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    KMT2A lysine (K)-specific methyltransferase 2A [ Homo sapiens (human) ]

    Gene ID: 4297, updated on 17-Jan-2016
    Official Symbol
    KMT2Aprovided by HGNC
    Official Full Name
    lysine (K)-specific methyltransferase 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:7132
    See related
    Ensembl:ENSG00000118058; HPRD:01162; MIM:159555; Vega:OTTHUMG00000166337
    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
    HRX; MLL; MLL1; TRX1; ALL-1; CXXC7; HTRX1; MLL1A; WDSTS; MLL-AF9; MLL/GAS7; TET1-MLL
    Summary
    This gene encodes a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The encoded protein contains multiple conserved functional domains. One of these domains, the SET domain, is responsible for its histone H3 lysine 4 (H3K4) methyltransferase activity which mediates chromatin modifications associated with epigenetic transcriptional activation. This protein is processed by the enzyme Taspase 1 into two fragments, MLL-C and MLL-N. These fragments reassociate and further assemble into different multiprotein complexes that regulate the transcription of specific target genes, including many of the HOX genes. Multiple chromosomal translocations involving this gene are the cause of certain acute lymphoid leukemias and acute myeloid leukemias. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]
    Orthologs
    See KMT2A in Epigenomics, MapViewer
    Location:
    11q23
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 11 NC_000011.10 (118436490..118526824)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118307205..118397539)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ubiquitination factor E4A Neighboring gene uncharacterized LOC100131626 Neighboring gene ATP synthase, H+ transporting, mitochondrial Fo complex subunit G Neighboring gene uncharacterized LOC101929089 Neighboring gene tetratricopeptide repeat domain 36 Neighboring gene transmembrane protein 25 Neighboring gene intraflagellar transport 46

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Wiedemann-Steiner syndrome
    MedGen: C1854630 OMIM: 605130 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2013-08-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Some evidence for dosage pathogenicity (Last evaluated (2013-08-22)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ11783

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    AT DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    core promoter sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone methyltransferase activity (H3-K4 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone methyltransferase activity (H3-K4 specific) IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    lysine-acetylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    unmethylated CpG binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA methylation IEA
    Inferred from Electronic Annotation
    more info
     
    anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin organization TAS
    Traceable Author Statement
    more info
     
    circadian regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    definitive hemopoiesis IEA
    Inferred from Electronic Annotation
    more info
     
    embryonic hemopoiesis TAS
    Traceable Author Statement
    more info
    PubMed 
    exploration behavior IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K4 dimethylation IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K4 methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H3-K4 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone H3-K4 trimethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H4-K16 acetylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    homeostasis of number of cells within a tissue IEA
    Inferred from Electronic Annotation
    more info
     
    membrane depolarization IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    peptidyl-lysine monomethylation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of cellular response to drug IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of histone H3-K4 methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    post-embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    protein complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of histone H3-K14 acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of histone H3-K27 acetylation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of histone H3-K9 acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of short-term neuronal synaptic plasticity IEA
    Inferred from Electronic Annotation
    more info
     
    response to potassium ion IEA
    Inferred from Electronic Annotation
    more info
     
    spleen development IEA
    Inferred from Electronic Annotation
    more info
     
    transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
    PubMed 
    visual learning IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    MLL1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
     
    histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Preferred Names
    histone-lysine N-methyltransferase 2A
    Names
    CDK6/MLL fusion protein
    CXXC-type zinc finger protein 7
    MLL-AF4 der(11) fusion protein
    MLL/ENL fusion protein
    MLL/GAS7 fusion protein
    MLL/GMPS fusion protein
    MLL/hCDCrel fusion protein
    lysine N-methyltransferase 2A
    mixed lineage leukemia 1
    myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
    rearranged MLL protein
    trithorax-like protein
    zinc finger protein HRX
    NP_001184033.1
    NP_005924.2

    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_027813.1 RefSeqGene

      Range
      5001..95335
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_613

    mRNA and Protein(s)

    1. NM_001197104.1NP_001184033.1  histone-lysine N-methyltransferase 2A isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AP000941, AP001267, BC065385, D14540, L04731
      Consensus CDS
      CCDS55791.1
      UniProtKB/Swiss-Prot
      Q03164
      Related
      ENSP00000436786, OTTHUMP00000232648, ENST00000534358, OTTHUMT00000389228
      Conserved Domains (12) summary
      cd05493
      Location:16501780
      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:36723755
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:38343954
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:39563972
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:38283972
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:11471194
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:20262076
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:21092275
      SOG2; RAM signalling pathway protein
      cd15588
      Location:14331479
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:14811530
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:15681627
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:18741986
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    2. NM_005933.3NP_005924.2  histone-lysine N-methyltransferase 2A isoform 2 precursor

      See identical proteins and their annotated locations for NP_005924.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AB209508, AP000941, AP001267, BC065385, D14540
      Consensus CDS
      CCDS31686.1
      UniProtKB/Swiss-Prot
      Q03164
      Related
      ENSP00000374157, OTTHUMP00000238461, ENST00000389506, OTTHUMT00000399085
      Conserved Domains (12) summary
      cd05493
      Location:16471777
      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:36693752
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:38313951
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:39533969
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:38253969
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:11471194
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:20232073
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:21062272
      SOG2; RAM signalling pathway protein
      cd15588
      Location:14331479
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:14811530
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:15681624
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:18711983
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p2 Primary Assembly

      Range
      118436490..118526824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542829.1XP_011541131.1  

      Conserved Domains (12) summary
      cd05493
      Location:16831813
      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:37053788
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:38673987
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:39894005
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:38614005
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:11801227
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:20592109
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:21422308
      SOG2; RAM signalling pathway protein
      cd15588
      Location:14661512
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:15141563
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:16011660
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:19072019
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    2. XM_011542831.1XP_011541133.1  

      Conserved Domains (12) summary
      cd05493
      Location:16801810
      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:37023785
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:38643984
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:39864002
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:38584002
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:11801227
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:20562106
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:21392305
      SOG2; RAM signalling pathway protein
      cd15588
      Location:14661512
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:15141563
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:16011657
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:19042016
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    3. XM_011542830.1XP_011541132.1  

      Conserved Domains (12) summary
      cd05493
      Location:16821812
      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:37043787
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:38663986
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:39884004
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:38604004
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:11801227
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:20582108
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:21412307
      SOG2; RAM signalling pathway protein
      cd15588
      Location:14661512
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:15141562
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:16001659
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:19062018
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    4. XM_011542832.1XP_011541134.1  

      Conserved Domains (12) summary
      cd05493
      Location:9521082
      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:29743057
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:31363256
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:32583274
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:31223274
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:449496
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:13281378
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:14111577
      SOG2; RAM signalling pathway protein
      cd15588
      Location:735781
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:783832
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:870929
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:11761288
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    5. XM_011542833.1XP_011541135.1  

      Conserved Domains (12) summary
      cd05493
      Location:844974
      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:28662949
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:30283148
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:31503166
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:30143166
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:341388
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:12201270
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:13031469
      SOG2; RAM signalling pathway protein
      cd15588
      Location:627673
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:675724
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:762821
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:10681180
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
    6. XM_006718839.2XP_006718902.2  

      Conserved Domains (12) summary
      cd05493
      Location:811941
      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:28332916
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:29953115
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:31173133
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:29813133
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:308355
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:11871237
      FYRN; F/Y-rich N-terminus
      pfam10428
      Location:12701436
      SOG2; RAM signalling pathway protein
      cd15588
      Location:594640
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:642691
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:729788
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:10351147
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      118193852..118284190
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024891.2: Suppressed sequence

      Description
      NM_024891.2: This RefSeq was permanently suppressed because it is primarily intronic sequence.