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

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; 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

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
Title: Targeting H3K36 methyltransferases NSDs: a promising strategy for tumor targeted therapy.
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.
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.
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.
NSD3S stabilizes MYC through hindering its interaction with FBXW7.
Title: NSD3S stabilizes MYC through hindering its interaction with FBXW7.
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.
Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
Title: Elevated NSD3 histone methylation activity drives squamous cell lung cancer.
Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
Title: Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G17256 (e-PCR)
- UniSTS:11055

WI-17448 (e-PCR)
- UniSTS:72513

SHGC-79887 (e-PCR)
- UniSTS:101459

MARC_17682-17683:1018452650:1 (e-PCR)
- UniSTS:268376

SHGC-57894 (e-PCR)
- UniSTS:35164

SHGC-2825 (e-PCR)
- UniSTS:10860

D8S1791 (e-PCR)
- UniSTS:3949

D8S1361E (e-PCR)
- UniSTS:151175

A006Q29 (e-PCR)
- UniSTS:25035

SHGC-64109 (e-PCR)
- UniSTS:61398

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

EC 2.1.1.370

EC 2.1.1.371

NP_075447.1

EC 2.1.1.370

EC 2.1.1.371

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

NG_023292.2 RefSeqGene

Range

5000..117567

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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)