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DNMT3B Gene(Protein Coding)

DNA Methyltransferase 3 Beta

GCID:
GC20P032762
GIFtS:
59
Genes Participants
UDN Logo

Aliases for DNMT3B Gene

Aliases for DNMT3B Gene

  • DNA Methyltransferase 3 Beta 2 3 5
  • DNA (Cytosine-5-)-Methyltransferase 3 Beta 2 3
  • DNA Methyltransferase HsaIIIB 3 4
  • DNA MTase HsaIIIB 3 4
  • EC 2.1.1.37 4 56
  • M.HsaIIIB 3 4
  • DNA Cytosine-5--Methyltransferase 3 Beta 3
  • DNA (Cytosine-5)-Methyltransferase 3B 3
  • Dnmt3b 4
  • ICF1 3
  • ICF 3

External Ids for DNMT3B Gene

Previous GeneCards Identifiers for DNMT3B Gene

  • GC20P031108
  • GC20P032018
  • GC20P032065
  • GC20P030813
  • GC20P031350
  • GC20P028137

Summaries for DNMT3B Gene

Entrez Gene Summary for DNMT3B 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]

GeneCards Summary for DNMT3B Gene

DNMT3B (DNA Methyltransferase 3 Beta) is a Protein Coding gene. Diseases associated with DNMT3B include Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome 1 and Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome. Among its related pathways are Mesodermal Commitment Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity and unmethylated CpG binding. An important paralog of this gene is DNMT3A.

UniProtKB/Swiss-Prot for DNMT3B Gene

  • Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1. Required for DUX4 silencing in somatic cells (PubMed:27153398).

Tocris Summary for DNMT3B Gene

  • Protein arginine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the arginine residues on histones and other proteins. The dysregulation of this methylation is critical in the development of certain cancers.

Gene Wiki entry for DNMT3B Gene

Additional gene information for DNMT3B Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DNMT3B Gene

Genomics for DNMT3B Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for DNMT3B Gene

Promoters and enhancers for DNMT3B Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH20I032760 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 559 +0.7 694 4.7 HDGF PKNOX1 FOXA2 ARNT SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF143 DNMT3B BAK1P1 MAPRE1 ASXL1 TM9SF4 PLAGL2 ENSG00000260257 ZNF341 C20orf203 BPIFB3
GH20I032779 Promoter/Enhancer 1.3 EPDnew ENCODE 550.4 +17.8 17837 2.7 CTCF PKNOX1 USF1 ZNF792 SAP130 SIN3A DMAP1 ZNF2 KMT2B SLC30A9 DNMT3B MAPRE1 COMMD7 ENSG00000260257 GC20P032809
GH20I031894 Enhancer 1.3 FANTOM5 Ensembl ENCODE 21.6 -867.1 -867052 1.5 HDGF ATF1 SMAD1 ZNF493 ZFP64 ZNF133 RFX5 ZNF335 ZNF213 ZNF302 ASXL1 TM9SF4 MCTS2P BAK1P1 DNMT3B REM1 TSPY26P RSL24D1P6 PDRG1 C20orf203
GH20I033665 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 10.1 +904.7 904745 3.1 HDGF PKNOX1 ATF1 SMAD1 SIN3A ZNF2 IRF4 ZNF48 YY1 ZNF143 ACTL10 CDK5RAP1 CBFA2T2 DNMT3B ZNF341-AS1 ENSG00000272945 E2F1 CHMP4B C20orf144 NECAB3
GH20I032580 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 2 -179.6 -179567 5.6 HDGF PKNOX1 SMAD1 ARNT ARID4B FEZF1 SLC30A9 ZNF766 ZNF263 SP5 ENSG00000228156 NOL4L ENSG00000233293 COMMD7 NOL4L-DT C20orf203 DNMT3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DNMT3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DNMT3B gene promoter:

Genomic Locations for DNMT3B Gene

Genomic Locations for DNMT3B Gene
chr20:32,762,385-32,809,356
(GRCh38/hg38)
Size:
46,972 bases
Orientation:
Plus strand
chr20:31,350,191-31,397,162
(GRCh37/hg19)

Genomic View for DNMT3B Gene

Genes around DNMT3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DNMT3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DNMT3B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DNMT3B Gene

Proteins for DNMT3B Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for DNMT3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBC3-DNM3B_HUMAN
    Recommended name:
    DNA (cytosine-5)-methyltransferase 3B
    Protein Accession:
    Q9UBC3
    Secondary Accessions:
    • A2A2E2
    • B4DSM8
    • B4DSU1
    • E1P5M6
    • E1P5M7
    • E7EN63
    • E9PBF2
    • Q9UBD4
    • Q9UJQ5
    • Q9UKA6
    • Q9UNE5
    • Q9Y5R9
    • Q9Y5S0

    Protein attributes for DNMT3B Gene

    Size:
    853 amino acids
    Molecular mass:
    95751 Da
    Quaternary structure:
    • Interacts with BAZ2A/TIP5, SUV39H1 and CBX4. Interacts with UHRF1 (By similarity). Interacts with DNMT1 and DNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1. Interacts with the PRC2/EED-EZH2 complex.

    Three dimensional structures from OCA and Proteopedia for DNMT3B Gene

    Alternative splice isoforms for DNMT3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DNMT3B Gene

Protein Expression for DNMT3B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for DNMT3B Gene

Q9UBC3:
  • LLGRSWSVPVIRHLFAPLK
  • EWGPFDLVIGGSPCNDLS
  • DGYQSYCT
  • CCRCFCVEC
  • VSAAHRARYFWGNLPGMNRP
  • RPKEGDDRPFFW
  • PIRVLSLFDGIATG
  • WFGDGKFS
  • FENVVAM
  • DKRDISRFLE
  • HYTDVSNM
  • SNSIKQGK
  • VNPARKGLYEGTGRLFFEFY

Post-translational modifications for DNMT3B Gene

Other Protein References for DNMT3B Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for DNMT3B Gene

Gene Families for DNMT3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for DNMT3B Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for DNMT3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UBC3

UniProtKB/Swiss-Prot:

DNM3B_HUMAN :
  • The PWWP domain is essential for targeting to pericentric heterochromatin.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.
Domain:
  • The PWWP domain is essential for targeting to pericentric heterochromatin.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.
genes like me logo Genes that share domains with DNMT3B: view

Function for DNMT3B Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for DNMT3B Gene

GENATLAS Biochemistry:
DNA (cytosine -5)-methyltransferase 3 beta ,abundantly expressed in ES cells in testis and thymus but barely detectable in differentiated cells and adult tissues,with at least two alternatively spliced isoforms essential for de novo DNA methylation and development (at least in mouse)
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by binding to the regulatory factor DNMT3L.
UniProtKB/Swiss-Prot Function:
Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1. Required for DUX4 silencing in somatic cells (PubMed:27153398).

Enzyme Numbers (IUBMB) for DNMT3B Gene

Phenotypes From GWAS Catalog for DNMT3B Gene

Gene Ontology (GO) - Molecular Function for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003714 transcription corepressor activity IMP 18567530
GO:0003886 DNA (cytosine-5-)-methyltransferase activity IDA,TAS 10433969
GO:0005515 protein binding IPI 11735126
genes like me logo Genes that share ontologies with DNMT3B: view
genes like me logo Genes that share phenotypes with DNMT3B: view

Human Phenotype Ontology for DNMT3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DNMT3B Gene

MGI Knock Outs for DNMT3B:

Animal Model Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for DNMT3B Gene

Localization for DNMT3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DNMT3B Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DNMT3B gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS 17303076
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with DNMT3B: view

Pathways & Interactions for DNMT3B Gene

genes like me logo Genes that share pathways with DNMT3B: view

Gene Ontology (GO) - Biological Process for DNMT3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 17303076
GO:0001666 response to hypoxia IEA --
GO:0006306 DNA methylation TAS 10433969
GO:0009636 response to toxic substance IEA --
GO:0010212 response to ionizing radiation IEA --
genes like me logo Genes that share ontologies with DNMT3B: view

No data available for SIGNOR curated interactions for DNMT3B Gene

Drugs & Compounds for DNMT3B Gene

Products:

  1. Drug

(17) Drugs for DNMT3B Gene - From: ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Thioguanine Approved Pharma Purine antimetabolite 83
Decitabine Approved, Investigational Pharma DNA methyltransferase inhibitor 267
Zebularine Experimental Pharma DNA methylation inhibitor, DNA methyltransferase and cytidine deaminase inhibitor 0
s-adenosylhomocysteine Experimental Pharma 0
5-Azacytidine Pharma DNA methyltransferase inhibitor., DNA methyltransferase inhibitor 0

(7) Additional Compounds for DNMT3B Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-methylcytosine
  • 4-Amino-5-methyl-2-(1H)-Pyrimidinone
  • 4-Amino-5-methyl-2-pyrimidinol
  • 5-Methyl-Cytosine
  • 5-Methylcytosine
  • 5-Methylcytosine>96
 554-01-8
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
 29908-03-0

(5) Tocris Compounds for DNMT3B Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor 320-67-2
Decitabine DNA methyltransferase inhibitor 2353-33-5
Lomeguatrib MGMT inhibitor 192441-08-0
RG 108 Non-nucleoside DNA methyltransferase inhibitor 48208-26-0
Zebularine DNA methyltransferase and cytidine deaminase inhibitor 3690-10-6

(10) ApexBio Compounds for DNMT3B Gene

Compound Action Cas Number
5-Azacytidine DNA methyltransferase inhibitor. 320-67-2
Decitabine (NSC127716, 5AZA-CdR) Deoxycytidine analog and cellular diifferentiation inducer 2353-33-5
Lomeguatrib MGMT inhibitor 192441-08-0
Nanaomycin A DNMT3B inhibitor 52934-83-5
Nanaomycin C 58286-55-8
RG 108 DNA methyltransferase inhibitor 48208-26-0
SGI-1027 DNMT inhibitor 1020149-73-8
SGI-110 DNA methyltransferases inhibitor,potent 929901-49-5
Thioguanine Purine antimetabolite 154-42-7
Zebularine DNA methylation inhibitor 3690-10-6
genes like me logo Genes that share compounds with DNMT3B: view

Drug Products

Transcripts for DNMT3B Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for DNMT3B Gene

(8) REFSEQ mRNAs :
(16) Additional mRNA sequences :
(103) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DNMT3B Gene

DNA (cytosine-5-)-methyltransferase 3 beta:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a ·
SP1: - - -
SP2: - -
SP3:
SP4:
SP5: - - - -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -
SP14: - - - -
SP15:
SP16: -
SP17:

ExUns: 16b · 16c ^ 17 ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b · 24c
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9: - - -
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for DNMT3B Gene

GeneLoc Exon Structure for
DNMT3B
ECgene alternative splicing isoforms for
DNMT3B

Expression for DNMT3B Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DNMT3B Gene

mRNA expression in normal human tissues for DNMT3B Gene
mRNA expression by BioGPS for DNMT3B GenemRNA expression by GTEx for DNMT3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DNMT3B Gene

This gene is overexpressed in Testis (x5.3) and Pancreas (x5.0).

Protein differential expression in normal tissues from HIPED for DNMT3B Gene

This gene is overexpressed in Bone marrow stromal cell (28.2), Heart (20.7), and Lung (20.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DNMT3B Gene



Protein tissue co-expression partners for DNMT3B Gene

NURSA nuclear receptor signaling pathways regulating expression of DNMT3B Gene:

DNMT3B

SOURCE GeneReport for Unigene cluster for DNMT3B Gene:

Hs.643024

mRNA Expression by UniProt/SwissProt for DNMT3B Gene:

Q9UBC3-DNM3B_HUMAN
Tissue specificity: Ubiquitous; highly expressed in fetal liver, heart, kidney, placenta, and at lower levels in spleen, colon, brain, liver, small intestine, lung, peripheral blood mononuclear cells, and skeletal muscle. Isoform 1 is expressed in all tissues except brain, skeletal muscle and PBMC, 3 is ubiquitous, 4 is expressed in all tissues except brain, skeletal muscle, lung and prostate and 5 is detectable only in testis and at very low level in brain and prostate.

Evidence on tissue expression from TISSUES for DNMT3B Gene

  • Intestine(4.5)
  • Nervous system(4.5)
  • Lung(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DNMT3B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • sinus
  • skull
  • tongue
Thorax:
  • bronchus
  • lung
Abdomen:
  • intestine
  • large intestine
  • small intestine
General:
  • blood
  • bone marrow
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with DNMT3B: view

Orthologs for DNMT3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for DNMT3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia DNMT3B 33 34
  • 99.49 (n)
cow
(Bos Taurus)
 Mammalia DNMT3B 34
  • 91 (a)
 OneToOne
LOC100848415 33
  • 88.65 (n)
dog
(Canis familiaris)
 Mammalia DNMT3B 33 34
  • 88.31 (n)
rat
(Rattus norvegicus)
 Mammalia Dnmt3b 33
  • 83.59 (n)
mouse
(Mus musculus)
 Mammalia Dnmt3b 33 16 34
  • 82.7 (n)
oppossum
(Monodelphis domestica)
 Mammalia DNMT3B 34
  • 66 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia DNMT3B 34
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves DNMT3B 33 34
  • 69.95 (n)
lizard
(Anolis carolinensis)
 Reptilia DNMT3B 34
  • 81 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii dnmt4 33 34
  • 66.36 (n)
-- 33
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 40 (a)
 OneToMany
Species where no ortholog for DNMT3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DNMT3B Gene

ENSEMBL:
Gene Tree for DNMT3B (if available)
TreeFam:
Gene Tree for DNMT3B (if available)

Paralogs for DNMT3B Gene

Paralogs for DNMT3B Gene

(1) SIMAP similar genes for DNMT3B Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for DNMT3B Gene

genes like me logo Genes that share paralogs with DNMT3B: view

Variants for DNMT3B Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for DNMT3B Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs121908939 pathogenic, Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency, Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860] 32,807,791(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs121908940 pathogenic, Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency, Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860] 32,807,793(+) G/A/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs121908941 Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860] 32,802,416(+) T/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121908942 pathogenic, Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency, Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860] 32,800,916(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121908943 pathogenic, Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency, Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860] 32,800,200(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for DNMT3B Gene

Variant ID Type Subtype PubMed ID
nsv1056411 CNV loss 25217958
nsv1072112 CNV deletion 25765185
nsv833956 CNV loss 17160897
nsv833957 CNV gain+loss 17160897
nsv979490 CNV duplication 23825009

Variation tolerance for DNMT3B Gene

Residual Variation Intolerance Score: 22.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.04; 50.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DNMT3B Gene

Human Gene Mutation Database (HGMD)
DNMT3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DNMT3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DNMT3B Gene

Disorders for DNMT3B Gene

MalaCards: The human disease database

(14) MalaCards diseases for DNMT3B Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

DNM3B_HUMAN
  • Facioscapulohumeral muscular dystrophy 2 (FSHD2) [MIM:158901]: A degenerative muscle disease characterized by slowly progressive weakness of the muscles of the face, upper-arm, and shoulder girdle. The onset of symptoms usually occurs in the first or second decade of life. Affected individuals usually present with impairment of upper extremity elevation. This tends to be followed by facial weakness, primarily involving the orbicularis oris and orbicularis oculi muscles. {ECO:0000269 PubMed:27153398}. Note=The disease is caused by mutations affecting the gene represented in this entry. DNMT3B mutations lead to DUX4 expression in somatic tissues, including muscle cells, when an haplotype on chromosome 4 is permissive for DUX4 expression. Ectopic expression of DUX4 in skeletal muscle activates the expression of stem cell and germline genes, and, when overexpressed in somatic cells, DUX4 can ultimately lead to cell death.
  • Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860]: A rare disorder characterized by a variable immunodeficiency resulting in recurrent infections, facial anomalies, and branching of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome in some, but not all, patients. {ECO:0000269 PubMed:10555141, ECO:0000269 PubMed:10588719, ECO:0000269 PubMed:10647011, ECO:0000269 PubMed:11102980, ECO:0000269 PubMed:15580563, ECO:0000269 PubMed:21120685, ECO:0000269 PubMed:27734333}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for DNMT3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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No data available for Genatlas for DNMT3B Gene

Publications for DNMT3B Gene

  1. Cloning, expression and chromosome locations of the human DNMT3 gene family. (PMID: 10433969) Xie S … Li E (Gene 1999) 2 3 4 22 58
  2. DNMT3B promoter polymorphism and risk of gastric cancer. (PMID: 19517237) Hu J … Xu H (Digestive diseases and sciences 2010) 3 22 44 58
  3. Association of the DNMT3B polymorphism with colorectal adenomatous polyps and adenocarcinoma. (PMID: 19626461) Guo X … Wang S (Molecular biology reports 2010) 3 22 44 58
  4. Effect of age on the association between p16CDKN2A methylation and DNMT3B polymorphism in head and neck carcinoma and patient survival. (PMID: 20514408) Farias LC … Guimarães AL (International journal of oncology 2010) 3 22 44 58
  5. Single nucleotide polymorphism in DNMT3B promoter and its association with hepatocellular carcinoma in a Moroccan population. (PMID: 19465161) Ezzikouri S … Benjelloun S (Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2009) 3 22 44 58

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