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

Gene ID: 54904, updated on 8-Jul-2021

Summary

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
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

See NSD3 in Genome Data Viewer
Location:
8p11.23
Exon count:
25
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (38269704..38382271, complement)
105.20201022 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 BAG cochaperone 4 Neighboring gene DDHD domain containing 2 Neighboring gene phospholipid phosphatase 5 Neighboring gene NUP98-NSD3 recombination region Neighboring gene uncharacterized LOC102723716 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 2 Neighboring gene fibroblast growth factor receptor 1 Neighboring gene ribosomal protein S20 pseudogene 22

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
Common variants on 8p12 and 1q24.2 confer risk of schizophrenia.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20353, MGC126766, MGC142029, DKFZp667H044

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone methyltransferase activity (H3-K36 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
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 
Component Evidence Code Pubs
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IC
Inferred by Curator
more info
PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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_023292.1 RefSeqGene

    Range
    5001..112231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017778.3NP_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:267383
    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_023034.2NP_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
    Q9BZ95
    Related
    ENSP00000313983.7, ENST00000317025.13
    Conserved Domains (10) summary
    cd05837
    Location:267383
    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:9581051
    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:10941144
    AWS; associated with SET domains
    smart00317
    Location:11451268
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5034
    Location:602746
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15649
    Location:703746
    PHD1_NSD3; PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15652
    Location:751797
    PHD2_NSD3; PHD finger 2 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15655
    Location:798850
    PHD3_NSD3; PHD finger 3 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15658
    Location:917952
    PHD4_NSD3; PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15661
    Location:13231365
    PHD5_NSD3; PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

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