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

Summary

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: mouse all
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Genomic context

Location:: 19q13.42

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (55339876..55348121)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (58435095..58443627)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (55851244..55859489)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC156606P1 (e-PCR)
- UniSTS:271408

PMC156606P2 (e-PCR)
- UniSTS:271409

D8S2278 (e-PCR)
- UniSTS:473906

sY3084 (e-PCR)
- UniSTS:515126

20922op (e-PCR)
- UniSTS:466077

D19S877 (e-PCR)
- UniSTS:15044

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
part_of 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
part_of 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

EC 2.1.1.361

EC 2.1.1.362

XP_006723505.1

EC 2.1.1.361

EC 2.1.1.362

XP_011525717.1

EC 2.1.1.361

EC 2.1.1.362

XP_047295511.1

EC 2.1.1.361

EC 2.1.1.362

XP_047295512.1

EC 2.1.1.361

EC 2.1.1.362

XP_054178384.1

EC 2.1.1.361

EC 2.1.1.362

XP_054178385.1

EC 2.1.1.361

EC 2.1.1.362

XP_054178386.1

EC 2.1.1.361

EC 2.1.1.362

XP_054178387.1

EC 2.1.1.361

EC 2.1.1.362

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)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

55339876..55348121

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0D9SF94

Related

ENSP00000486397.1, ENST00000630497.1
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
XM_047439556.1 → XP_047295512.1 histone-lysine N-methyltransferase KMT5C isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

58435095..58443627

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q86Y97, Q8WZ10, Q9BRZ6
XM_054322410.1 → XP_054178385.1 histone-lysine N-methyltransferase KMT5C isoform X2

UniProtKB/TrEMBL

A0A0D9SF94
XM_054322411.1 → XP_054178386.1 histone-lysine N-methyltransferase KMT5C isoform X2

UniProtKB/TrEMBL

A0A0D9SF94
XM_054322412.1 → XP_054178387.1 histone-lysine N-methyltransferase KMT5C isoform X3