Seroatlas · Human Serome Atlas

DNMT3B

DNA (cytosine-5)-methyltransferase 3B

Also known as: DNM3B_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9UBC3
Gene: DNMT3B
Ensembl: ENSG00000088305
Chromosome: 20
Canonical length: 853 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined. [provided by RefSeq, May 2011]

Canonical amino-acid sequenceUniProt

853 residues, UniProt reviewed canonical sequence.

>Q9UBC3|DNMT3B
     1  MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV
    61  SSLLSYTQDL TGDGDGEDGD GSDTPVMPKL FRETRTRSES PAVRTRNNNS VSSRERHRPS
   121  PRSTRGRQGR NHVDESPVEF PATRSLRRRA TASAGTPWPS PPSSYLTIDL TDDTEDTHGT
   181  PQSSSTPYAR LAQDSQQGGM ESPQVEADSG DGDSSEYQDG KEFGIGDLVW GKIKGFSWWP
   241  AMVVSWKATS KRQAMSGMRW VQWFGDGKFS EVSADKLVAL GLFSQHFNLA TFNKLVSYRK
   301  AMYHALEKAR VRAGKTFPSS PGDSLEDQLK PMLEWAHGGF KPTGIEGLKP NNTQPVVNKS
   361  KVRRAGSRKL ESRKYENKTR RRTADDSATS DYCPAPKRLK TNCYNNGKDR GDEDQSREQM
   421  ASDVANNKSS LEDGCLSCGR KNPVSFHPLF EGGLCQTCRD RFLELFYMYD DDGYQSYCTV
   481  CCEGRELLLC SNTSCCRCFC VECLEVLVGT GTAAEAKLQE PWSCYMCLPQ RCHGVLRRRK
   541  DWNVRLQAFF TSDTGLEYEA PKLYPAIPAA RRRPIRVLSL FDGIATGYLV LKELGIKVGK
   601  YVASEVCEES IAVGTVKHEG NIKYVNDVRN ITKKNIEEWG PFDLVIGGSP CNDLSNVNPA
   661  RKGLYEGTGR LFFEFYHLLN YSRPKEGDDR PFFWMFENVV AMKVGDKRDI SRFLECNPVM
   721  IDAIKVSAAH RARYFWGNLP GMNRPVIASK NDKLELQDCL EYNRIAKLKK VQTITTKSNS
   781  IKQGKNQLFP VVMNGKEDVL WCTELERIFG FPVHYTDVSN MGRGARQKLL GRSWSVPVIR
   841  HLFAPLKDYF ACE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against DNMT3B 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): 0.4
Highest tissue expression: 5.8 nTPM

Expression across tissuesHPA

Tissue

pancreas: 5.8 nTPM
testis: 5.7 nTPM
cerebellum: 2.8 nTPM
skin: 2.7 nTPM
thymus: 2.7 nTPM
kidney: 1.6 nTPM

Single-cell type

sertoli cells: 62 nCPM
megakaryocyte progenitors: 56 nCPM
hematopoietic stem cells: 47 nCPM
megakaryocyte-erythroid progenitors: 27 nCPM
pancreatic acinar cells: 21 nCPM
retinal amacrine cells: 19 nCPM

Immune cell

myeloid DC: 0.1 nTPM
naive CD4 T-cell: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM

Brain region

cerebellum: 1.9 nTPM
hypothalamus: 1.2 nTPM
cerebral cortex: 1.1 nTPM
medulla oblongata: 1 nTPM
hippocampal formation: 0.9 nTPM
midbrain: 0.9 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about DNMT3B.

Disease | AllUniProt

Conditions DNMT3B is implicated in, by any mechanism.

Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) MIM:242860
Facioscapulohumeral muscular dystrophy 4, digenic (FSHD4) MIM:619478

Disease | GeneticClinVar

42 pathogenic / likely-pathogenic of 958 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency
Immunodeficiency-centromeric instability-facial anomalies syndrome 1
Facioscapulohumeral muscular dystrophy 4, digenic

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): 0.38
gnomAD pLI: 0.2
gnomAD missense Z: 1.5
DepMap mean gene effect: 0.06
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

DNA (cytosine-5-)-methyltransferase activity
DNA binding
DNA-methyltransferase activity
transcription corepressor activity
zinc ion binding
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of DNMT3B 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 DNMT3B as an antibody target. Whether an autoantibody or antibody against DNMT3B could matter depends on whether native DNMT3B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

DNMT3B 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 DNMT3B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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