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    NSD1 nuclear receptor binding SET domain protein 1 [ Homo sapiens (human) ]

    Gene ID: 64324, updated on 20-Apr-2017
    Official Symbol
    NSD1provided by HGNC
    Official Full Name
    nuclear receptor binding SET domain protein 1provided by HGNC
    Primary source
    HGNC:HGNC:14234
    See related
    Ensembl:ENSG00000165671 MIM:606681; Vega:OTTHUMG00000130846
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    STO; KMT3B; SOTOS; ARA267; SOTOS1
    Summary
    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]
    Orthologs
    Location:
    5q35.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (177133079..177300213)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176560026..176727214)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 346 Neighboring gene fibroblast growth factor receptor 4 Neighboring gene ribosomal protein L21 pseudogene 60 Neighboring gene protein arginine methyltransferase 1 pseudogene 1 Neighboring gene PRELI domain containing 1 Neighboring gene RAB24, member RAS oncogene family Neighboring gene MAX dimerization protein 3

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Beckwith-Wiedemann syndrome
    MedGen: C0004903 OMIM: 130650 GeneReviews: Beckwith-Wiedemann Syndrome
    Compare labs
    Sotos syndrome 1
    MedGen: CN035106 OMIM: 117550 GeneReviews: Sotos Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2011-10-06)

    ClinGen Genome Curation Page
    Triplosensitivity

    Little evidence for dosage pathogenicity (Last evaluated (2011-10-06)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    NHGRI GWA Catalog
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Histone Modifications, organism-specific biosystem (from WikiPathways)
      Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
    • Lysine degradation, organism-specific biosystem (from KEGG)
      Lysine degradation, organism-specific biosystem
      Lysine degradation
    • Lysine degradation, conserved biosystem (from KEGG)
      Lysine degradation, conserved biosystem
      Lysine degradation
    • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
      PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...
    • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
      Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ10684, FLJ22263, FLJ44628, DKFZp666C163

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA polymerase II core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    androgen receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    estrogen receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone methyltransferase activity (H3-K36 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone methyltransferase activity (H3-K36 specific) ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone methyltransferase activity (H4-K20 specific) ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone-lysine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    retinoic acid receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    retinoid X receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    thyroid hormone receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription cofactor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    histone H3-K36 methylation IEA
    Inferred from Electronic Annotation
    more info
     
    histone H4-K20 methylation IEA
    Inferred from Electronic Annotation
    more info
     
    histone methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of RNA polymerase II regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of histone H3-K36 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of peptidyl-serine phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
    Names
    H3-K36-HMTase
    H4-K20-HMTase
    NR-binding SET domain-containing protein
    androgen receptor coactivator 267 kDa protein
    androgen receptor-associated coregulator 267
    androgen receptor-associated protein of 267 kDa
    lysine N-methyltransferase 3B
    nuclear receptor-binding SET domain-containing protein 1
    NP_071900.2
    NP_758859.1

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009821.1 RefSeqGene

      Range
      5001..172135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_512

    mRNA and Protein(s)

    1. NM_022455.4NP_071900.2  histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific isoform b

      See identical proteins and their annotated locations for NP_071900.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as ARA267-beta, represents the longer transcript, and encodes the longer isoform b.
      Source sequence(s)
      AC027314, AC146507, AF395588, AY049721, CK300021
      Consensus CDS
      CCDS4412.1
      UniProtKB/Swiss-Prot
      Q96L73
      Related
      ENSP00000395929.2, OTTHUMP00000161431, ENST00000439151.6, OTTHUMT00000253412
      Conserved Domains (10) summary
      cd05837
      Location:319429
      MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
      cd05838
      Location:17541848
      WHSC1_related; The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as ...
      smart00570
      Location:18911941
      AWS; associated with SET domains
      smart00317
      Location:19422065
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5034
      Location:14311587
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15648
      Location:15451587
      PHD1_NSD1_2; PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2
      cd15650
      Location:15921638
      PHD2_NSD1; PHD finger 2 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15653
      Location:16391692
      PHD3_NSD1; PHD finger 3 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15656
      Location:17091748
      PHD4_NSD1; PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15659
      Location:21202162
      PHD5_NSD1; PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
    2. NM_172349.2NP_758859.1  histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific isoform a

      See identical proteins and their annotated locations for NP_758859.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as ARA267-alpha, differs in the 5' UTR and coding region, compared to variant 2. It encodes a shorter isoform (a), that has a distinct N-terminus compared to isoform b.
      Source sequence(s)
      AC146507, AF380302, AK056667, CK300021, CN333750
      Consensus CDS
      CCDS4413.1
      UniProtKB/Swiss-Prot
      Q96L73
      UniProtKB/TrEMBL
      Q96MN8
      Related
      ENSP00000346111.4, ENST00000354179.8
      Conserved Domains (10) summary
      cd05837
      Location:50160
      MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
      cd05838
      Location:14851579
      WHSC1_related; The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as ...
      smart00570
      Location:16221672
      AWS; associated with SET domains
      smart00317
      Location:16731796
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5034
      Location:11621318
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15648
      Location:12761318
      PHD1_NSD1_2; PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2
      cd15650
      Location:13231369
      PHD2_NSD1; PHD finger 2 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15653
      Location:13701423
      PHD3_NSD1; PHD finger 3 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15656
      Location:14401479
      PHD4_NSD1; PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)
      cd15659
      Location:18511893
      PHD5_NSD1; PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

      Range
      177133079..177300213
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      175992834..176160257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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