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KMT2D lysine methyltransferase 2D [ Homo sapiens (human) ]

Gene ID: 8085, updated on 1-Jun-2020

Summary

Official Symbol
KMT2Dprovided by HGNC
Official Full Name
lysine methyltransferase 2Dprovided by HGNC
Primary source
HGNC:HGNC:7133
See related
Ensembl:ENSG00000167548 MIM:602113
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
ALR; KMS; MLL2; MLL4; AAD10; KABUK1; TNRC21; CAGL114
Summary
The protein encoded by this gene is a histone methyltransferase that methylates the Lys-4 position of histone H3. The encoded protein is part of a large protein complex called ASCOM, which has been shown to be a transcriptional regulator of the beta-globin and estrogen receptor genes. Mutations in this gene have been shown to be a cause of Kabuki syndrome. [provided by RefSeq, Oct 2010]
Expression
Ubiquitous expression in bone marrow (RPKM 10.0), skin (RPKM 5.8) and 25 other tissues See more
Orthologs

Genomic context

See KMT2D in Genome Data Viewer
Location:
12q13.12
Exon count:
56
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (49018975..49060884, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49412758..49453935, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene DDN and PRKAG1 antisense RNA 1 Neighboring gene dendrin Neighboring gene protein kinase AMP-activated non-catalytic subunit gamma 1 Neighboring gene RHEB like 1 Neighboring gene uncharacterized LOC105369759 Neighboring gene GATA motif-containing MPRA enhancer 293 Neighboring gene desert hedgehog signaling molecule

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

Associated conditions

Description Tests
Kabuki syndrome 1
MedGen: CN030661 OMIM: 147920 GeneReviews: Kabuki Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2020-01-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2020-01-23)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K4 specific) TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
beta-catenin-TCF complex assembly TAS
Traceable Author Statement
more info
 
chromatin silencing ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K4 dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 methylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
histone H3-K4 monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
oocyte growth ISS
Inferred from Sequence or Structural Similarity
more info
 
oogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of intracellular estrogen receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of megakaryocyte differentiation TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
response to estrogen IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
MLL3/4 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
MLL3/4 complex IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase complex IPI
Inferred from Physical Interaction
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase 2D
Names
ALL1-related protein
Kabuki make-up syndrome
Kabuki mental retardation syndrome
histone-lysine N-methyltransferase MLL2
lysine (K)-specific methyltransferase 2D
lysine N-methyltransferase 2D
myeloid/lymphoid or mixed-lineage leukemia 2
trinucleotide repeat containing 21
truncated lysine methyltransferase 2D
NP_003473.3
XP_006719677.1
XP_006719679.1
XP_011537072.1
XP_011537073.1
XP_011537074.1
XP_011537075.1
XP_011537076.1
XP_011537078.1

NCBI Reference Sequences (RefSeq)

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_027827.1 RefSeqGene

    Range
    5001..41350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003482.4NP_003473.3  histone-lysine N-methyltransferase 2D

    See identical proteins and their annotated locations for NP_003473.3

    Status: REVIEWED

    Source sequence(s)
    AC011603
    Consensus CDS
    CCDS44873.1
    UniProtKB/Swiss-Prot
    O14686
    UniProtKB/TrEMBL
    Q59FG6, Q6PIA1
    Related
    ENSP00000301067.7, ENST00000301067.11
    Conserved Domains (11) summary
    smart00398
    Location:20212072
    HMG; high mobility group
    smart00542
    Location:52405327
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:53975519
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50325138
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51825232
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    49018975..49060884 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719614.4XP_006719677.1  histone-lysine N-methyltransferase 2D isoform X6

    UniProtKB/Swiss-Prot
    O14686
    Conserved Domains (11) summary
    smart00398
    Location:20242075
    HMG; high mobility group
    smart00542
    Location:52435330
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54005522
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50355141
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51855235
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  2. XM_006719616.3XP_006719679.1  histone-lysine N-methyltransferase 2D isoform X8

    Conserved Domains (11) summary
    smart00398
    Location:20202071
    HMG; high mobility group
    smart00542
    Location:52395326
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:53965518
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14281474
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13771427
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15051555
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50315137
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51815231
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  3. XM_011538774.2XP_011537076.1  histone-lysine N-methyltransferase 2D isoform X5

    Conserved Domains (11) summary
    smart00398
    Location:20172068
    HMG; high mobility group
    smart00542
    Location:52365323
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54095531
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50285134
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51785228
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  4. XM_011538773.2XP_011537075.1  histone-lysine N-methyltransferase 2D isoform X4

    Conserved Domains (11) summary
    smart00398
    Location:20202071
    HMG; high mobility group
    smart00542
    Location:52395326
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54125534
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14281474
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13771427
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15051555
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50315137
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51815231
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  5. XM_011538771.2XP_011537073.1  histone-lysine N-methyltransferase 2D isoform X2

    Conserved Domains (11) summary
    smart00398
    Location:20232074
    HMG; high mobility group
    smart00542
    Location:52425329
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54155537
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14281474
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13771427
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15051555
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50345140
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51845234
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  6. XM_011538772.2XP_011537074.1  histone-lysine N-methyltransferase 2D isoform X3

    Conserved Domains (11) summary
    smart00398
    Location:20212072
    HMG; high mobility group
    smart00542
    Location:52405327
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54135535
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50325138
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51825232
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  7. XM_011538776.2XP_011537078.1  histone-lysine N-methyltransferase 2D isoform X9

    Conserved Domains (11) summary
    smart00398
    Location:20242075
    HMG; high mobility group
    smart00542
    Location:52125299
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:53855507
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50045110
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51545204
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily
  8. XM_011538770.2XP_011537072.1  histone-lysine N-methyltransferase 2D isoform X1

    Conserved Domains (11) summary
    smart00398
    Location:20242075
    HMG; high mobility group
    smart00542
    Location:52435330
    FYRC; FY-rich domain, C-terminal region
    smart00317
    Location:54165538
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd15509
    Location:228273
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15513
    Location:14291475
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15597
    Location:13781428
    PHD3_KMT2D; PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15601
    Location:15061556
    PHD5_KMT2D; PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D)
    cd15695
    Location:134217
    ePHD1_KMT2D; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D)
    cd15698
    Location:50355141
    ePHD2_KMT2D; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D)
    pfam05964
    Location:51855235
    FYRN; F/Y-rich N-terminus
    cl22851
    Location:275320
    PHD_SF; PHD finger superfamily

RNA

  1. XR_001748874.1 RNA Sequence

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