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

    Gene ID: 4297, updated on 5-Jan-2025

    Summary

    Official Symbol
    KMT2Aprovided by HGNC
    Official Full Name
    lysine methyltransferase 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:7132
    See related
    Ensembl:ENSG00000118058 MIM:159555; AllianceGenome:HGNC:7132
    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; ALL1; GAS7; HTRX; MLL1; TRX1; ALL-1; CXXC7; HTRX1; MLL1A; WDSTS
    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]
    Expression
    Ubiquitous expression in ovary (RPKM 12.8), lymph node (RPKM 6.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See KMT2A in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118436492..118526832)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118455794..118546121)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118307207..118397547)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5590 Neighboring gene ubiquitination factor E4A Neighboring gene uncharacterized LOC100131626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118272182-118273045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118273504-118274094 Neighboring gene ATP synthase membrane subunit g Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:118306179-118307176 and GRCh37_chr11:118307177-118308175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118308176-118309173 Neighboring gene Sharpr-MPRA regulatory region 11577 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118358704-118358932 Neighboring gene TTC36 and KMT2A antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3947 Neighboring gene tetratricopeptide repeat domain 36 Neighboring gene transmembrane protein 25 Neighboring gene intraflagellar transport 46

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (138 hits/1268 screens)

    Associated conditions

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2018-05-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2018-05-23)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol The IN catalytic core domain has a higher binding affinity (Kd) for PSIP1 (LEDGF/p75) than the physiological binding partner, KMT2A (MML1) PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • FLJ11783

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding  
    enables histone H3K4 methyltransferase activity PubMed 
    enables histone H3K4 methyltransferase activity  
    enables histone H3K4 methyltransferase activity PubMed 
    enables histone H3K4 methyltransferase activity PubMed 
    enables histone H3K4 methyltransferase activity  
    enables histone H3K4 monomethyltransferase activity  
    enables histone H3K4 trimethyltransferase activity PubMed 
    enables identical protein binding PubMed 
    enables lysine-acetylated histone binding PubMed 
    enables minor groove of adenine-thymine-rich DNA binding PubMed 
    enables protein binding PubMed 
    enables protein homodimerization activity PubMed 
    enables protein-cysteine methyltransferase activity PubMed 
    enables unmethylated CpG binding PubMed 
    enables zinc ion binding PubMed 
    Items 1 - 25 of 26
    Process Evidence Code Pubs
    involved_in T-helper 2 cell differentiation PubMed 
    involved_in anterior/posterior pattern specification  
    involved_in apoptotic process  
    involved_in cellular response to transforming growth factor beta stimulus  
    involved_in circadian regulation of gene expression  
    involved_in definitive hemopoiesis  
    involved_in embryonic hemopoiesis PubMed 
    involved_in exploration behavior  
    involved_in fibroblast proliferation  
    involved_in homeostasis of number of cells within a tissue  
    involved_in membrane depolarization  
    involved_in methylation  
    involved_in negative regulation of DNA methylation-dependent heterochromatin formation PubMed 
    involved_in negative regulation of fibroblast proliferation  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in post-embryonic development  
    involved_in protein modification process  
    involved_in protein-containing complex assembly PubMed 
    involved_in regulation of short-term neuronal synaptic plasticity  
    involved_in response to potassium ion  
    involved_in spleen development  
    involved_in transcription initiation-coupled chromatin remodeling PubMed 
    involved_in transcription initiation-coupled chromatin remodeling PubMed 
    involved_in visual learning  
    Items 1 - 25 of 26
    Component Evidence Code Pubs
    part_of MLL1 complex PubMed 
    part_of MLL1 complex PubMed 
    located_in cytosol  
    located_in cytosol  
    part_of histone methyltransferase complex  
    part_of histone methyltransferase complex PubMed 
    located_in nucleoplasm  
    located_in nucleoplasm  
    located_in nucleus PubMed 
    located_in nucleus PubMed 

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase 2A
    Names
    Acute lymphocytic 1
    CXXC-type zinc finger protein 7
    lysine (K)-specific methyltransferase 2A
    lysine N-methyltransferase 2A
    mixed lineage leukemia 1
    myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
    trithorax-like protein
    zinc finger protein HRX
    NP_001184033.1
    NP_001399526.1
    NP_005924.2
    XP_006718902.2
    XP_011541131.1
    XP_011541132.1
    XP_011541135.1
    XP_047282919.1
    XP_047282920.1
    XP_054224805.1
    XP_054224806.1
    XP_054224807.1
    XP_054224808.1
    XP_054224809.1
    XP_054224810.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001197104.2 → NP_001184033.1  histone-lysine N-methyltransferase 2A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.
      Source sequence(s)
      AI500057, AP000941, AP001267, BC065385, D14540, L04731
      Consensus CDS
      CCDS55791.1
      UniProtKB/TrEMBL
      A0A8I5KXR3
      Related
      ENSP00000436786.2, ENST00000534358.8
      Conserved Domains (9) summary
      cd05493
      Location:1650 → 1780
      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:3672 → 3755
      FYRC; FY-rich domain, C-terminal region
      cd15588
      Location:1433 → 1479
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:1481 → 1530
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:1568 → 1627
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1874 → 1986
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam02008
      Location:1147 → 1194
      zf-CXXC; CXXC zinc finger domain
      pfam05964
      Location:2027 → 2074
      FYRN; F/Y-rich N-terminus
      cd19170
      Location:3819 → 3972
      SET_KMT2A_2B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins
    2. NM_001412597.1 → NP_001399526.1  histone-lysine N-methyltransferase 2A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AP000941, AP001267
      UniProtKB/TrEMBL
      A0A8I5KXR3, A0AA34QVI8
      Related
      ENSP00000518343.1, ENST00000710560.1
    3. NM_005933.4 → NP_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) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the coding region, compared to variant 3. This results in a shorter protein (isoform 2), compared to isoform 3.
      Source sequence(s)
      AB209508, AP000941, AP001267, BC065385, D14540
      Consensus CDS
      CCDS31686.1
      UniProtKB/Swiss-Prot
      E9PQG7, Q03164, Q13743, Q13744, Q14845, Q16364, Q59FF2, Q6UBD1, Q9HBJ3, Q9UD94, Q9UMA3
      UniProtKB/TrEMBL
      A0A8I5KXR3
      Related
      ENSP00000374157.5, ENST00000389506.10
      Conserved Domains (11) summary
      cd05493
      Location:1647 → 1777
      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:3669 → 3752
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:3831 → 3951
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:3953 → 3969
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:3825 → 3969
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:1147 → 1194
      zf-CXXC; CXXC zinc finger domain
      cd15588
      Location:1433 → 1479
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:1481 → 1530
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:1568 → 1624
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1871 → 1983
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam05964
      Location:2025 → 2071
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      118436492..118526832
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542829.3 → XP_011541131.1  histone-lysine N-methyltransferase 2A isoform X1

      UniProtKB/TrEMBL
      A0A8I5KXR3, E9PR05
      Related
      ENSP00000432391.3, ENST00000531904.7
      Conserved Domains (11) summary
      cd05493
      Location:1683 → 1813
      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:3705 → 3788
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:3867 → 3987
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:3989 → 4005
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:3861 → 4005
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:1180 → 1227
      zf-CXXC; CXXC zinc finger domain
      cd15588
      Location:1466 → 1512
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:1514 → 1563
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:1601 → 1660
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1907 → 2019
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam05964
      Location:2061 → 2107
      FYRN; F/Y-rich N-terminus
    2. XM_011542830.3 → XP_011541132.1  histone-lysine N-methyltransferase 2A isoform X2

      UniProtKB/TrEMBL
      A0A8I5KXR3
      Conserved Domains (11) summary
      cd05493
      Location:1682 → 1812
      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:3704 → 3787
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:3866 → 3986
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:3988 → 4004
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:3860 → 4004
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:1180 → 1227
      zf-CXXC; CXXC zinc finger domain
      cd15588
      Location:1466 → 1512
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:1514 → 1562
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:1600 → 1659
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1906 → 2018
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam05964
      Location:2060 → 2106
      FYRN; F/Y-rich N-terminus
    3. XM_047426963.1 → XP_047282919.1  histone-lysine N-methyltransferase 2A isoform X3

      UniProtKB/TrEMBL
      A0A8I5KXR3
    4. XM_011542833.3 → XP_011541135.1  histone-lysine N-methyltransferase 2A isoform X4

      Conserved Domains (11) summary
      cd05493
      Location:844 → 974
      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:2866 → 2949
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:3028 → 3148
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:3150 → 3166
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:3014 → 3166
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:341 → 388
      zf-CXXC; CXXC zinc finger domain
      cd15588
      Location:627 → 673
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:675 → 724
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:762 → 821
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1068 → 1180
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam05964
      Location:1222 → 1268
      FYRN; F/Y-rich N-terminus
    5. XM_006718839.4 → XP_006718902.2  histone-lysine N-methyltransferase 2A isoform X5

      Conserved Domains (11) summary
      cd05493
      Location:811 → 941
      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:2833 → 2916
      FYRC; FY-rich domain, C-terminal region
      smart00317
      Location:2995 → 3115
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:3117 → 3133
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:2981 → 3133
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      pfam02008
      Location:308 → 355
      zf-CXXC; CXXC zinc finger domain
      cd15588
      Location:594 → 640
      PHD1_KMT2A; PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15590
      Location:642 → 691
      PHD2_KMT2A; PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15592
      Location:729 → 788
      PHD3_KMT2A; PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A)
      cd15693
      Location:1035 → 1147
      ePHD_KMT2A; Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A)
      pfam05964
      Location:1189 → 1235
      FYRN; F/Y-rich N-terminus
    6. XM_047426964.1 → XP_047282920.1  histone-lysine N-methyltransferase 2A isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      118455794..118546121
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368830.1 → XP_054224805.1  histone-lysine N-methyltransferase 2A isoform X1

      UniProtKB/TrEMBL
      A0A8I5KXR3, E9PR05
    2. XM_054368831.1 → XP_054224806.1  histone-lysine N-methyltransferase 2A isoform X2

      UniProtKB/TrEMBL
      A0A8I5KXR3
    3. XM_054368832.1 → XP_054224807.1  histone-lysine N-methyltransferase 2A isoform X3

      UniProtKB/TrEMBL
      A0A8I5KXR3
    4. XM_054368833.1 → XP_054224808.1  histone-lysine N-methyltransferase 2A isoform X4

    5. XM_054368834.1 → XP_054224809.1  histone-lysine N-methyltransferase 2A isoform X5

    6. XM_054368835.1 → XP_054224810.1  histone-lysine N-methyltransferase 2A isoform X6

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