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

Gene ID: 26013, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43507697..43550954)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45240962..45284158)
105.20220307 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. 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
  2. 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
  3. 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
  4. 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
  5. Imprinting of the human L3MBTL gene, a polycomb family member located in a region of chromosome 20 deleted in human myeloid malignancies. Li J, et al. Proc Natl Acad Sci U S A, 2004 May 11. PMID 15123827, Free PMC Article

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)

Genotypes

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
part_of 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_2023_10

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

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