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    NSD3 nuclear receptor binding SET domain protein 3 [ Homo sapiens (human) ]

    Gene ID: 54904, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NSD3provided by HGNC
    Official Full Name
    nuclear receptor binding SET domain protein 3provided by HGNC
    Primary source
    HGNC:HGNC:12767
    See related
    Ensembl:ENSG00000147548 MIM:607083; AllianceGenome:HGNC:12767
    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
    KMT3F; KMT3G; WHISTLE; WHSC1L1; pp14328
    Summary
    This gene is related to the Wolf-Hirschhorn syndrome candidate-1 gene and encodes a protein with PWWP (proline-tryptophan-tryptophan-proline) domains. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. Two alternatively spliced variants have been described. [provided by RefSeq, May 2015]
    Expression
    Ubiquitous expression in ovary (RPKM 10.0), brain (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NSD3 in Genome Data Viewer
    Location:
    8p11.23
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38269704..38382271, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38546659..38659240, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38127222..38239789, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38033837-38034694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27246 Neighboring gene BAG cochaperone 4 Neighboring gene Sharpr-MPRA regulatory region 4585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38089405-38089904 Neighboring gene DDHD domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19119 Neighboring gene phospholipid phosphatase 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19120 Neighboring gene NUP98-NSD3 recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27247 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38235530-38236031 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38238312-38238846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38239137-38239927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38242638-38243268 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:38243269-38243898 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38244052-38244553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19125 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38247000-38247501 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38248280-38248781 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38257600-38258101 Neighboring gene uncharacterized LOC102723716 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38261681-38262180 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38262831-38263332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19126 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38269931-38270603 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38270604-38271277 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38272896-38273666 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38274107-38274772 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38275681-38276444 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38277305-38277806 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38277908-38278453 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38278454-38278998 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38278999-38279544 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38279545-38280088 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280202-38280702 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280703-38281203 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38282951-38283642 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38285189-38286186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38287183-38288180 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289284-38289961 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289962-38290638 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38292133-38292640 Neighboring gene fibroblast growth factor receptor 1 Neighboring gene ribosomal protein S20 pseudogene 22

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Elevated expression of nuclear receptor-binding SET domain 3 promotes pancreatic cancer cell growth. Sun Y, et al. Cell Death Dis, 2021 Oct 6. PMID 34615858, Free PMC Article
    2. The NSD3L histone methyltransferase regulates cell cycle and cell invasion in breast cancer cells. Zhou Z, et al. Biochem Biophys Res Commun, 2010 Jul 30. PMID 20599755
    3. Development of mammary hyperplasia, dysplasia, and invasive ductal carcinoma in transgenic mice expressing the 8p11 amplicon oncogene NSD3. Turner-Ivey B, et al. Breast Cancer Res Treat, 2017 Jul. PMID 28484924, Free PMC Article
    4. Silencing of histone methyltransferase NSD3 reduces cell viability in osteosarcoma with induction of apoptosis. Liu Z, et al. Oncol Rep, 2017 Nov. PMID 28901481, Free PMC Article
    5. NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines. Angrand PO, et al. Genomics, 2001 May 15. PMID 11374904

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histones Methyltransferase NSD3 Inhibits Lung Adenocarcinoma Glycolysis Through Interacting with PPP1CB to Decrease STAT3 Signaling Pathway.
      Title: Histones Methyltransferase NSD3 Inhibits Lung Adenocarcinoma Glycolysis Through Interacting with PPP1CB to Decrease STAT3 Signaling Pathway.
    2. The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors.
      Title: The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors.
    3. Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
      Title: Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
    4. Elevated expression of nuclear receptor-binding SET domain 3 promotes pancreatic cancer cell growth.
      Title: Elevated expression of nuclear receptor-binding SET domain 3 promotes pancreatic cancer cell growth.
    5. A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins.
      Title: A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins.
    6. Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.
      Title: Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.
    7. NSD3S stabilizes MYC through hindering its interaction with FBXW7.
      Title: NSD3S stabilizes MYC through hindering its interaction with FBXW7.
    8. NSD3-Induced Methylation of H3K36 Activates NOTCH Signaling to Drive Breast Tumor Initiation and Metastatic Progression.
      Title: NSD3-Induced Methylation of H3K36 Activates NOTCH Signaling to Drive Breast Tumor Initiation and Metastatic Progression.
    9. Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
      Title: Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
    10. Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
      Title: Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common variants on 8p12 and 1q24.2 confer risk of schizophrenia.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20353, MGC126766, MGC142029, DKFZp667H044

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables histone H3K27 dimethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27 trimethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K36 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K4 dimethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription regulator activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in 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
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase NSD3
    Names
    Wolf-Hirschhorn syndrome candidate 1-like 1
    nuclear SET domain-containing protein 3
    protein whistle
    NP_060248.2
    NP_075447.1

    NCBI Reference Sequences (RefSeq)

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    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_023292.2 RefSeqGene

      Range
      5000..117567
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017778.3 → NP_060248.2  histone-lysine N-methyltransferase NSD3 isoform short

      See identical proteins and their annotated locations for NP_060248.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (short) contains an alternative 3' end sequence. The shorter protein encoded has a different carboxy terminus than the protein encoded by variant long.
      Source sequence(s)
      AF332468
      Consensus CDS
      CCDS6105.1
      UniProtKB/Swiss-Prot
      Q9BZ95
      Related
      ENSP00000313410.3, ENST00000316985.7
      Conserved Domains (1) summary
      cd05837
      Location:267 → 383
      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 ...

    2. NM_023034.2 → NP_075447.1  histone-lysine N-methyltransferase NSD3 isoform long

      See identical proteins and their annotated locations for NP_075447.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (long) contains an alternative 3' end sequence. The longer protein encoded has a different carboxy terminus than the protein encoded by variant short.
      Source sequence(s)
      AC087362, AF332469
      Consensus CDS
      CCDS43729.1
      UniProtKB/Swiss-Prot
      B7ZL11, D3DSX1, Q1RMD3, Q3B796, Q6ZSA5, Q9BYU8, Q9BYU9, Q9BZ95, Q9H2M8, Q9H9W9, Q9NXA6
      Related
      ENSP00000313983.7, ENST00000317025.13
      Conserved Domains (10) summary
      cd05837
      Location:267 → 383
      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:958 → 1051
      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:1094 → 1144
      AWS; associated with SET domains
      smart00317
      Location:1145 → 1268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5034
      Location:602 → 746
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15649
      Location:703 → 746
      PHD1_NSD3; PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3)
      cd15652
      Location:751 → 797
      PHD2_NSD3; PHD finger 2 found in nuclear SET domain-containing protein 3 (NSD3)
      cd15655
      Location:798 → 850
      PHD3_NSD3; PHD finger 3 found in nuclear SET domain-containing protein 3 (NSD3)
      cd15658
      Location:917 → 952
      PHD4_NSD3; PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3)
      cd15661
      Location:1323 → 1365
      PHD5_NSD3; PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      38269704..38382271 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      38546659..38659240 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZ95.1 GenPept UniProtKB/Swiss-Prot:Q9BZ95

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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