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

    Gene ID: 64324, updated on 6-Jun-2024

    Summary

    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; AllianceGenome:HGNC:14234
    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. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Sep 2018]
    Expression
    Ubiquitous expression in testis (RPKM 4.4), thyroid (RPKM 4.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NSD1 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177131798..177300213)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177675008..177843448)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176560016..176727214)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176449401-176449938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176449939-176450475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16670 Neighboring gene zinc finger protein 346 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176488686-176489885 Neighboring gene FGFR4 5' regulatory region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176537235-176537734 Neighboring gene fibroblast growth factor receptor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176558105-176558658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr5:176559765-176560316 and GRCh37_chr5:176560317-176560870 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176560871-176561422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176561423-176561976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176692158-176693050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176693051-176693942 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:176696443-176697642 Neighboring gene ribosomal protein L21 pseudogene 60 Neighboring gene protein arginine methyltransferase 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176722701-176723202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176723203-176723702 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176727388-176727581 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176728411-176729610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16677 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176730775-176731652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23700 Neighboring gene PRELI domain containing 1 Neighboring gene RAB24, member RAS oncogene family Neighboring gene MAX dimerization protein 3

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Sotos syndrome
    MedGen: C0175695 OMIM: 117550 GeneReviews: Sotos Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-07-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-27)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10684, FLJ22263, FLJ44628, DKFZp666C163

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables histone H3K36 dimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K36 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K36 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables histone H3K36 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H4K20 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nuclear androgen receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear estrogen receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nuclear retinoic acid receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nuclear retinoid X receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nuclear thyroid hormone receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase, H3 lysine-36 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
    histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
    lysine N-methyltransferase 3B
    nuclear receptor SET domain-containing protein 1
    nuclear receptor-binding SET domain-containing protein 1
    NP_001352613.2
    NP_001396230.1
    NP_001396231.1
    NP_001396232.1
    NP_001396233.1
    NP_001396234.1
    NP_001396235.1
    NP_001396236.1
    NP_001396237.1
    NP_001396238.1
    NP_071900.2
    NP_758859.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001365684.2NP_001352613.2  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform a

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      Consensus CDS
      CCDS4413.1
      UniProtKB/TrEMBL
      A0A8I5QJP2, B2RWP5, D6RA58
      Related
      ENSP00000343209.5, ENST00000347982.9
    2. NM_001409301.1NP_001396230.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform b

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/Swiss-Prot
      Q96L73, Q96PD8, Q96RN7
      UniProtKB/TrEMBL
      B2RWP5
    3. NM_001409302.1NP_001396231.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform b

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/Swiss-Prot
      Q96L73, Q96PD8, Q96RN7
      UniProtKB/TrEMBL
      B2RWP5
    4. NM_001409303.1NP_001396232.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform b

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/Swiss-Prot
      Q96L73, Q96PD8, Q96RN7
      UniProtKB/TrEMBL
      B2RWP5
      Related
      ENSP00000508426.1, ENST00000687453.1
    5. NM_001409304.1NP_001396233.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform c

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      B2RWP5
      Related
      ENST00000688613.1
    6. NM_001409305.1NP_001396234.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform d

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      B2RWP5
    7. NM_001409306.1NP_001396235.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform e

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      B2RWP5
    8. NM_001409307.1NP_001396236.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform e

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      B2RWP5
    9. NM_001409308.1NP_001396237.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform a

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      A0A8I5QJP2, B2RWP5, D6RA58
      Related
      ENSP00000423372.3, ENST00000508896.7
    10. NM_001409309.1NP_001396238.1  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform f

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      UniProtKB/TrEMBL
      B2RWP5
    11. NM_022455.5NP_071900.2  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform b

      See identical proteins and their annotated locations for NP_071900.2

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      Consensus CDS
      CCDS4412.1
      UniProtKB/Swiss-Prot
      Q96L73, Q96PD8, Q96RN7
      UniProtKB/TrEMBL
      B2RWP5
      Related
      ENSP00000395929.2, ENST00000439151.7
      Conserved Domains (12) 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
      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)
      cl26267
      Location:14311587
      ING; Inhibitor of growth proteins N-terminal histone-binding
      cl26386
      Location:24382663
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
      cl26464
      Location:22082574
      Atrophin-1; Atrophin-1 family
    12. NM_172349.5NP_758859.2  histone-lysine N-methyltransferase, H3 lysine-36 specific isoform a

      Status: REVIEWED

      Source sequence(s)
      AC008570, AC027314, AC146507
      Consensus CDS
      CCDS4413.1
      UniProtKB/TrEMBL
      A0A8I5QJP2, B2RWP5, D6RA58
      Related
      ENSP00000346111.5, ENST00000354179.9

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      177131798..177300213
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      177675008..177843448
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)