Seroatlas · Human Serome Atlas

NSD2

Histone-lysine N-methyltransferase NSD2

Also known as: KMT3G, MMSET, NSD2_HUMAN, WHSC1

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O96028
Gene: NSD2
Ensembl: ENSG00000109685
Chromosome: 4
Canonical length: 1365 aa
Protein class: Cancer-related genes, Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm,Nucleoli

OverviewNCBI Gene

This gene encodes a protein that contains four domains present in other developmental proteins: a PWWP domain, an HMG box, a SET domain, and a PHD-type zinc finger. It is expressed ubiquitously in early development. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene maps to the 165 kb WHS critical region and has also been involved in the chromosomal translocation t(4;14)(p16.3;q32.3) in multiple myelomas. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. Some transcript variants are nonsense-mediated mRNA (NMD) decay candidates, hence not represented as reference sequences. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1365 residues, UniProt reviewed canonical sequence.

>O96028|NSD2
     1  MEFSIKQSPL SVQSVVKCIK MKQAPEILGS ANGKTPSCEV NRECSVFLSK AQLSSSLQEG
    61  VMQKFNGHDA LPFIPADKLK DLTSRVFNGE PGAHDAKLRF ESQEMKGIGT PPNTTPIKNG
   121  SPEIKLKITK TYMNGKPLFE SSICGDSAAD VSQSEENGQK PENKARRNRK RSIKYDSLLE
   181  QGLVEAALVS KISSPSDKKI PAKKESCPNT GRDKDHLLKY NVGDLVWSKV SGYPWWPCMV
   241  SADPLLHSYT KLKGQKKSAR QYHVQFFGDA PERAWIFEKS LVAFEGEGQF EKLCQESAKQ
   301  APTKAEKIKL LKPISGKLRA QWEMGIVQAE EAASMSVEER KAKFTFLYVG DQLHLNPQVA
   361  KEAGIAAESL GEMAESSGVS EEAAENPKSV REECIPMKRR RRAKLCSSAE TLESHPDIGK
   421  STPQKTAEAD PRRGVGSPPG RKKTTVSMPR SRKGDAASQF LVFCQKHRDE VVAEHPDASG
   481  EEIEELLRSQ WSLLSEKQRA RYNTKFALVA PVQAEEDSGN VNGKKRNHTK RIQDPTEDAE
   541  AEDTPRKRLR TDKHSLRKRD TITDKTARTS SYKAMEAASS LKSQAATKNL SDACKPLKKR
   601  NRASTAASSA LGFSKSSSPS ASLTENEVSD SPGDEPSESP YESADETQTE VSVSSKKSER
   661  GVTAKKEYVC QLCEKPGSLL LCEGPCCGAF HLACLGLSRR PEGRFTCSEC ASGIHSCFVC
   721  KESKTDVKRC VVTQCGKFYH EACVKKYPLT VFESRGFRCP LHSCVSCHAS NPSNPRPSKG
   781  KMMRCVRCPV AYHSGDACLA AGCSVIASNS IICTAHFTAR KGKRHHAHVN VSWCFVCSKG
   841  GSLLCCESCP AAFHPDCLNI EMPDGSWFCN DCRAGKKLHF QDIIWVKLGN YRWWPAEVCH
   901  PKNVPPNIQK MKHEIGEFPV FFFGSKDYYW THQARVFPYM EGDRGSRYQG VRGIGRVFKN
   961  ALQEAEARFR EIKLQREARE TQESERKPPP YKHIKVNKPY GKVQIYTADI SEIPKCNCKP
  1021  TDENPCGFDS ECLNRMLMFE CHPQVCPAGE FCQNQCFTKR QYPETKIIKT DGKGWGLVAK
  1081  RDIRKGEFVN EYVGELIDEE ECMARIKHAH ENDITHFYML TIDKDRIIDA GPKGNYSRFM
  1141  NHSCQPNCET LKWTVNGDTR VGLFAVCDIP AGTELTFNYN LDCLGNEKTV CRCGASNCSG
  1201  FLGDRPKTST TLSSEEKGKK TKKKTRRRRA KGEGKRQSED ECFRCGDGGQ LVLCDRKFCT
  1261  KAYHLSCLGL GKRPFGKWEC PWHHCDVCGK PSTSFCHLCP NSFCKEHQDG TAFSCTPDGR
  1321  SYCCEHDLGA ASVRSTKTEK PPPEPGKPKG KRRRRRGWRR VTEGK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against NSD2 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.46
Highest tissue expression: 56 nTPM

Expression across tissuesHPA

Tissue

thymus: 56 nTPM
bone marrow: 51 nTPM
testis: 35 nTPM
retina: 26 nTPM
lymph node: 24 nTPM
tonsil: 23 nTPM

Single-cell type

erythrocyte progenitors: 342 nCPM
early primary spermatocytes: 281 nCPM
monocyte progenitors: 242 nCPM
rod photoreceptor cells: 194 nCPM
megakaryocyte progenitors: 178 nCPM
gonadotrophs: 173 nCPM

Immune cell

basophil: 4 nTPM
neutrophil: 3.3 nTPM
T-reg: 2.9 nTPM
plasmacytoid DC: 2.1 nTPM
naive B-cell: 1.7 nTPM
memory CD4 T-cell: 1.5 nTPM

Brain region

cerebellum: 93 nTPM
cerebral cortex: 76 nTPM
white matter: 74 nTPM
hypothalamus: 71 nTPM
basal ganglia: 71 nTPM
pons: 69 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about NSD2.

Disease | AllUniProt

Conditions NSD2 is implicated in, by any mechanism.

Rauch-Steindl syndrome (RAUST) MIM:619695

Disease | GeneticClinVar

84 pathogenic / likely-pathogenic of 736 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Rauch-Steindl syndrome
4p partial monosomy syndrome
NSD2-related disorder
Wolf-Hirschhorn like syndrome
Inborn genetic diseases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.12
gnomAD pLI: 1
DepMap mean gene effect: -0.06
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

PWWP domain
SET domain
Zinc finger, RING-type
Zinc finger, PHD-type
Post-SET domain
AWS domain
High mobility group box domain
Zinc finger, FYVE/PHD-type
Zinc finger, RING/FYVE/PHD-type
Zinc finger, PHD-type, conserved site
Zinc finger, PHD-finger
High mobility group box domain superfamily
NSD, Cys-His rich domain
SET domain superfamily
Histone-lysine N-methyltransferase NSD1 / NSD2, first PHD finger
SET2 Histone-Lysine N-Methyltransferase
Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger
Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1
HMG (high mobility group) box
PHD-finger
PWWP domain
SET domain
AWS domain
NSD Cys-His rich domain
Histone-lysine N-methyltransferase NSD-like, PHD zinc finger
Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger
Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1
Nuclear SET domain-containing protein 2, first PWWP domain
Nuclear SET domain-containing protein 2, second PWWP domain
Nuclear SET domain-containing protein 2, SET domain
Nuclear SET domain-containing protein 2, second PHD finger
Nuclear SET domain-containing protein 2, third PHD finger
Nuclear SET domain-containing protein 2, fifth PHD finger
Nuclear SET domain-containing protein 2, HMG box

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of NSD2 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads NSD2 as an antibody target. Whether an autoantibody or antibody against NSD2 could matter depends on whether native NSD2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

NSD2 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label NSD2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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