This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of t... See more...

Aliases for L3MBTL3 Gene

Aliases for L3MBTL3 Gene

  • L3MBTL Histone Methyl-Lysine Binding Protein 3 2 3 5
  • L3MBTL3, Histone Methyl-Lysine Binding Protein 2 3
  • Lethal(3)Malignant Brain Tumor-Like Protein 3 3 4
  • H-L(3)Mbt-Like Protein 3 3 4
  • MBT-1 3 4
  • MBT1 3 4
  • L(3)Mbt-Like 3 (Drosophila) 2
  • L(3)Mbt-Like Protein 3 4
  • L(3)Mbt-Like 3 3
  • KIAA1798 4

External Ids for L3MBTL3 Gene

Previous GeneCards Identifiers for L3MBTL3 Gene

  • GC06P130320
  • GC06P130381
  • GC06P127920
  • GC06P130013

Summaries for L3MBTL3 Gene

Entrez Gene Summary for L3MBTL3 Gene

  • This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of this gene has been observed in human patients with medulloblastoma. [provided by RefSeq, Oct 2016]

GeneCards Summary for L3MBTL3 Gene

L3MBTL3 (L3MBTL Histone Methyl-Lysine Binding Protein 3) is a Protein Coding gene. Diseases associated with L3MBTL3 include Lipodystrophy, Familial Partial, Type 1 and Gastric Dilatation. An important paralog of this gene is L3MBTL4.

UniProtKB/Swiss-Prot Summary for L3MBTL3 Gene

  • Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility. Required for normal maturation of myeloid progenitor cells (By similarity).

Additional gene information for L3MBTL3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for L3MBTL3 Gene

Genomics for L3MBTL3 Gene

GeneHancer (GH) Regulatory Elements for L3MBTL3 Gene

Promoters and enhancers for L3MBTL3 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
GH06J130017 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 511.8 +40.9 40925 4.1 HNRNPK CTCF SIN3A NRF1 ZFX ZNF639 POLR2A ZBTB10 ZBTB26 TRIM28 L3MBTL3 RPL5P21 ARHGAP18 SAMD3 RF00017-5774 LOC105378000
GH06J130027 Enhancer 0.7 Ensembl ENCODE 36.7 +49.6 49596 4.4 ZNF316 ZNF384 MAFF MAFK MAFG JUNB BCL3 EMSY L3MBTL3 RF00017-5774 LOC105378000
GH06J130033 Enhancer 0.9 Ensembl ENCODE 24.3 +55.5 55496 3 JUND FOS ZBTB11 TRIM28 ZNF510 OSR2 WT1 FOXA2 NCOR1 SPI1 L3MBTL3 RF00017-5774 LOC105378000
GH06J129677 Enhancer 1.5 FANTOM5 ENCODE dbSUPER 11.2 -295.9 -295899 11.3 CTCF NRF1 TCF12 POLR2G USF1 SP1 NCOR1 JUND PHB2 FOS ARHGAP18 RPL5P21 L3MBTL3 piR-43104-047 RF00017-5772
GH06J130036 Enhancer 0.5 Ensembl 23.1 +58.0 57997 1.6 CTCF ZNF384 PKNOX1 RAD21 ZNF350 ARID3A SMC3 L3MBTL3 RF00017-5774 LOC105378000
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around L3MBTL3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for L3MBTL3

Top Transcription factor binding sites by QIAGEN in the L3MBTL3 gene promoter:
  • CREB
  • deltaCREB
  • Evi-1
  • Nkx2-5
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • SRF
  • SRF (504 AA)

Genomic Locations for L3MBTL3 Gene

Genomic Locations for L3MBTL3 Gene
chr6:129,978,804-130,141,451
(GRCh38/hg38)
Size:
162,648 bases
Orientation:
Plus strand
chr6:130,334,844-130,462,594
(GRCh37/hg19)
Size:
127,751 bases
Orientation:
Plus strand

Genomic View for L3MBTL3 Gene

Genes around L3MBTL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
L3MBTL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for L3MBTL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for L3MBTL3 Gene

Proteins for L3MBTL3 Gene

  • Protein details for L3MBTL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JM7-LMBL3_HUMAN
    Recommended name:
    Lethal(3)malignant brain tumor-like protein 3
    Protein Accession:
    Q96JM7
    Secondary Accessions:
    • Q4VXE1
    • Q5VUM9
    • Q6P9B5

    Protein attributes for L3MBTL3 Gene

    Size:
    780 amino acids
    Molecular mass:
    88337 Da
    Quaternary structure:
    • Interacts with RNF2.
    SequenceCaution:
    • Sequence=BAB47427.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for L3MBTL3 Gene

    Alternative splice isoforms for L3MBTL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for L3MBTL3 Gene

Post-translational modifications for L3MBTL3 Gene

  • Ubiquitination at Lys692
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for L3MBTL3 Gene

Domains & Families for L3MBTL3 Gene

Gene Families for L3MBTL3 Gene

Protein Domains for L3MBTL3 Gene

Blocks:
  • Sterile alpha motif SAM
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for L3MBTL3 Gene

GenScript: Design optimal peptide antigens:
  • MBT-1 (LMBL3_HUMAN)
genes like me logo Genes that share domains with L3MBTL3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for L3MBTL3 Gene

Function for L3MBTL3 Gene

Molecular function for L3MBTL3 Gene

UniProtKB/Swiss-Prot Function:
Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility. Required for normal maturation of myeloid progenitor cells (By similarity).

Phenotypes From GWAS Catalog for L3MBTL3 Gene

Gene Ontology (GO) - Molecular Function for L3MBTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003700 DNA-binding transcription factor activity IEA --
GO:0005515 protein binding IPI,IEA 17517653
GO:0008270 zinc ion binding IEA --
GO:0140110 transcription regulator activity IEA --
genes like me logo Genes that share ontologies with L3MBTL3: view
genes like me logo Genes that share phenotypes with L3MBTL3: view

Animal Models for L3MBTL3 Gene

MGI Knock Outs for L3MBTL3:

Animal Model Products

CRISPR Products

miRNA for L3MBTL3 Gene

miRTarBase miRNAs that target L3MBTL3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for L3MBTL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for L3MBTL3 Gene

Localization for L3MBTL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for L3MBTL3 Gene

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 L3MBTL3 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for L3MBTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with L3MBTL3: view

Pathways & Interactions for L3MBTL3 Gene

PathCards logo

SuperPathways for L3MBTL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for L3MBTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0030099 myeloid cell differentiation IEA --
GO:0030225 macrophage differentiation IEA --
GO:0030851 granulocyte differentiation IEA --
genes like me logo Genes that share ontologies with L3MBTL3: view

No data available for Pathways by source and SIGNOR curated interactions for L3MBTL3 Gene

Drugs & Compounds for L3MBTL3 Gene

No Compound Related Data Available

Transcripts for L3MBTL3 Gene

mRNA/cDNA for L3MBTL3 Gene

4 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for L3MBTL3

Alternative Splicing Database (ASD) splice patterns (SP) for L3MBTL3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23
SP1: - -
SP2: -
SP3:

Relevant External Links for L3MBTL3 Gene

GeneLoc Exon Structure for
L3MBTL3

Expression for L3MBTL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for L3MBTL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for L3MBTL3 Gene

This gene is overexpressed in CD8 Tcells (27.8), Ovary (21.7), and CD4 Tcells (16.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for L3MBTL3 Gene



Protein tissue co-expression partners for L3MBTL3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for L3MBTL3

SOURCE GeneReport for Unigene cluster for L3MBTL3 Gene:

Hs.658051

Evidence on tissue expression from TISSUES for L3MBTL3 Gene

  • Nervous system(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with L3MBTL3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for L3MBTL3 Gene

Orthologs for L3MBTL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for L3MBTL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia L3MBTL3 31 30
  • 99.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia L3MBTL3 31 30
  • 91.56 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 89 (a)
OneToMany
-- 31
  • 84 (a)
OneToMany
mouse
(Mus musculus)
Mammalia L3mbtl3 17 31 30
  • 86.09 (n)
dog
(Canis familiaris)
Mammalia L3MBTL3 31 30
  • 84.54 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia L3mbtl3 30
  • 84.19 (n)
oppossum
(Monodelphis domestica)
Mammalia L3MBTL3 31
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves L3MBTL3 31 30
  • 75.39 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia L3MBTL3 31
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia l3mbtl3 30
  • 60.96 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5963 30
zebrafish
(Danio rerio)
Actinopterygii l3mbtl3 31
  • 59 (a)
OneToOne
l3mbtl1b 30
  • 57.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(3)mbt 31 30
  • 47.03 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 45 (a)
OneToMany
Species where no ortholog for L3MBTL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for L3MBTL3 Gene

ENSEMBL:
Gene Tree for L3MBTL3 (if available)
TreeFam:
Gene Tree for L3MBTL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for L3MBTL3: view image

Paralogs for L3MBTL3 Gene

(5) SIMAP similar genes for L3MBTL3 Gene using alignment to 3 proteins:

  • LMBL3_HUMAN
  • E9PI01_HUMAN
  • E9PLL7_HUMAN
genes like me logo Genes that share paralogs with L3MBTL3: view

Variants for L3MBTL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for L3MBTL3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
732722 Likely Benign: not provided 130,055,161(+) C/A INTRON_VARIANT
768109 Benign: not provided 130,068,424(+) A/G INTRON_VARIANT
771405 Benign: not provided 130,060,116(+) G/A SYNONYMOUS_VARIANT
rs386352323 Uncertain Significance: not provided 130,092,751(+) T/C MISSENSE_VARIANT
rs9388768 - p.Thr183Asn

Additional dbSNP identifiers (rs#s) for L3MBTL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for L3MBTL3 Gene

Variant ID Type Subtype PubMed ID
esv3610778 CNV gain 21293372
esv3610781 CNV gain 21293372
nsv1073588 CNV deletion 25765185
nsv473251 CNV novel sequence insertion 20440878
nsv604663 CNV gain 21841781

Variation tolerance for L3MBTL3 Gene

Residual Variation Intolerance Score: 6.81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.69; 32.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for L3MBTL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
L3MBTL3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for L3MBTL3 Gene

Disorders for L3MBTL3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for L3MBTL3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lipodystrophy, familial partial, type 1
  • fpld1
gastric dilatation
  • stomach dilatation
n syndrome
  • nsx
medulloblastoma
  • mdb
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for L3MBTL3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with L3MBTL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for L3MBTL3 Gene

Publications for L3MBTL3 Gene

  1. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H … Hirschhorn JN (Nature 2010) 3 41 54
  2. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 41 54
  3. Screening of LRRK2 interactants by yeast 2-hybrid analysis. (PMID: 19001729) Zheng XY … Zhang ZH (Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences 2008) 3 23 54
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for L3MBTL3 Gene

Sources for L3MBTL3 Gene