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    L3MBTL4 L3MBTL histone methyl-lysine binding protein 4 [ Homo sapiens (human) ]

    Gene ID: 91133, updated on 27-Nov-2024

    Summary

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    Official Symbol
    L3MBTL4provided by HGNC
    Official Full Name
    L3MBTL histone methyl-lysine binding protein 4provided by HGNC
    Primary source
    HGNC:HGNC:26677
    See related
    Ensembl:ENSG00000154655 MIM:617135; AllianceGenome:HGNC:26677
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HsT1031
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 2.4), ovary (RPKM 1.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See L3MBTL4 in Genome Data Viewer
    Location:
    18p11.31
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (5954717..6415259, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (6114833..6575726, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (5954716..6415258, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene MIR3976 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9264 Neighboring gene microRNA 3976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:5891299-5891826 Neighboring gene uncharacterized LOC121725015 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:5899993-5901192 Neighboring gene transmembrane protein 200C Neighboring gene OCT4 hESC enhancer GRCh37_chr18:5941844-5942352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:5964119-5964619 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:5964978-5965478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13058 Neighboring gene Sharpr-MPRA regulatory region 6254 Neighboring gene RNA, U5F small nuclear 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:6146293-6146793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13059 Neighboring gene L3MBTL4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13060 Neighboring gene uncharacterized LOC124904240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:6382344-6383130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:6383131-6383916 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9267 Neighboring gene microRNA 4317 Neighboring gene RNA, U6 small nuclear 349, pseudogene Neighboring gene ribosomal protein L6 pseudogene 27

    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. Loss, mutation and deregulation of L3MBTL4 in breast cancers. Addou-Klouche L, et al. Mol Cancer, 2010 Aug 10. PMID 20698951, Free PMC Article
    2. Genome Wide Association Study Identifies L3MBTL4 as a Novel Susceptibility Gene for Hypertension. Liu X, et al. Sci Rep, 2016 Aug 2. PMID 27480026, Free PMC Article
    3. Molecular cloning and chemical synthesis of a region of platelet glycoprotein IIb involved in adhesive function. Loftus JC, et al. Proc Natl Acad Sci U S A, 1987 Oct. PMID 2444974, Free PMC Article
    4. A genome-wide association study of sleep habits and insomnia. Byrne EM, et al. Am J Med Genet B Neuropsychiatr Genet, 2013 Jul. PMID 23728906, Free PMC Article
    5. Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency. Ferreira RC, et al. Nat Genet, 2010 Sep. PMID 20694011

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Findings pinpointed L3MBTL4 as a critical contributor to the development and progression of hypertension.
      Title: Genome Wide Association Study Identifies L3MBTL4 as a Novel Susceptibility Gene for Hypertension.
    2. identified L3MBTL4 as a potential tumor suppressor gene of chromosome arm 18p. The gene is targeted by deletion, breakage and mutations and its mRNA is downregulated in breast tumors
      Title: Loss, mutation and deregulation of L3MBTL4 in breast cancers.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study of sleep habits and insomnia.
    EBI GWAS Catalog
    Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lethal(3)malignant brain tumor-like protein 4
    Names
    H-l(3)mbt-like protein 4
    L3MBTL4, histone methyl-lysine binding protein

    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.

    mRNA and Protein(s)

    1. NM_001330559.2 → NP_001317488.1  lethal(3)malignant brain tumor-like protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228, CA313345
      Consensus CDS
      CCDS82238.1
      UniProtKB/TrEMBL
      F8W9S8
      Related
      ENSP00000318543.7, ENST00000317931.12
      Conserved Domains (3) summary
      cd09582
      Location:531 → 596
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    2. NM_001365765.2 → NP_001352694.1  lethal(3)malignant brain tumor-like protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228
      Consensus CDS
      CCDS82238.1
      UniProtKB/TrEMBL
      F8W9S8
      Conserved Domains (3) summary
      cd09582
      Location:531 → 596
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    3. NM_001365766.2 → NP_001352695.1  lethal(3)malignant brain tumor-like protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228
      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    4. NM_001365767.2 → NP_001352696.1  lethal(3)malignant brain tumor-like protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AP001021, AP005060, BC039316
      Consensus CDS
      CCDS92428.1
      Related
      ENSP00000382975.3, ENST00000400104.7
      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    5. NM_001365768.2 → NP_001352697.1  lethal(3)malignant brain tumor-like protein 4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228
      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    6. NM_001365769.2 → NP_001352698.1  lethal(3)malignant brain tumor-like protein 4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228
      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    7. NM_001365770.2 → NP_001352699.1  lethal(3)malignant brain tumor-like protein 4 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AK093255, AP001021
      Consensus CDS
      CCDS11839.2
      UniProtKB/Swiss-Prot
      A8MTL8, Q8IXS3, Q8NA19
      Related
      ENSP00000382976.2, ENST00000400105.6
      Conserved Domains (3) summary
      cd09582
      Location:540 → 605
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    8. NM_173464.4 → NP_775735.2  lethal(3)malignant brain tumor-like protein 4 isoform 1

      See identical proteins and their annotated locations for NP_775735.2

      Status: VALIDATED

      Source sequence(s)
      AK026733, AK093255, CA313345, DB455331
      Consensus CDS
      CCDS11839.2
      UniProtKB/Swiss-Prot
      A8MTL8, Q8IXS3, Q8NA19
      Conserved Domains (3) summary
      cd09582
      Location:540 → 605
      SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 407
      zf-C2HC; Zinc finger, C2HC type

    RNA

    1. NR_158609.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228

    2. NR_158610.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228

    3. NR_158611.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP000874, AP001021, AP005060, AP005228

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      5954717..6415259 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437914.1 → XP_047293870.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    2. XM_017026074.2 → XP_016881563.1  lethal(3)malignant brain tumor-like protein 4 isoform X4

    3. XM_011525760.2 → XP_011524062.1  lethal(3)malignant brain tumor-like protein 4 isoform X2

      Conserved Domains (3) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:531 → 560
      SAM_superfamily; SAM (Sterile alpha motif )

    4. XM_011525757.2 → XP_011524059.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011524059.1

      Conserved Domains (3) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:540 → 569
      SAM_superfamily; SAM (Sterile alpha motif )

    5. XM_047437919.1 → XP_047293875.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    6. XM_011525759.2 → XP_011524061.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011524061.1

      Conserved Domains (3) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:540 → 569
      SAM_superfamily; SAM (Sterile alpha motif )

    7. XM_047437917.1 → XP_047293873.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    8. XM_011525758.2 → XP_011524060.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011524060.1

      Conserved Domains (3) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:540 → 569
      SAM_superfamily; SAM (Sterile alpha motif )

    9. XM_047437920.1 → XP_047293876.1  lethal(3)malignant brain tumor-like protein 4 isoform X7

    10. XM_047437918.1 → XP_047293874.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    11. XM_047437916.1 → XP_047293872.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    12. XM_047437915.1 → XP_047293871.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    13. XM_011525767.3 → XP_011524069.1  lethal(3)malignant brain tumor-like protein 4 isoform X10

      Conserved Domains (3) summary
      smart00561
      Location:1 → 75
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:90 → 116
      zf-C2HC; Zinc finger, C2HC type
      cl15755
      Location:251 → 280
      SAM_superfamily; SAM (Sterile alpha motif )

    14. XM_011525762.3 → XP_011524064.1  lethal(3)malignant brain tumor-like protein 4 isoform X5

      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type

    15. XM_006722364.3 → XP_006722427.1  lethal(3)malignant brain tumor-like protein 4 isoform X8

      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type

    16. XM_011525763.3 → XP_011524065.1  lethal(3)malignant brain tumor-like protein 4 isoform X6

      Conserved Domains (2) summary
      smart00561
      Location:273 → 364
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam01530
      Location:379 → 405
      zf-C2HC; Zinc finger, C2HC type

    17. XM_017026077.2 → XP_016881566.1  lethal(3)malignant brain tumor-like protein 4 isoform X9

    RNA

    1. XR_007066253.1 RNA Sequence

    2. XR_935072.2 RNA Sequence

    3. XR_007066252.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      6114833..6575726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319328.1 → XP_054175303.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    2. XM_054319337.1 → XP_054175312.1  lethal(3)malignant brain tumor-like protein 4 isoform X4

    3. XM_054319333.1 → XP_054175308.1  lethal(3)malignant brain tumor-like protein 4 isoform X2

    4. XM_054319327.1 → XP_054175302.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    5. XM_054319336.1 → XP_054175311.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    6. XM_054319332.1 → XP_054175307.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    7. XM_054319334.1 → XP_054175309.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    8. XM_054319329.1 → XP_054175304.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    9. XM_054319340.1 → XP_054175315.1  lethal(3)malignant brain tumor-like protein 4 isoform X7

    10. XM_054319335.1 → XP_054175310.1  lethal(3)malignant brain tumor-like protein 4 isoform X3

      UniProtKB/TrEMBL
      F8W9S8

    11. XM_054319331.1 → XP_054175306.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    12. XM_054319330.1 → XP_054175305.1  lethal(3)malignant brain tumor-like protein 4 isoform X1

    13. XM_054319343.1 → XP_054175318.1  lethal(3)malignant brain tumor-like protein 4 isoform X10

    14. XM_054319338.1 → XP_054175313.1  lethal(3)malignant brain tumor-like protein 4 isoform X5

    15. XM_054319341.1 → XP_054175316.1  lethal(3)malignant brain tumor-like protein 4 isoform X8

    16. XM_054319339.1 → XP_054175314.1  lethal(3)malignant brain tumor-like protein 4 isoform X6

    17. XM_054319342.1 → XP_054175317.1  lethal(3)malignant brain tumor-like protein 4 isoform X9

    RNA

    1. XR_008485033.1 RNA Sequence

    2. XR_008485034.1 RNA Sequence

    3. XR_008485032.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NA19.2 GenPept UniProtKB/Swiss-Prot:Q8NA19

    Gene LinkOut

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

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