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    KMT2B lysine methyltransferase 2B [ Homo sapiens (human) ]

    Gene ID: 9757, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KMT2Bprovided by HGNC
    Official Full Name
    lysine methyltransferase 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:15840
    See related
    Ensembl:ENSG00000272333 MIM:606834; AllianceGenome:HGNC:15840
    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
    HRX2; MLL2; MLL4; TRX2; WBP7; DYT28; MLL1B; MRD68; WBP-7; CXXC10
    Summary
    This gene encodes a protein which contains multiple domains including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains, and a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain. The SET domain is a conserved C-terminal domain that characterizes proteins of the MLL (mixed-lineage leukemia) family. This gene is ubiquitously expressed in adult tissues. It is also amplified in solid tumor cell lines, and may be involved in human cancer. Two alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene, however, the full length nature of the shorter transcript is not known. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 15.2), spleen (RPKM 7.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KMT2B in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35718003..35738878)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38263317..38284192)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36208905..36229779)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36174493-36174994 Neighboring gene thymidylate synthetase pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14492 Neighboring gene zinc finger and BTB domain containing 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10532 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:36207458-36208017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:36209137-36209694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36230671-36231301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14497 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36234871-36235031 Neighboring gene IGF like family receptor 1 Neighboring gene U2 small nuclear RNA auxiliary factor 1 like 4 Neighboring gene presenilin enhancer, gamma-secretase subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia. Meyer E, et al. Nat Genet, 2017 Feb. PMID 27992417
    2. Identification of a novel de novo KMT2B variant in a Greek dystonia patient via exome sequencing genotype-phenotype correlations of all published cases. Marogianni C, et al. Mol Biol Rep, 2021 Jan. PMID 33300088
    3. KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation. Cif L, et al. Brain, 2020 Dec 5. PMID 33150406, Free PMC Article
    4. Clinical phenotypes, genotypes and treatment in Chinese dystonia patients with KMT2B variants. Li XY, et al. Parkinsonism Relat Disord, 2020 Aug. PMID 32634684
    5. Frequency and phenotypic spectrum of KMT2B dystonia in childhood: A single-center cohort study. Carecchio M, et al. Mov Disord, 2019 Oct. PMID 31216378

    See all (130) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MLL4 binds TET3.
      Title: MLL4 binds TET3.
    2. [Phenotypic and genotypic spectrum of KMT2B dystonia. Description of three Colombian patients].
      Title: [Phenotypic and genotypic spectrum of KMT2B dystonia. Description of three Colombian patients].
    3. Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4.
      Title: Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4.
    4. LncRNA SEMA3B-AS1 suppresses the tumor-initiating characteristics of triple negative breast cancer via engaging in MLL4-mediated H3K4 trimethylation.
      Title: LncRNA SEMA3B-AS1 suppresses the tumor-initiating characteristics of triple negative breast cancer via engaging in MLL4-mediated H3K4 trimethylation.
    5. Histone Methyltransferase KMT2B Promotes Metastasis and Angiogenesis of Cervical Cancer by Upregulating EGF Expression.
      Title: Histone Methyltransferase KMT2B Promotes Metastasis and Angiogenesis of Cervical Cancer by Upregulating EGF Expression.
    6. Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4).
      Title: Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4).
    7. Comparison of methylation episignatures in KMT2B- and KMT2D-related human disorders.
      Title: Comparison of methylation episignatures in KMT2B- and KMT2D-related human disorders.
    8. Blood DNA methylation provides an accurate biomarker of KMT2B-related dystonia and predicts onset.
      Title: Blood DNA methylation provides an accurate biomarker of KMT2B-related dystonia and predicts onset.
    9. Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile.
      Title: Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile.
    10. A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members.
      Title: A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    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

    Associated conditions

    Description Tests
    Dystonia 28, childhood-onset
    MedGen: C4310633 OMIM: 617284 GeneReviews: Hereditary Dystonia Overview, KMT2B-Related Dystonia
    		not available
    Intellectual developmental disorder, autosomal dominant 68
    MedGen: C5677008 OMIM: 619934 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2017-05-11)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2017-05-11)

    ClinGen Genome Curation PagePubMed

    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

    Homology

    Clone Names

    • KIAA0304

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		  
    enables histone H3K4 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K4 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables unmethylated CpG binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of MLL1/2 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of histone methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase 2B
    Names
    WW domain binding protein 7
    histone-lysine N-methyltransferase MLL4
    lysine (K)-specific methyltransferase 2B
    mixed lineage leukemia gene homolog 2
    myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4
    myeloid/lymphoid or mixed-lineage leukemia protein 4
    trithorax homologue 2
    NP_055542.1
    XP_011525863.3
    XP_011525864.1
    XP_047295743.1
    XP_054178770.1
    XP_054178771.1
    XP_054178772.1

    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_052906.1 RefSeqGene

      Range
      4985..25860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014727.3 → NP_055542.1  histone-lysine N-methyltransferase 2B

      See identical proteins and their annotated locations for NP_055542.1

      Status: REVIEWED

      Source sequence(s)
      AD000671, AJ007041
      Consensus CDS
      CCDS46055.1
      UniProtKB/Swiss-Prot
      O15022, O95836, Q96GP2, Q96IP3, Q9UK25, Q9UMN6, Q9Y668, Q9Y669
      UniProtKB/TrEMBL
      A0A8I5KPK0
      Related
      ENSP00000398837.2, ENST00000420124.4
      Conserved Domains (10) summary
      cd05493
      Location:1374 → 1516
      Bromo_ALL-1; Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many ...
      smart00542
      Location:2413 → 2497
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:2577 → 2697
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG2940
      Location:2559 → 2715
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:958 → 1005
      zf-CXXC; CXXC zinc finger domain
      cd15589
      Location:1203 → 1249
      PHD1_KMT2B; PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15591
      Location:1251 → 1300
      PHD2_KMT2B; PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15593
      Location:1337 → 1393
      PHD3_KMT2B; PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15694
      Location:1581 → 1685
      ePHD_KMT2B; Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B)
      pfam05964
      Location:1734 → 1780
      FYRN; F/Y-rich N-terminus

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      35718003..35738878
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439787.1 → XP_047295743.1  histone-lysine N-methyltransferase 2B isoform X2

      UniProtKB/TrEMBL
      A0A8I5KPK0

    2. XM_011527561.3 → XP_011525863.3  histone-lysine N-methyltransferase 2B isoform X3

      UniProtKB/TrEMBL
      A0A669KBI7, A0A8I5KPK0
      Related
      ENSP00000501283.1, ENST00000673918.2

    3. XM_011527562.3 → XP_011525864.1  histone-lysine N-methyltransferase 2B isoform X1

      UniProtKB/TrEMBL
      A0A8I5KPK0
      Conserved Domains (8) summary
      cd05493
      Location:1374 → 1516
      Bromo_ALL-1; Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many ...
      smart00542
      Location:2413 → 2497
      FYRC; FY-rich domain, C-terminal region
      pfam02008
      Location:958 → 1005
      zf-CXXC; CXXC zinc finger domain
      cd15589
      Location:1203 → 1249
      PHD1_KMT2B; PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15591
      Location:1251 → 1300
      PHD2_KMT2B; PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15593
      Location:1337 → 1393
      PHD3_KMT2B; PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B)
      cd15694
      Location:1581 → 1685
      ePHD_KMT2B; Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B)
      pfam05964
      Location:1734 → 1780
      FYRN; F/Y-rich N-terminus

    RNA

    1. XR_935878.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      38263317..38284192
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322796.1 → XP_054178771.1  histone-lysine N-methyltransferase 2B isoform X2

      UniProtKB/TrEMBL
      A0A8I5KPK0

    2. XM_054322797.1 → XP_054178772.1  histone-lysine N-methyltransferase 2B isoform X3

      UniProtKB/TrEMBL
      A0A8I5KPK0

    3. XM_054322795.1 → XP_054178770.1  histone-lysine N-methyltransferase 2B isoform X1

      UniProtKB/TrEMBL
      A0A8I5KPK0

    RNA

    1. XR_008485225.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UMN6.1 GenPept UniProtKB/Swiss-Prot:Q9UMN6

    Gene LinkOut

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

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