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

Gene ID: 54904, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38269704..38382271, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38546659..38659240, complement)
105.20220307 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
  • 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. NSD3-Induced Methylation of H3K36 Activates NOTCH Signaling to Drive Breast Tumor Initiation and Metastatic Progression. Jeong GY, et al. Cancer Res, 2021 Jan 1. PMID 32967925
  3. 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
  4. 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
  5. The histone methyltransferase Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) is involved in human carcinogenesis. Kang D, et al. Genes Chromosomes Cancer, 2013 Feb. PMID 23011637

See all (75) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
    Title: Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
  3. 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.
  4. 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.
  5. 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.
  6. NSD3S stabilizes MYC through hindering its interaction with FBXW7.
    Title: NSD3S stabilizes MYC through hindering its interaction with FBXW7.
  7. 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.
  8. Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
    Title: Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
  9. Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
    Title: Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
  10. The observation that certain metabolic pathways are differentially regulated by NSD3s and Pdp3 suggests that, despite the structural similarity between their PWWP domains, the two proteins act by unique mechanisms and may recruit different downstream signaling complexes.
    Title: (1) H NMR metabolomics reveals increased glutaminolysis upon overexpression of NSD3s or Pdp3 in Saccharomyces cerevisiae.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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
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
  
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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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_2023_10

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

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