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    L3MBTL1 L3MBTL histone methyl-lysine binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 26013, updated on 10-Dec-2024

    Summary

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    Official Symbol
    L3MBTL1provided by HGNC
    Official Full Name
    L3MBTL histone methyl-lysine binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:15905
    See related
    Ensembl:ENSG00000185513 MIM:608802; AllianceGenome:HGNC:15905
    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
    L3MBTL; ZC2HC3; H-L(3)MBT; dJ138B7.3
    Summary
    This gene represents a polycomb group gene. The encoded protein functions to regulate gene activity, likely via chromatin modification. The encoded protein may also be necessary for mitosis. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
    Expression
    Broad expression in testis (RPKM 4.3), brain (RPKM 2.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See L3MBTL1 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43507697..43550954)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45240962..45284158)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42136337..42179594)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42086334-42087281 Neighboring gene serine and arginine rich splicing factor 6 Neighboring gene RNA, U6 small nuclear 1251, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12927 Neighboring gene transmembrane protein 14C-like Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42173308-42173524 Neighboring gene serum/glucocorticoid regulated kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42236005-42236846 Neighboring gene intraflagellar transport 52 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42266543-42266756

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets. Wang WK, et al. Structure, 2003 Jul. PMID 12842041, Free PMC Article
    2. L3MBTL1 deficiency directs the differentiation of human embryonic stem cells toward trophectoderm. Hoya-Arias R, et al. Stem Cells Dev, 2011 Nov. PMID 21341991, Free PMC Article
    3. Depletion of L3MBTL1 promotes the erythroid differentiation of human hematopoietic progenitor cells: possible role in 20q- polycythemia vera. Perna F, et al. Blood, 2010 Oct 14. PMID 20585043, Free PMC Article
    4. Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Li H, et al. Mol Cell, 2007 Nov 30. PMID 18042461, Free PMC Article
    5. Characterization of the imprinted polycomb gene L3MBTL, a candidate 20q tumour suppressor gene, in patients with myeloid malignancies. Bench AJ, et al. Br J Haematol, 2004 Dec. PMID 15566354

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression and DNA Methylation Status of the Imprinted Genes PEG10 and L3MBTL1 in the Umbilical Cord Blood and Placenta of the Offspring of Assisted Reproductive Technology.
      Title: Expression and DNA Methylation Status of the Imprinted Genes PEG10 and L3MBTL1 in the Umbilical Cord Blood and Placenta of the Offspring of Assisted Reproductive Technology.
    2. results revealed that the three RNAs-based biomarker network (long non-coding intergenic RNA-[lncRNA RP11-909B2.1], Homo sapiens microRNA-595 [hsa-miRNA-595], and L3MBTL1 mRNA), had high sensitivity and specificity for discriminating CRC from healthy controls and also from benign colorectal neoplasm.
      Title: Competing endogenous RNA network crosstalk reveals novel molecular markers in colorectal cancer.
    3. Loss of the paternally derived allele of the imprinted L3MBTL1 gene is associated with Shwachman-Diamond syndrome.
      Title: Parental origin of the deletion del(20q) in Shwachman-Diamond patients and loss of the paternally derived allele of the imprinted L3MBTL1 gene.
    4. The polycomb group protein L3MBTL1 represses a SMAD5-mediated hematopoietic transcriptional program in human pluripotent stem cells.
      Title: The polycomb group protein L3MBTL1 represses a SMAD5-mediated hematopoietic transcriptional program in human pluripotent stem cells.
    5. Data indicate that germline genes, some of which drive oncogenesis in Drosophila melanogaster, are similarly ectopically activated in a wide range of human cancers.
      Title: Meta-analysis of expression of l(3)mbt tumor-associated germline genes supports the model that a soma-to-germline transition is a hallmark of human cancers.
    6. High expression of L3MBTL1 was associated with low grade and hormone receptor-positive tumors, as well as low risk of disease recurrence and breast cancer death.
      Title: Physical activity and breast cancer survival: an epigenetic link through reduced methylation of a tumor suppressor gene L3MBTL1.
    7. depletion of L3MBTL1 does not affect hESC self-renewal, rather it enhances differentiation toward extra-embryonic trophoblast tissues
      Title: L3MBTL1 deficiency directs the differentiation of human embryonic stem cells toward trophectoderm.
    8. Data suggest that the loss of L3MBTL1 contributes to the development of 20q(-) hematopoietic malignancies by inducing replicative stress, DNA damage, and genomic instability.
      Title: L3MBTL1 polycomb protein, a candidate tumor suppressor in del(20q12) myeloid disorders, is essential for genome stability.
    9. SET8-mediated methylation of p53 at Lys-382 promotes the interaction between L3MBTL1 and p53 in cells.
      Title: The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression.
    10. haploinsufficiency of L3MBTL1 contributes to some (20q-) myeloproliferative neoplasms, especially polycythemia vera, by promoting erythroid differentiation
      Title: Depletion of L3MBTL1 promotes the erythroid differentiation of human hematopoietic progenitor cells: possible role in 20q- polycythemia vera.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-08-29)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-08-29)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: SGK2

    Homology

    Clone Names

    • FLJ41181, KIAA0681, DKFZp586P1522

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SAM domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables nucleosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in hemopoiesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell cycle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of megakaryocyte differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of mitotic nuclear division IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chromatin lock complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lethal(3)malignant brain tumor-like protein 1
    Names
    L3MBTL1, histone methyl-lysine binding protein
    l(3)mbt protein homolog
    l(3)mbt-like 1
    lethal (3) malignant brain tumor l(3)

    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

    1. NG_009238.3 RefSeqGene

      Range
      5018..48275
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1049

    mRNA and Protein(s)

    1. NM_001377303.1 → NP_001364232.1  lethal(3)malignant brain tumor-like protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93043.1
      UniProtKB/TrEMBL
      A0A3F2YNZ1, A0A994J4Z1
      Related
      ENSP00000398516.2, ENST00000418998.7
      Conserved Domains (4) summary
      smart00561
      Location:407 → 503
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      PRK07764
      Location:27 → 188
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01530
      Location:643 → 671
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:770 → 798
      SAM_superfamily; SAM (Sterile alpha motif )

    2. NM_001377306.1 → NP_001364235.1  lethal(3)malignant brain tumor-like protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93044.1
      UniProtKB/TrEMBL
      A0A3B3ISS0, A0A994J4Z1
      Related
      ENSP00000497566.1, ENST00000649917.1
      Conserved Domains (4) summary
      smart00561
      Location:407 → 503
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      PRK07764
      Location:27 → 188
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01530
      Location:643 → 671
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:770 → 814
      SAM_superfamily; SAM (Sterile alpha motif )

    3. NM_001377307.1 → NP_001364236.1  lethal(3)malignant brain tumor-like protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      UniProtKB/TrEMBL
      A0A994J4Z1
      Conserved Domains (3) summary
      cd09582
      Location:685 → 750
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:558 → 586
      zf-C2HC; Zinc finger, C2HC type

    4. NM_001377308.1 → NP_001364237.1  lethal(3)malignant brain tumor-like protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93046.1
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000410139.2, ENST00000422861.3
      Conserved Domains (3) summary
      cd09582
      Location:680 → 745
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 581
      zf-C2HC; Zinc finger, C2HC type

    5. NM_001377309.1 → NP_001364238.1  lethal(3)malignant brain tumor-like protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL031681, BC034398, Z98752
      Consensus CDS
      CCDS93045.1
      UniProtKB/TrEMBL
      A0A0A0MRR4, A0A994J4Z1
      Related
      ENSP00000362226.1, ENST00000373134.5

    6. NM_001377310.1 → NP_001364239.1  lethal(3)malignant brain tumor-like protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      UniProtKB/TrEMBL
      A0A994J4Z1
      Conserved Domains (3) summary
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 581
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:680 → 708
      SAM_superfamily; SAM (Sterile alpha motif )

    7. NM_001377311.1 → NP_001364240.1  lethal(3)malignant brain tumor-like protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Consensus CDS
      CCDS93047.1
      UniProtKB/TrEMBL
      A0A994J4Z1, B0QYN5
      Related
      ENSP00000415971.2, ENST00000434666.6
      Conserved Domains (3) summary
      cd09582
      Location:640 → 705
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:277 → 373
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:513 → 541
      zf-C2HC; Zinc finger, C2HC type

    8. NM_015478.7 → NP_056293.4  lethal(3)malignant brain tumor-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_056293.4

      Status: REVIEWED

      Source sequence(s)
      AK310345, BC039820, BG956397, BU741824
      Consensus CDS
      CCDS13319.1
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000362227.3, ENST00000373135.8
      Conserved Domains (3) summary
      smart00561
      Location:317 → 413
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:553 → 579
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:680 → 708
      SAM_superfamily; SAM (Sterile alpha motif )

    9. NM_032107.5 → NP_115479.4  lethal(3)malignant brain tumor-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK299199, BC039820, BG956397, BU741824, DR003568
      Consensus CDS
      CCDS46602.2
      UniProtKB/Swiss-Prot
      B4DRC9, E1P5W7, Q5H8Y8, Q5H8Y9, Q8IUV7, Q9H1E6, Q9H1G5, Q9UG06, Q9UJB9, Q9Y468, Q9Y4C9
      UniProtKB/TrEMBL
      A0A994J4Z1
      Related
      ENSP00000402107.4, ENST00000427442.8
      Conserved Domains (4) summary
      smart00561
      Location:385 → 481
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:621 → 649
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:748 → 776
      SAM_superfamily; SAM (Sterile alpha motif )
      cl26386
      Location:5 → 166
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    RNA

    1. NR_165189.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    2. NR_165190.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Related
      ENST00000648570.1

    3. NR_165191.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    4. NR_165192.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    5. NR_165193.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    6. NR_165194.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752
      Related
      ENST00000649501.1

    7. NR_165195.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    8. NR_165196.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031681, Z98752

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      43507697..43550954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      45240962..45284158
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y468.4 GenPept UniProtKB/Swiss-Prot:Q9Y468

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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