This protein may act as a nucleus-localized, basic transcriptional factor and also as a bifunctional transcriptional regulator. Mutations of this gene have been associated with Sotos syndrome and Weaver syndrome. One version of childhood acute myeloid leukemia is the result of a cryptic translocation with the breakpoints occurring within nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1 on chromosome 5 and nucleoporin, 98-kd on chromosome 11. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for NSD1 Gene

NSD1 (Nuclear Receptor Binding SET Domain Protein 1) is a Protein Coding gene. Diseases associated with NSD1 include Sotos Syndrome 1 and Beckwith-Wiedemann Syndrome. Among its related pathways are Lysine degradation and PKMTs methylate histone lysines. GO annotations related to this gene include chromatin binding and transcription cofactor activity. An important paralog of this gene is NSD2.

UniProtKB/Swiss-Prot for NSD1 Gene

  • Histone methyltransferase. Preferentially methylates Lys-36 of histone H3 and Lys-20 of histone H4 (in vitro). Transcriptional intermediary factor capable of both negatively or positively influencing transcription, depending on the cellular context.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NSD1 Gene

Genomics for NSD1 Gene

Regulatory Elements for NSD1 Gene

Enhancers for NSD1 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
GH05G177021 1.2 ENCODE 10.6 -110.5 -110485 2.7 CREB3L1 DMAP1 YY1 ZNF416 ZNF143 ZNF263 SP3 SSRP1 ZNF610 GLIS1 FAF2 ENSG00000251414 ENSG00000250909 ZNF346 ENSG00000247679 LOC202181 ZNF346-IT1 RPL21P60 FGFR4 NSD1
GH05G177111 0.9 ENCODE 12.8 -21.0 -20991 0.2 ELF3 HDGF RB1 ARID4B ZNF2 ZNF48 RAD21 GLIS2 ELK1 ZNF366 FGFR4 NSD1 PRELID1 RAB24 MXD3 RGS14
GH05G177070 1 Ensembl ENCODE 10.9 -61.3 -61291 2.8 CTCF ARID4B RAD21 ZNF316 ZNF143 SMC3 ZNF600 MAFK KLF11 ZNF654 ZNF346 FGFR4 NSD1 MXD3 UIMC1 PIR44333 GC05P177068 GC05M177054
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NSD1 on UCSC Golden Path with GeneCards custom track

Promoters for NSD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000191308 675 2601 HDGF ATF1 ARNT SIN3A ZNF2 YY1 ZNF766 GLIS2 ELK1 ZNF143

Genomic Location for NSD1 Gene

177,133,025 bp from pter
177,300,215 bp from pter
167,191 bases
Plus strand

Genomic View for NSD1 Gene

Genes around NSD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSD1 Gene

Proteins for NSD1 Gene

  • Protein details for NSD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
    Protein Accession:
    Secondary Accessions:
    • Q96PD8
    • Q96RN7

    Protein attributes for NSD1 Gene

    2696 amino acids
    Molecular mass:
    296652 Da
    Quaternary structure:
    • Interacts with the ligand-binding domains of RARA and THRA in the absence of ligand; in the presence of ligand the interaction is severely disrupted but some binding still occurs. Interacts with the ligand-binding domains of RXRA and ESRRA only in the presence of ligand. Interacts with ZNF496 (By similarity). Interacts with AR DNA- and ligand-binding domains.

    Three dimensional structures from OCA and Proteopedia for NSD1 Gene

    Alternative splice isoforms for NSD1 Gene


neXtProt entry for NSD1 Gene

Selected DME Specific Peptides for NSD1 Gene


Post-translational modifications for NSD1 Gene

  • Ubiquitination at Lys865 and Lys886
  • Modification sites at PhosphoSitePlus

Domains & Families for NSD1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with NSD1: view

Function for NSD1 Gene

Molecular function for NSD1 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-36 of histone H3 and Lys-20 of histone H4 (in vitro). Transcriptional intermediary factor capable of both negatively or positively influencing transcription, depending on the cellular context.

Enzyme Numbers (IUBMB) for NSD1 Gene

Gene Ontology (GO) - Molecular Function for NSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding IDA 20837538
GO:0003682 chromatin binding ISS --
GO:0003712 transcription cofactor activity IDA 11509567
GO:0003714 transcription corepressor activity ISS --
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with NSD1: view
genes like me logo Genes that share phenotypes with NSD1: view

Human Phenotype Ontology for NSD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NSD1 Gene

MGI Knock Outs for NSD1:

Animal Model Products

CRISPR Products

miRNA for NSD1 Gene

miRTarBase miRNAs that target NSD1

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for NSD1 Gene

Localization for NSD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSD1 Gene

Nucleus. Chromosome.

Subcellular locations from

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 NSD1 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for NSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with NSD1: view

Pathways & Interactions for NSD1 Gene

genes like me logo Genes that share pathways with NSD1: view

Pathways by source for NSD1 Gene

1 GeneTex pathway for NSD1 Gene
1 KEGG pathway for NSD1 Gene

SIGNOR curated interactions for NSD1 Gene


Gene Ontology (GO) - Biological Process for NSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0000414 regulation of histone H3-K36 methylation IMP 20837538
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010452 histone H3-K36 methylation IEA --
genes like me logo Genes that share ontologies with NSD1: view

Drugs & Compounds for NSD1 Gene

(3) Drugs for NSD1 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 NSD1: view

Transcripts for NSD1 Gene

Unigene Clusters for NSD1 Gene

Nuclear receptor binding SET domain protein 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NSD1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23a · 23b ^
SP1: - -
SP2: - -

ExUns: 24

Relevant External Links for NSD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NSD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NSD1 Gene

Protein differential expression in normal tissues from HIPED for NSD1 Gene

This gene is overexpressed in Fetal Brain (13.2), Liver (10.0), Pancreas (9.2), Fetal gut (8.6), and Blymphocyte (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NSD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NSD1 Gene:


SOURCE GeneReport for Unigene cluster for NSD1 Gene:


mRNA Expression by UniProt/SwissProt for NSD1 Gene:

Tissue specificity: Expressed in the fetal/adult brain, kidney, skeletal muscle, spleen, and the thymus, and faintly in the lung.

Evidence on tissue expression from TISSUES for NSD1 Gene

  • Nervous system(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NSD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
  • tongue
  • tooth
  • vocal cord
  • breast
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • adrenal gland
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • ureter
  • urinary bladder
  • uterus
  • vagina
  • vas deferens
  • vulva
  • 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
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with NSD1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for NSD1 Gene

Orthologs for NSD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NSD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NSD1 35 34
  • 99.77 (n)
(Bos Taurus)
Mammalia NSD1 34 35
  • 91.72 (n)
(Canis familiaris)
Mammalia NSD1 35 34
  • 91.6 (n)
(Mus musculus)
Mammalia Nsd1 16 35 34
  • 86.04 (n)
(Rattus norvegicus)
Mammalia Nsd1 34
  • 85.46 (n)
(Monodelphis domestica)
Mammalia NSD1 35
  • 70 (a)
(Ornithorhynchus anatinus)
Mammalia NSD1 35
  • 64 (a)
(Gallus gallus)
Aves NSD1 35 34
  • 65.31 (n)
(Anolis carolinensis)
Reptilia NSD1 35
  • 52 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20360 34
(Danio rerio)
Actinopterygii nsd1a 35
  • 45 (a)
nsd1b 35
  • 43 (a)
Dr.19744 34
fruit fly
(Drosophila melanogaster)
Insecta Mes-4 35
  • 25 (a)
(Caenorhabditis elegans)
Secernentea lin-59 35
  • 14 (a)
(Oryza sativa)
Liliopsida Os.27622 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9549 35
  • 51 (a)
Species where no ortholog for NSD1 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 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 NSD1 Gene

Gene Tree for NSD1 (if available)
Gene Tree for NSD1 (if available)

Paralogs for NSD1 Gene

Variants for NSD1 Gene

Sequence variations from dbSNP and Humsavar for NSD1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs121908068 Pathogenic, Sotos syndrome 1 (SOTOS1) [MIM:117550] 177,292,124(+) TACCA(C/G/T)GCAGA reference, synonymous-codon
rs121908069 Pathogenic, Sotos syndrome 1 (SOTOS1) [MIM:117550] 177,293,916(+) CTTTT(C/G)TAAGC reference, missense
rs587784169 Pathogenic, Sotos syndrome 1 (SOTOS1) [MIM:117550] 177,282,523(+) AGCTC(A/G)AATTC reference, missense
rs587784174 Pathogenic, Sotos syndrome 1 (SOTOS1) [MIM:117550] 177,283,791(+) GGACC(A/G)AATCA reference, missense
rs587784176 Pathogenic, Sotos syndrome 1 (SOTOS1) [MIM:117550] 177,283,826(+) ATGCT(A/C/T)GGTTC reference, synonymous-codon, missense

Structural Variations from Database of Genomic Variants (DGV) for NSD1 Gene

Variant ID Type Subtype PubMed ID
dgv363n21 CNV gain 19592680
esv1011107 CNV deletion 20482838
esv2659977 CNV deletion 23128226
esv2664525 CNV deletion 23128226
esv2759396 CNV gain 17122850
esv3607687 CNV loss 21293372
esv3607688 CNV loss 21293372
nsv1131929 CNV deletion 24896259
nsv428132 CNV gain 18775914
nsv509101 CNV insertion 20534489
nsv515632 CNV gain 19592680
nsv521574 CNV loss 19592680
nsv521575 CNV gain 19592680
nsv525027 CNV gain 19592680
nsv600364 CNV loss 21841781
nsv823351 CNV gain 20364138
nsv980763 CNV duplication 23825009

Variation tolerance for NSD1 Gene

Residual Variation Intolerance Score: 0.91% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.94; 87.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NSD1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSD1 Gene

Disorders for NSD1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for NSD1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
sotos syndrome 1
  • sotos syndrome
beckwith-wiedemann syndrome
  • wiedemann-beckwith syndrome
beckwith-wiedemann syndrome due to nsd1 mutation
weaver syndrome 1
  • weaver syndrome
5q35 microduplication syndrome
  • dup(5)(q35)
- elite association - COSMIC cancer census association via MalaCards
Search NSD1 in MalaCards View complete list of genes associated with diseases


  • Beckwith-Wiedemann syndrome (BWS) [MIM:130650]: A disorder characterized by anterior abdominal wall defects including exomphalos (omphalocele), pre- and postnatal overgrowth, and macroglossia. Additional less frequent complications include specific developmental defects and a predisposition to embryonal tumors. {ECO:0000269 PubMed:14997421}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving NSD1 is found in an adult form of myelodysplastic syndrome (MDS). Insertion of NUP98 into NSD1 generates a NUP98-NSD1 fusion product. {ECO:0000269 PubMed:15382262}.
  • Note=A chromosomal aberration involving NSD1 is found in childhood acute myeloid leukemia. Translocation t(5;11)(q35;p15.5) with NUP98.
  • Sotos syndrome 1 (SOTOS1) [MIM:117550]: A childhood overgrowth syndrome characterized by pre- and postnatal overgrowth, developmental delay, mental retardation, advanced bone age, and abnormal craniofacial morphology including macrodolichocephaly with frontal bossing, frontoparietal sparseness of hair, apparent hypertelorism, downslanting palpebral fissures, and facial flushing. Common oral findings include: premature eruption of teeth; high, arched palate; pointed chin and, more rarely, prognathism. {ECO:0000269 PubMed:11896389, ECO:0000269 PubMed:12464997, ECO:0000269 PubMed:12807965, ECO:0000269 PubMed:14997421}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NSD1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with NSD1: view

No data available for Genatlas for NSD1 Gene

Publications for NSD1 Gene

  1. Haploinsufficiency of NSD1 causes Sotos syndrome. (PMID: 11896389) Kurotaki N. … Matsumoto N. (Nat. Genet. 2002) 2 3 4 22 64
  2. MLPA analysis in 30 Sotos syndrome patients revealed one total NSD1 deletion and two partial deletions not previously reported. (PMID: 19596467) Fagali C. … Koiffmann C.P. (Eur J Med Genet 2009) 3 22 46 64
  3. Heterogeneity of NSD1 alterations in 116 patients with Sotos syndrome. (PMID: 17565729) Saugier-Veber P. … BA1rglen L. (Hum. Mutat. 2007) 3 22 46 64
  4. Mutation analysis of the NSD1 gene in patients with autism spectrum disorders and macrocephaly. (PMID: 18001468) Buxbaum J.D. … Betancur C. (BMC Med. Genet. 2007) 3 22 46 64
  5. Psychosocial, cognitive, and motor functioning in patients with suspected Sotos syndrome: a comparison between patients with and without NSD1 gene alterations. (PMID: 16780628) de Boer L. … Wit J.M. (Dev Med Child Neurol 2006) 3 22 46 64

Products for NSD1 Gene

Sources for NSD1 Gene

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