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    KMT5B lysine methyltransferase 5B [ Homo sapiens (human) ]

    Gene ID: 51111, updated on 3-Nov-2024

    Summary

    Official Symbol
    KMT5Bprovided by HGNC
    Official Full Name
    lysine methyltransferase 5Bprovided by HGNC
    Primary source
    HGNC:HGNC:24283
    See related
    Ensembl:ENSG00000110066 MIM:610881; AllianceGenome:HGNC:24283
    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
    CGI85; MRD51; CGI-85; SUV420H1
    Summary
    This gene encodes a protein that contains a SET domain. SET domains appear to be protein-protein interaction domains that mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). The function of this gene has not been determined. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 12.1), endometrium (RPKM 8.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KMT5B in Genome Data Viewer
    Location:
    11q13.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (68154863..68213648, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68158479..68217261, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67922330..67981115, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67834020-67834520 Neighboring gene choline kinase alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67850572-67850749 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67861600-67861729 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67870988-67871188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67886638-67887154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67888828-67889593 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67889594-67890360 Neighboring gene CHKA divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67907579-67907779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67981441-67982143 Neighboring gene Sharpr-MPRA regulatory region 2086 Neighboring gene MPRA-validated peak1319 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:68034746-68035945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68039550-68040404 Neighboring gene uncharacterized LOC105369363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3666 Neighboring gene chromosome 11 open reading frame 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5134

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 51
    MedGen: C4540474 OMIM: 617788 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-06-13)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2023-06-13)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of suppressor of variegation 4-20 homolog 1 (SUV420H1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC703, MGC21161, MGC118906, MGC118909

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 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 
    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 muscle organ development 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 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
     

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase KMT5B
    Names
    [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
    [histone H4]-lysine20 N-methyltransferase KMT5B
    histone-lysine N-methyltransferase SUV420H1
    lysine (K)-specific methyltransferase 5B
    lysine N-methyltransferase 5B
    lysine-specific methyltransferase 5B
    su(var)4-20 homolog 1
    suppressor of variegation 4-20 homolog 1
    NP_001287836.1
    NP_001287837.1
    NP_001287838.1
    NP_001350495.1
    NP_001356353.1
    NP_001356354.1
    NP_001356355.1
    NP_001356356.1
    NP_001356357.1
    NP_001356358.1
    NP_001356359.1
    NP_001356360.1
    NP_001356361.1
    NP_001356362.1
    NP_057112.3
    NP_060105.3
    XP_005274092.2
    XP_005274093.2
    XP_006718644.1
    XP_011543394.1
    XP_024304338.1
    XP_047283027.1
    XP_047283028.1
    XP_047283029.1
    XP_054225022.1
    XP_054225023.1
    XP_054225024.1
    XP_054225025.1
    XP_054225026.1
    XP_054225027.1
    XP_054225028.1
    XP_054225029.1

    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_052873.1 RefSeqGene

      Range
      5477..63910
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001300907.1NP_001287836.1  histone-lysine N-methyltransferase KMT5B isoform 3

      See identical proteins and their annotated locations for NP_001287836.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon and uses a downstream start codon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AP002992, BC108304
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. NM_001300908.2NP_001287837.1  histone-lysine N-methyltransferase KMT5B isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate first exon and an alternate splice junction at the 5' end of an exon, and uses a downstream start codon compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK314336, AP002992, CR997801
      Conserved Domains (1) summary
      pfam00856
      Location:2168
      SET; SET domain
    3. NM_001300909.2NP_001287838.1  histone-lysine N-methyltransferase KMT5B isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate first exon, lacks an alternate in-frame exon, and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AK299201, AP002992, BC002522, CR997801, KC877427
      Consensus CDS
      CCDS76444.1
      UniProtKB/TrEMBL
      B7WNX0, B7Z5N2
      Related
      ENSP00000384724.2, ENST00000402185.6
      Conserved Domains (1) summary
      smart00317
      Location:180291
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    4. NM_001363566.2NP_001350495.1  histone-lysine N-methyltransferase KMT5B isoform 6

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS86221.1
      UniProtKB/TrEMBL
      B5MCB3, B7Z5N2
      Related
      ENSP00000385005.1, ENST00000402789.5
      Conserved Domains (1) summary
      cd19184
      Location:192335
      SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
    5. NM_001369424.1NP_001356353.1  histone-lysine N-methyltransferase KMT5B isoform 7

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Related
      ENST00000700525.1
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    6. NM_001369425.1NP_001356354.1  histone-lysine N-methyltransferase KMT5B isoform 8

      Status: REVIEWED

      Source sequence(s)
      AP002992
      Consensus CDS
      CCDS91519.1
      UniProtKB/TrEMBL
      B7Z5N2, C9JFG1
      Related
      ENSP00000403233.2, ENST00000458496.2
      Conserved Domains (1) summary
      smart00317
      Location:132243
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    7. NM_001369426.1NP_001356355.1  histone-lysine N-methyltransferase KMT5B isoform 1

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS31623.1
      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
      Conserved Domains (1) summary
      cd19184
      Location:192335
      SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
    8. NM_001369427.1NP_001356356.1  histone-lysine N-methyltransferase KMT5B isoform 2

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS44660.1
      UniProtKB/TrEMBL
      B7Z5N2
      Related
      ENSP00000385640.1, ENST00000405515.5
      Conserved Domains (1) summary
      smart00317
      Location:203314
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    9. NM_001369428.1NP_001356357.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    10. NM_001369429.1NP_001356358.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Related
      ENSP00000515030.1, ENST00000700523.1
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    11. NM_001369430.1NP_001356359.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    12. NM_001369431.1NP_001356360.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    13. NM_001369432.1NP_001356361.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    14. NM_001369433.1NP_001356362.1  histone-lysine N-methyltransferase KMT5B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
      Consensus CDS
      CCDS91518.1
      UniProtKB/TrEMBL
      A0A8V8TQB9
      Conserved Domains (1) summary
      smart00317
      Location:31142
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    15. NM_016028.4NP_057112.3  histone-lysine N-methyltransferase KMT5B isoform 2

      See identical proteins and their annotated locations for NP_057112.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate 3' exon and utilizes an upstream stop codon, compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC002522, BM152996
      Consensus CDS
      CCDS44660.1
      UniProtKB/TrEMBL
      B7Z5N2
      Related
      ENSP00000385965.2, ENST00000401547.6
      Conserved Domains (1) summary
      smart00317
      Location:203314
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    16. NM_017635.5NP_060105.3  histone-lysine N-methyltransferase KMT5B isoform 1

      See identical proteins and their annotated locations for NP_060105.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AP002992, BC099714, BC108304
      Consensus CDS
      CCDS31623.1
      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
      Related
      ENSP00000305899.4, ENST00000304363.9
      Conserved Domains (1) summary
      cd19184
      Location:192335
      SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins

    RNA

    1. NR_161378.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
    2. NR_161379.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427
    3. NR_161380.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP002992, KC877427

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      68154863..68213648 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427072.1XP_047283028.1  histone-lysine N-methyltransferase KMT5B isoform X4

    2. XM_011545092.4XP_011543394.1  histone-lysine N-methyltransferase KMT5B isoform X3

      UniProtKB/TrEMBL
      C9J6S5
      Related
      ENSP00000406377.2, ENST00000453170.6
      Conserved Domains (1) summary
      smart00317
      Location:132243
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    3. XM_005274036.5XP_005274093.2  histone-lysine N-methyltransferase KMT5B isoform X2

      See identical proteins and their annotated locations for XP_005274093.2

      Conserved Domains (1) summary
      smart00317
      Location:180291
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    4. XM_005274035.5XP_005274092.2  histone-lysine N-methyltransferase KMT5B isoform X1

      See identical proteins and their annotated locations for XP_005274092.2

      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
      Conserved Domains (1) summary
      cd19184
      Location:192335
      SET_KMT5B; SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins
    5. XM_006718581.2XP_006718644.1  histone-lysine N-methyltransferase KMT5B isoform X2

      See identical proteins and their annotated locations for XP_006718644.1

      Conserved Domains (1) summary
      smart00317
      Location:180291
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    6. XM_047427071.1XP_047283027.1  histone-lysine N-methyltransferase KMT5B isoform X1

      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    7. XM_047427073.1XP_047283029.1  histone-lysine N-methyltransferase KMT5B isoform X5

    8. XM_024448570.2XP_024304338.1  histone-lysine N-methyltransferase KMT5B isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      68158479..68217261 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369052.1XP_054225027.1  histone-lysine N-methyltransferase KMT5B isoform X4

    2. XM_054369051.1XP_054225026.1  histone-lysine N-methyltransferase KMT5B isoform X3

      UniProtKB/TrEMBL
      C9J6S5
    3. XM_054369049.1XP_054225024.1  histone-lysine N-methyltransferase KMT5B isoform X2

    4. XM_054369047.1XP_054225022.1  histone-lysine N-methyltransferase KMT5B isoform X1

      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    5. XM_054369050.1XP_054225025.1  histone-lysine N-methyltransferase KMT5B isoform X2

    6. XM_054369048.1XP_054225023.1  histone-lysine N-methyltransferase KMT5B isoform X1

      UniProtKB/Swiss-Prot
      A0A0A0MT19, B7WNX7, Q3SX56, Q4FZB7, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
    7. XM_054369053.1XP_054225028.1  histone-lysine N-methyltransferase KMT5B isoform X5

    8. XM_054369054.1XP_054225029.1  histone-lysine N-methyltransferase KMT5B isoform X5