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    KMT2C lysine methyltransferase 2C [ Homo sapiens (human) ]

    Gene ID: 58508, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KMT2Cprovided by HGNC
    Official Full Name
    lysine methyltransferase 2Cprovided by HGNC
    Primary source
    HGNC:HGNC:13726
    See related
    Ensembl:ENSG00000055609 MIM:606833; AllianceGenome:HGNC:13726
    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
    HALR; MLL3; KLEFS2
    Summary
    This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 8.7), bone marrow (RPKM 8.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KMT2C in Genome Data Viewer
    Location:
    7q36.1
    Exon count:
    59
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (152134925..152436003, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (153307815..153608900, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (151832010..152133088, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 11 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:151778343-151779337 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:151804574-151805773 Neighboring gene uncharacterized LOC731075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26876 Neighboring gene Y-box binding protein 1 pseudogene 4 Neighboring gene MPRA-validated peak6855 silencer Neighboring gene Sharpr-MPRA regulatory region 15588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26877 Neighboring gene septin 7 pseudogene 6 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:152091085-152091724 Neighboring gene Sharpr-MPRA regulatory region 5889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18833 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:152138204-152138404 Neighboring gene fatty acid binding protein 5 pseudogene 3 Neighboring gene chaperonin containing TCP1 subunit 8 like 1, pseudogene

    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 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. Association between histone lysine methyltransferase KMT2C mutation and clinicopathological factors in breast cancer. Chen X, et al. Biomed Pharmacother, 2019 Aug. PMID 31146111
    2. Downregulation of MLL3 in esophageal squamous cell carcinoma is required for the growth and metastasis of cancer cells. Xia M, et al. Tumour Biol, 2015 Feb. PMID 25273170
    3. Interaction between MLL3 genetic polymorphisms, smoking, and alcohol drinking in laryngeal cancer: a case-control study. Chen D, et al. Cancer Med, 2016 Mar. PMID 26818916, Free PMC Article
    4. The modification role and tumor association with a methyltransferase: KMT2C. Jiao Y, et al. Front Immunol, 2024. PMID 39165358, Free PMC Article
    5. Association of KMT2C Genetic Variants with the Clinicopathologic Development of Oral Cancer. Shieu MK, et al. Int J Environ Res Public Health, 2022 Mar 27. PMID 35409657, Free PMC Article

    See all (162) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The modification role and tumor association with a methyltransferase: KMT2C.
      Title: The modification role and tumor association with a methyltransferase: KMT2C.
    2. Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes.
      Title: Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes.
    3. A novel 11 base pair deletion in KMT2C resulting in Kleefstra syndrome 2.
      Title: A novel 11 base pair deletion in KMT2C resulting in Kleefstra syndrome 2.
    4. Association of KMT2C/D loss-of-function variants with response to immune checkpoint blockades in colorectal cancer.
      Title: Association of KMT2C/D loss-of-function variants with response to immune checkpoint blockades in colorectal cancer.
    5. Mutations in epigenetic regulator KMT2C detected by liquid biopsy are associated with worse survival in prostate cancer patients.
      Title: Mutations in epigenetic regulator KMT2C detected by liquid biopsy are associated with worse survival in prostate cancer patients.
    6. MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer.
      Title: MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer.
    7. Association of MLL3 and TGF-beta signaling gene polymorphisms with the susceptibility and prognostic outcomes of Stanford type B aortic dissection : MLL3 with TGF-beta signal pathway association with Stanford type B AD.
      Title: Association of MLL3 and TGF-β signaling gene polymorphisms with the susceptibility and prognostic outcomes of Stanford type B aortic dissection : MLL3 with TGF-β signal pathway association with Stanford type B AD.
    8. MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state.
      Title: MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state.
    9. KMT2C Induced by FABP5P3 Aggravates Keratinocyte Hyperproliferation and Psoriasiform Skin Inflammation by Upregulating the Transcription of PIK3R3.
      Title: KMT2C Induced by FABP5P3 Aggravates Keratinocyte Hyperproliferation and Psoriasiform Skin Inflammation by Upregulating the Transcription of PIK3R3.
    10. Histone methyltransferase KMT2C plays an oncogenic role in prostate cancer.
      Title: Histone methyltransferase KMT2C plays an oncogenic role in prostate cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (72)

    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
    Kleefstra syndrome 2
    MedGen: C4540395 OMIM: 617768 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2018-01-24)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2018-01-24)

    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

    • FLJ12625, FLJ38309, KIAA1506, MGC119851, MGC119852, MGC119853, DKFZp686C08112

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables acyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		 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 histone methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein-containing complex organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to electrical stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MLL3/4 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of MLL3/4 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm 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
    		 PubMed 

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase 2C
    Names
    ALR-like protein
    histone-lysine N-methyltransferase MLL3
    histone-lysine N-methyltransferase, H3 lysine-4 specific
    homologous to ALR protein
    lysine (K)-specific methyltransferase 2C
    myeloid/lymphoid or mixed-lineage leukemia protein 3
    NP_733751.2

    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_033948.1 RefSeqGene

      Range
      5003..306081
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_170606.3 → NP_733751.2  histone-lysine N-methyltransferase 2C

      See identical proteins and their annotated locations for NP_733751.2

      Status: REVIEWED

      Source sequence(s)
      AF264750, AK025911, AY024361, BP281562, BU623509, BU685177, CD513584
      Consensus CDS
      CCDS5931.1
      UniProtKB/Swiss-Prot
      Q8NC02, Q8NDF6, Q8NEZ4, Q9H9P4, Q9NR13, Q9P222, Q9UDR7
      UniProtKB/TrEMBL
      A0A7P0TAI3
      Related
      ENSP00000262189.6, ENST00000262189.11
      Conserved Domains (17) summary
      smart00317
      Location:4772 → 4893
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4895 → 4911
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:4725 → 4911
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      sd00025
      Location:1084 → 1106
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      cd15509
      Location:343 → 388
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15511
      Location:466 → 517
      PHD3_KMT2C; PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15513
      Location:1009 → 1055
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:390 → 435
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:952 → 1008
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15600
      Location:1086 → 1136
      PHD6_KMT2C; PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15696
      Location:247 → 330
      ePHD1_KMT2C; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4402 → 4506
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam05964
      Location:4552 → 4602
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4608 → 4689
      FYRC; F/Y rich C-terminus
      pfam11176
      Location:1692 → 1775
      DUF2962; Protein of unknown function (DUF2962)
      pfam15233
      Location:3181 → 3270
      SYCE1; Synaptonemal complex central element protein 1
      cl00082
      Location:1654 → 1705
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      152134925..152436003 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      153307815..153608900 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_021230.2: Suppressed sequence

      Description
      NM_021230.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NEZ4.3 GenPept UniProtKB/Swiss-Prot:Q8NEZ4

    Gene LinkOut

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

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