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

Gene ID: 58508, updated on 14-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
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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 Variation Viewer (GRCh37.p13)

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 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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