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

    Gene ID: 387893, updated on 27-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KMT5A in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123384132..123409353)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123380646..123405922)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in 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

    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)

    NEW Try the new Transcript table

    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_001324504.2NP_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:194311
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. NM_001324505.2NP_001311434.1  N-lysine methyltransferase KMT5A isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC137767, AC145423
      UniProtKB/TrEMBL
      C9JKQ0
      Conserved Domains (1) summary
      smart00317
      Location:167284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    3. NM_001324506.2NP_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:116233
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    4. NM_001367386.2NP_001354315.1  N-lysine methyltransferase KMT5A isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC137767, AC145423
      UniProtKB/Swiss-Prot
      A8K9D0, Q86W83, Q8TD09, Q9NQR1
    5. NM_001367388.2NP_001354317.1  N-lysine methyltransferase KMT5A isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC137767, AC145423
      UniProtKB/TrEMBL
      C9JKQ0
    6. NM_001367389.2NP_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_020382.7NP_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:200339
      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_2024_08

    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_047428836.1XP_047284792.1  N-lysine methyltransferase KMT5A isoform X1

    2. XM_047428837.1XP_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_054372041.1XP_054228016.1  N-lysine methyltransferase KMT5A isoform X3

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

    RNA

    1. XR_008488584.1 RNA Sequence