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KMT5C lysine methyltransferase 5C [ Homo sapiens (human) ]

Gene ID: 84787, updated on 27-Nov-2024

Summary

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Official Symbol
KMT5Cprovided by HGNC
Official Full Name
lysine methyltransferase 5Cprovided by HGNC
Primary source
HGNC:HGNC:28405
See related
Ensembl:ENSG00000133247 MIM:613198; AllianceGenome:HGNC:28405
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SUV420H2; Suv4-20h2
Summary
SUV420H2 and the related enzyme SUV420H1 (MIM 610881) function as histone methyltransferases that specifically trimethylate nucleosomal histone H4 (see MIM 602822) on lysine-20 (K20) (Schotta et al., 2004 [PubMed 15145825]).[supplied by OMIM, Dec 2009]
Expression
Ubiquitous expression in bone marrow (RPKM 1.9), placenta (RPKM 1.5) and 25 other tissues See more
Orthologs
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Genomic context

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See KMT5C in Genome Data Viewer
Location:
19q13.42
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55339876..55348121)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58435095..58443627)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55851244..55859489)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55781781-55782280 Neighboring gene HSPA (Hsp70) binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55789069-55789569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11021 Neighboring gene BR serine/threonine kinase 1 Neighboring gene Sharpr-MPRA regulatory region 11129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55824387-55824912 Neighboring gene transmembrane protein 150B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55849388-55850162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55850163-55850936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11023 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55855204-55856008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55856009-55856814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55858005-55858699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11025 Neighboring gene cytochrome c oxidase subunit 6B2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55871113-55871613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55874435-55875039 Neighboring gene golgi associated RAB2 interactor family member 5B

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
  • 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. Lysine methyltransferase 5C increases the proliferation and metastatic abilities of clear cell renal cell carcinoma via aerobic glycolysis. Zeng B, et al. Int J Oncol, 2024 Apr. PMID 38426605, Free PMC Article
  2. Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression. Boonsanay V, et al. Gastroenterology, 2023 Feb. PMID 36402192, Free PMC Article
  3. Impact of Histone Lysine Methyltransferase SUV4-20H2 on Cancer Onset and Progression with Therapeutic Potential. Papadaki S, et al. Int J Mol Sci, 2024 Feb 21. PMID 38473745, Free PMC Article
  4. Specificity of the SUV4-20H1 and SUV4-20H2 protein lysine methyltransferases and methylation of novel substrates. Weirich S, et al. J Mol Biol, 2016 Jun 5. PMID 27105552
  5. Histone H4 Methyltransferase Suv420h2 Maintains Fidelity of Osteoblast Differentiation. Khani F, et al. J Cell Biochem, 2017 May. PMID 27862226, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Impact of Histone Lysine Methyltransferase SUV4-20H2 on Cancer Onset and Progression with Therapeutic Potential.
    Title: Impact of Histone Lysine Methyltransferase SUV4-20H2 on Cancer Onset and Progression with Therapeutic Potential.
  2. Lysine methyltransferase 5C increases the proliferation and metastatic abilities of clear cell renal cell carcinoma via aerobic glycolysis.
    Title: Lysine methyltransferase 5C increases the proliferation and metastatic abilities of clear cell renal cell carcinoma via aerobic glycolysis.
  3. Epigenetic regulation of DHRS2 by SUV420H2 inhibits cell apoptosis in renal cell carcinoma.
    Title: Epigenetic regulation of DHRS2 by SUV420H2 inhibits cell apoptosis in renal cell carcinoma.
  4. Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression.
    Title: Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression.
  5. Loss of KMT5C Promotes EGFR Inhibitor Resistance in NSCLC via LINC01510-Mediated Upregulation of MET.
    Title: Loss of KMT5C Promotes EGFR Inhibitor Resistance in NSCLC via LINC01510-Mediated Upregulation of MET.
  6. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells.
    Title: H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells.
  7. The analysis of human pancreatic cancer biopsies was concordant with these findings, because high levels of SUV420H2 correlated with a loss of epithelial characteristics in progressively invasive cancer. Together, these data indicate that SUV420H2 is an upstream epigenetic regulator of epithelial/mesenchymal state control.
    Title: SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer.
  8. Study provides evidence that Suv420h2 controls the H4K20 methylome of osteoblasts and is critical for normal progression of osteoblastogenesis.
    Title: Histone H4 Methyltransferase Suv420h2 Maintains Fidelity of Osteoblast Differentiation.
  9. Altogether, these results reveal Suv4-20h-mediated histone H4K20 tri-methylation as a critical determinant in the selection of active replication initiation sites in heterochromatin regions of mammalian genomes.
    Title: Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication.
  10. The sequences surrounding both methylation sites do not fit to the specificity profile of SUV4-20H1.
    Title: Specificity of the SUV4-20H1 and SUV4-20H2 protein lysine methyltransferases and methylation of novel substrates.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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

EBI GWAS Catalog

Description
Loci at chromosomes 13, 19 and 20 influence age at natural menopause.
EBI GWAS Catalog

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

  • MGC2705, FLJ51466, FLJ98627

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables S-adenosyl-L-methionine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H4 methyltransferase activity TAS
Traceable Author Statement
more info
  
enables histone H4K20 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H4K20 methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H4K20 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4K20me methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in condensed chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
  
located_in heterochromatin 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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in pericentric heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
histone-lysine N-methyltransferase KMT5C
Names
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
[histone H4]-lysine20 N-methyltransferase KMT5B
histone-lysine N-methyltransferase SUV420H2
lysine (K)-specific methyltransferase 5C
lysine N-methyltransferase 5C
lysine-specific methyltransferase 5C
su(var)4-20 homolog 2
suppressor of variegation 4-20 homolog 2
NP_116090.2
XP_006723505.1
XP_011525717.1
XP_047295511.1
XP_047295512.1
XP_054178384.1
XP_054178385.1
XP_054178386.1
XP_054178387.1

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.

mRNA and Protein(s)

  1. NM_032701.4 → NP_116090.2  histone-lysine N-methyltransferase KMT5C

    See identical proteins and their annotated locations for NP_116090.2

    Status: VALIDATED

    Source sequence(s)
    AK308586, AW248704, BC044889
    Consensus CDS
    CCDS12922.1
    UniProtKB/Swiss-Prot
    Q86Y97, Q8WZ10, Q9BRZ6
    Related
    ENSP00000255613.3, ENST00000255613.8
    Conserved Domains (1) summary
    cd19185
    Location:102 → 243
    SET_KMT5C; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5C (KMT5C) and similar proteins

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
    55339876..55348121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011527415.4 → XP_011525717.1  histone-lysine N-methyltransferase KMT5C isoform X1

    See identical proteins and their annotated locations for XP_011525717.1

    UniProtKB/Swiss-Prot
    Q86Y97, Q8WZ10, Q9BRZ6
    Conserved Domains (1) summary
    cd19185
    Location:102 → 243
    SET_KMT5C; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5C (KMT5C) and similar proteins

  2. XM_047439555.1 → XP_047295511.1  histone-lysine N-methyltransferase KMT5C isoform X2

    UniProtKB/TrEMBL
    A0A0D9SF94
    Related
    ENSP00000486397.1, ENST00000630497.1

  3. XM_006723442.4 → XP_006723505.1  histone-lysine N-methyltransferase KMT5C isoform X2

    See identical proteins and their annotated locations for XP_006723505.1

    UniProtKB/TrEMBL
    A0A0D9SF94
    Conserved Domains (1) summary
    smart00317
    Location:5 → 109
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

  4. XM_047439556.1 → XP_047295512.1  histone-lysine N-methyltransferase KMT5C isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    58435095..58443627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322409.1 → XP_054178384.1  histone-lysine N-methyltransferase KMT5C isoform X1

    UniProtKB/Swiss-Prot
    Q86Y97, Q8WZ10, Q9BRZ6

  2. XM_054322410.1 → XP_054178385.1  histone-lysine N-methyltransferase KMT5C isoform X2

    UniProtKB/TrEMBL
    A0A0D9SF94

  3. XM_054322411.1 → XP_054178386.1  histone-lysine N-methyltransferase KMT5C isoform X2

    UniProtKB/TrEMBL
    A0A0D9SF94

  4. XM_054322412.1 → XP_054178387.1  histone-lysine N-methyltransferase KMT5C isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86Y97.1 GenPept UniProtKB/Swiss-Prot:Q86Y97

Gene LinkOut

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