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KMT2B lysine methyltransferase 2B [ Homo sapiens (human) ]

Gene ID: 9757, updated on 7-Apr-2024

Summary

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Official Symbol
KMT2Bprovided by HGNC
Official Full Name
lysine methyltransferase 2Bprovided by HGNC
Primary source
HGNC:HGNC:15840
See related
Ensembl:ENSG00000272333 MIM:606834; AllianceGenome:HGNC:15840
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
HRX2; MLL2; MLL4; TRX2; WBP7; DYT28; MLL1B; MRD68; WBP-7; CXXC10
Summary
This gene encodes a protein which contains multiple domains including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains, and a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain. The SET domain is a conserved C-terminal domain that characterizes proteins of the MLL (mixed-lineage leukemia) family. This gene is ubiquitously expressed in adult tissues. It is also amplified in solid tumor cell lines, and may be involved in human cancer. Two alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene, however, the full length nature of the shorter transcript is not known. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 15.2), spleen (RPKM 7.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
19q13.12
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35718003..35738878)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38263317..38284192)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36208905..36229779)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36174493-36174994 Neighboring gene thymidylate synthetase pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14492 Neighboring gene zinc finger and BTB domain containing 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10532 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:36207458-36208017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:36209137-36209694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36230671-36231301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14497 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36234871-36235031 Neighboring gene IGF like family receptor 1 Neighboring gene U2 small nuclear RNA auxiliary factor 1 like 4 Neighboring gene presenilin enhancer, gamma-secretase subunit

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. Histone Methyltransferase KMT2B Promotes Metastasis and Angiogenesis of Cervical Cancer by Upregulating EGF Expression. Zhao D, et al. Int J Biol Sci, 2023. PMID 36594087, Free PMC Article
  2. A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members. Owczarzak LR, et al. Tremor Other Hyperkinet Mov (N Y), 2022. PMID 35415007, Free PMC Article
  3. Blood DNA methylation provides an accurate biomarker of KMT2B-related dystonia and predicts onset. Mirza-Schreiber N, et al. Brain, 2022 Apr 18. PMID 34590685
  4. Novel KMT2B mutation causes cerebellar ataxia: Expanding the clinical phenotype. Damásio J, et al. Clin Genet, 2021 Dec. PMID 34477219
  5. Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile. Ciolfi A, et al. Clin Epigenetics, 2021 Aug 11. PMID 34380541, Free PMC Article

See all (116) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4.
    Title: Histone H4K16ac Binding Function of the Triple PHD Finger Cassette of MLL4.
  2. LncRNA SEMA3B-AS1 suppresses the tumor-initiating characteristics of triple negative breast cancer via engaging in MLL4-mediated H3K4 trimethylation.
    Title: LncRNA SEMA3B-AS1 suppresses the tumor-initiating characteristics of triple negative breast cancer via engaging in MLL4-mediated H3K4 trimethylation.
  3. Histone Methyltransferase KMT2B Promotes Metastasis and Angiogenesis of Cervical Cancer by Upregulating EGF Expression.
    Title: Histone Methyltransferase KMT2B Promotes Metastasis and Angiogenesis of Cervical Cancer by Upregulating EGF Expression.
  4. Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4).
    Title: Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4).
  5. Comparison of methylation episignatures in KMT2B- and KMT2D-related human disorders.
    Title: Comparison of methylation episignatures in KMT2B- and KMT2D-related human disorders.
  6. Blood DNA methylation provides an accurate biomarker of KMT2B-related dystonia and predicts onset.
    Title: Blood DNA methylation provides an accurate biomarker of KMT2B-related dystonia and predicts onset.
  7. Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile.
    Title: Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile.
  8. A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members.
    Title: A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members.
  9. KMT2B promotes SHPRH expression to regulate (131)I sensitivity in thyroid carcinoma cells by affecting FYN protein stability.
    Title: KMT2B promotes SHPRH expression to regulate (131)I sensitivity in thyroid carcinoma cells by affecting FYN protein stability.
  10. Novel KMT2B mutation causes cerebellar ataxia: Expanding the clinical phenotype.
    Title: Novel KMT2B mutation causes cerebellar ataxia: Expanding the clinical phenotype.
Submit: New GeneRIF Correction See all GeneRIFs (39)

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2017-05-11)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2017-05-11)

ClinGen Genome Curation PagePubMed

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

Clone Names

  • KIAA0304

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
  
enables histone H3K4 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables unmethylated CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
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 DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of MLL1/2 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
histone-lysine N-methyltransferase 2B
Names
WW domain binding protein 7
histone-lysine N-methyltransferase MLL4
lysine (K)-specific methyltransferase 2B
mixed lineage leukemia gene homolog 2
myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4
myeloid/lymphoid or mixed-lineage leukemia protein 4
trithorax homologue 2
NP_055542.1
XP_011525863.3
XP_011525864.1
XP_047295743.1
XP_054178770.1
XP_054178771.1
XP_054178772.1

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_052906.1 RefSeqGene

    Range
    4985..25860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014727.3 → NP_055542.1  histone-lysine N-methyltransferase 2B

    See identical proteins and their annotated locations for NP_055542.1

    Status: REVIEWED

    Source sequence(s)
    AD000671, AJ007041
    Consensus CDS
    CCDS46055.1
    UniProtKB/Swiss-Prot
    O15022, O95836, Q96GP2, Q96IP3, Q9UK25, Q9UMN6, Q9Y668, Q9Y669
    UniProtKB/TrEMBL
    A0A8I5KPK0
    Related
    ENSP00000398837.2, ENST00000420124.4
    Conserved Domains (10) summary
    cd05493
    Location:1374 → 1516
    Bromo_ALL-1; Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many ...
    smart00542
    Location:2413 → 2497
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:2577 → 2697
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG2940
    Location:2559 → 2715
    SET; SET domain-containing protein (function unknown) [General function prediction only]
    pfam02008
    Location:958 → 1005
    zf-CXXC; CXXC zinc finger domain
    cd15589
    Location:1203 → 1249
    PHD1_KMT2B; PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15591
    Location:1251 → 1300
    PHD2_KMT2B; PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15593
    Location:1337 → 1393
    PHD3_KMT2B; PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15694
    Location:1581 → 1685
    ePHD_KMT2B; Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B)
    pfam05964
    Location:1734 → 1780
    FYRN; F/Y-rich N-terminus

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    35718003..35738878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439787.1 → XP_047295743.1  histone-lysine N-methyltransferase 2B isoform X2

  2. XM_011527561.3 → XP_011525863.3  histone-lysine N-methyltransferase 2B isoform X3

    UniProtKB/TrEMBL
    A0A669KBI7
    Related
    ENSP00000501283.1, ENST00000673918.2

  3. XM_011527562.3 → XP_011525864.1  histone-lysine N-methyltransferase 2B isoform X1

    UniProtKB/TrEMBL
    A0A8I5KPK0
    Conserved Domains (8) summary
    cd05493
    Location:1374 → 1516
    Bromo_ALL-1; Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many ...
    smart00542
    Location:2413 → 2497
    FYRC; FY-rich domain, C-terminal region
    pfam02008
    Location:958 → 1005
    zf-CXXC; CXXC zinc finger domain
    cd15589
    Location:1203 → 1249
    PHD1_KMT2B; PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15591
    Location:1251 → 1300
    PHD2_KMT2B; PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15593
    Location:1337 → 1393
    PHD3_KMT2B; PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B)
    cd15694
    Location:1581 → 1685
    ePHD_KMT2B; Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B)
    pfam05964
    Location:1734 → 1780
    FYRN; F/Y-rich N-terminus

RNA

  1. XR_935878.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38263317..38284192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322796.1 → XP_054178771.1  histone-lysine N-methyltransferase 2B isoform X2

  2. XM_054322797.1 → XP_054178772.1  histone-lysine N-methyltransferase 2B isoform X3

  3. XM_054322795.1 → XP_054178770.1  histone-lysine N-methyltransferase 2B isoform X1

RNA

  1. XR_008485225.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UMN6.1 GenPept UniProtKB/Swiss-Prot:Q9UMN6

Gene LinkOut

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