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KMT5A lysine methyltransferase 5A [ Homo sapiens (human) ]

Gene ID: 387893, updated on 7-Apr-2024

Summary

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Official Symbol
KMT5Aprovided by HGNC
Official Full Name
lysine methyltransferase 5Aprovided by HGNC
Primary source
HGNC:HGNC:29489
See related
Ensembl:ENSG00000183955 MIM:607240; AllianceGenome:HGNC:29489
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
SET8; SET07; SETD8; PR-Set7; PR/SET07
Summary
The protein encoded by this gene is a protein-lysine N-methyltransferase that can monomethylate Lys-20 of histone H4 to effect transcriptional repression of some genes. The encoded protein is required for cell proliferation and plays a role in chromatin condensation. [provided by RefSeq, May 2016]
Expression
Ubiquitous expression in prostate (RPKM 17.6), esophagus (RPKM 16.8) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12q24.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123384132..123409353)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123380646..123405922)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123868679..123893900)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene strawberry notch homolog 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7260 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123855180-123855353 Neighboring gene SBNO1 antisense RNA 1 Neighboring gene microRNA 8072 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123867650-123867872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123867837-123868567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5043 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123886419-123887182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7266 Neighboring gene Rab interacting lysosomal protein like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123920207-123921136 Neighboring gene uncharacterized LOC124903041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123942373-123943239 Neighboring gene COP9 signalosome subunit 5 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123943240-123944105 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123949657-123950158 Neighboring gene Sharpr-MPRA regulatory region 13608 Neighboring gene small nuclear ribonucleoprotein U11/U12 subunit 35 Neighboring gene Rab interacting lysosomal protein like 1

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. SETD8 promotes glycolysis in colorectal cancer via regulating HIF1α/HK2 axis. Ke B, et al. Tissue Cell, 2023 Jun. PMID 36921492
  2. KMT5A Knockdown Suppresses Osteosarcoma Cell Proliferation and Metastasis Through Ꞵ-Catenin Signalling. An J, et al. Clin Invest Med, 2022 Sep 21. PMID 36149050
  3. Integrative bioinformatics analysis the clinical value of KMT5A in different subtypes of lung cancer. Liu S, et al. Comput Biol Chem, 2022 Feb. PMID 34894606
  4. SET8, a novel regulator to ameliorate vascular calcification via activating PI3K/Akt mediated anti-apoptotic effects. Bai Y, et al. Biochem Cell Biol, 2022 Apr. PMID 34846946
  5. Epigenetic Modifier SETD8 as a Therapeutic Target for High-Grade Serous Ovarian Cancer. Wada M, et al. Biomolecules, 2020 Dec 16. PMID 33339442, Free PMC Article

See all (115) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification.
    Title: Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification.
  2. SETD8 promotes glycolysis in colorectal cancer via regulating HIF1alpha/HK2 axis.
    Title: SETD8 promotes glycolysis in colorectal cancer via regulating HIF1α/HK2 axis.
  3. KMT5A Knockdown Suppresses Osteosarcoma Cell Proliferation and Metastasis Through -Catenin Signalling.
    Title: KMT5A Knockdown Suppresses Osteosarcoma Cell Proliferation and Metastasis Through Ꞵ-Catenin Signalling.
  4. KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling.
    Title: KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling.
  5. SET8, a novel regulator to ameliorate vascular calcification via activating PI3K/Akt mediated anti-apoptotic effects.
    Title: SET8, a novel regulator to ameliorate vascular calcification via activating PI3K/Akt mediated anti-apoptotic effects.
  6. SETD8 induces stemness and epithelial-mesenchymal transition of pancreatic cancer cells by regulating ROR1 expression.
    Title: SETD8 induces stemness and epithelial-mesenchymal transition of pancreatic cancer cells by regulating ROR1 expression.
  7. Integrative bioinformatics analysis the clinical value of KMT5A in different subtypes of lung cancer.
    Title: Integrative bioinformatics analysis the clinical value of KMT5A in different subtypes of lung cancer.
  8. ets1 associates with KMT5A to participate in high glucose-mediated EndMT via upregulation of PFN2 expression in diabetic nephropathy.
    Title: ets1 associates with KMT5A to participate in high glucose-mediated EndMT via upregulation of PFN2 expression in diabetic nephropathy.
  9. LncRNA LINC00473 is involved in the progression of invasive pituitary adenoma by upregulating KMT5A via ceRNA-mediated miR-502-3p evasion.
    Title: LncRNA LINC00473 is involved in the progression of invasive pituitary adenoma by upregulating KMT5A via ceRNA-mediated miR-502-3p evasion.
  10. SETD8 is a prognostic biomarker that contributes to stem-like cell properties in non-small cell lung cancer.
    Title: SETD8 is a prognostic biomarker that contributes to stem-like cell properties in non-small cell lung cancer.
Submit: New GeneRIF Correction See all GeneRIFs (84)

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
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
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)

Genotypes

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 TAS
Traceable Author Statement
more info
  
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic chromosome condensation TAS
Traceable Author Statement
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in peptidyl-lysine monomethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA damage response, signal transduction by p53 class mediator IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA damage response, signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
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
  
is_active_in polytene chromosome IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
N-lysine methyltransferase KMT5A
Names
H4-K20-HMTase KMT5A
H4-K20-HMTase SETD8
H4-K20-specific histone methyltransferase
N-lysine methyltransferase SETD8
PR/SET domain containing protein 8
PR/SET domain-containing protein 07
SET domain containing (lysine methyltransferase) 8
SET domain-containing protein 8
histone-lysine N-methyltransferase KMT5A
histone-lysine N-methyltransferase SETD8
lysine (K)-specific methyltransferase 5A
lysine N-methyltransferase 5A
lysine-specific methylase 5A
NP_001311433.1
NP_001311434.1
NP_001311435.1
NP_001354315.1
NP_001354317.1
NP_001354318.1
NP_065115.3
XP_047284792.1
XP_047284793.1
XP_054228016.1
XP_054228017.1

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.

Genomic

  1. NG_050615.2 RefSeqGene

    Range
    5002..30223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001324504.2 → NP_001311433.1  N-lysine methyltransferase KMT5A isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423
    UniProtKB/Swiss-Prot
    A8K9D0, Q86W83, Q8TD09, Q9NQR1
    UniProtKB/TrEMBL
    E3VVS3
    Conserved Domains (1) summary
    smart00317
    Location:194 → 311
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

  2. NM_001324505.2 → NP_001311434.1  N-lysine methyltransferase KMT5A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423
    UniProtKB/TrEMBL
    C9JKQ0
    Conserved Domains (1) summary
    smart00317
    Location:167 → 284
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

  3. NM_001324506.2 → NP_001311435.1  N-lysine methyltransferase KMT5A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variant 8, encodes isoform 4.
    Source sequence(s)
    AC137767, AC145423
    UniProtKB/Swiss-Prot
    Q9NQR1
    Conserved Domains (1) summary
    smart00317
    Location:116 → 233
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

  4. NM_001367386.2 → NP_001354315.1  N-lysine methyltransferase KMT5A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423
    UniProtKB/Swiss-Prot
    A8K9D0, Q86W83, Q8TD09, Q9NQR1

  5. NM_001367388.2 → NP_001354317.1  N-lysine methyltransferase KMT5A isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423
    UniProtKB/TrEMBL
    C9JKQ0

  6. NM_001367389.2 → NP_001354318.1  N-lysine methyltransferase KMT5A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variant 4, encodes isoform 4.
    Source sequence(s)
    AC137767, AC145423

  7. NM_020382.7 → NP_065115.3  N-lysine methyltransferase KMT5A isoform 1

    See identical proteins and their annotated locations for NP_065115.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC137767, AC145423
    Consensus CDS
    CCDS9247.1
    UniProtKB/Swiss-Prot
    A8K9D0, Q86W83, Q8TD09, Q9NQR1
    Related
    ENSP00000384629.3, ENST00000402868.8
    Conserved Domains (1) summary
    cd10528
    Location:200 → 339
    SET_SETD8; SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins

RNA

  1. NR_136910.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    123384132..123409353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428836.1 → XP_047284792.1  N-lysine methyltransferase KMT5A isoform X1

  2. XM_047428837.1 → XP_047284793.1  N-lysine methyltransferase KMT5A isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123380646..123405922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372041.1 → XP_054228016.1  N-lysine methyltransferase KMT5A isoform X3

  2. XM_054372042.1 → XP_054228017.1  N-lysine methyltransferase KMT5A isoform X2

RNA

  1. XR_008488584.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQR1.3 GenPept UniProtKB/Swiss-Prot:Q9NQR1

Gene LinkOut

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Chemical Information
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