Free for academic non-profit institutions. Other users need a Commercial license

Aliases for KDM6A Gene

Aliases for KDM6A Gene

  • Lysine Demethylase 6A 2 3 5
  • Lysine (K)-Specific Demethylase 6A 2 3
  • Histone Demethylase UTX 3 4
  • UTX 3 4
  • BA386N14.2 (Ubiquitously Transcribed X Chromosome Tetratricopeptide Repeat Protein (UTX)) 3
  • Ubiquitously-Transcribed X Chromosome Tetratricopeptide Repeat Protein 4
  • Ubiquitously Transcribed Tetratricopeptide Repeat Protein X-Linked 3
  • Ubiquitously Transcribed Tetratricopeptide Repeat, X Chromosome 2
  • Ubiquitously-Transcribed TPR Protein On The X Chromosome 4
  • Ubiquitously-Transcribed TPR Gene On The X Chromosome 3
  • Lysine-Specific Demethylase 6A 3
  • EC 1.14.11.- 4
  • BA386N14.2 3
  • EC 1.14.11 61
  • KABUK2 3

External Ids for KDM6A Gene

Previous HGNC Symbols for KDM6A Gene

  • UTX

Previous GeneCards Identifiers for KDM6A Gene

  • GC0XP044619
  • GC0XP044732
  • GC0XP042453

Summaries for KDM6A Gene

Entrez Gene Summary for KDM6A Gene

  • This gene is located on the X chromosome and is the corresponding locus to a Y-linked gene which encodes a tetratricopeptide repeat (TPR) protein. The encoded protein of this gene contains a JmjC-domain and catalyzes the demethylation of tri/dimethylated histone H3. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]

GeneCards Summary for KDM6A Gene

KDM6A (Lysine Demethylase 6A) is a Protein Coding gene. Diseases associated with KDM6A include Kabuki Syndrome 2 and Kabuki Syndrome 1. Among its related pathways are Mesodermal Commitment Pathway and Transcriptional misregulation in cancer. GO annotations related to this gene include identical protein binding and dioxygenase activity. An important paralog of this gene is UTY.

UniProtKB/Swiss-Prot for KDM6A Gene

  • Histone demethylase that specifically demethylates Lys-27 of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-27 (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of Lys-27 of histone H3 is concomitant with methylation of Lys-4 of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849).

Gene Wiki entry for KDM6A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM6A Gene

Genomics for KDM6A Gene

Regulatory Elements for KDM6A Gene

Enhancers for KDM6A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG044870 1.7 FANTOM5 ENCODE dbSUPER 19.5 +0.5 545 5.6 HDGF PKNOX1 FOXA2 AGO1 SIN3A FEZF1 ZNF2 YY1 ZNF143 FOS KDM6A GC0XP045033
GH0XG044897 1.1 Ensembl ENCODE 5.6 +26.0 25993 2.5 HDGF ZSCAN4 TCF12 ZNF766 SCRT2 RELB IKZF2 EGR2 ZBTB2 TBX21 KDM6A GC0XP045033
GH0XG044913 1.3 Ensembl ENCODE 4.4 +42.0 41968 2.8 PKNOX1 FOXA2 ATF1 MLX ARNT ARID4B FEZF1 YY1 TCF12 ZNF766 KDM6A GC0XP045033
GH0XG044949 1 Ensembl ENCODE 5.4 +77.7 77738 2.2 ZSCAN4 ZNF2 BCL11B ZNF101 POLR2A PATZ1 SCRT2 ZNF239 PRDM10 SCRT1 KDM6A GC0XP045033
GH0XG044973 1 Ensembl ENCODE 4.4 +101.9 101939 2.4 TFAP4 KLF1 JUN HIC1 GATA2 ZNF169 FOS GATAD2A ZNF680 FOXA3 CXorf36 KDM6A GC0XP045033
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM6A on UCSC Golden Path with GeneCards custom track

Promoters for KDM6A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000246189 526 5000 HDGF PKNOX1 FOXA2 SIN3A FEZF1 ZNF2 YY1 ZNF143 FOS ZNF263

Genomic Location for KDM6A Gene

Chromosome:
X
Start:
44,873,175 bp from pter
End:
45,112,779 bp from pter
Size:
239,605 bases
Orientation:
Plus strand

Genomic View for KDM6A Gene

Genes around KDM6A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM6A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM6A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM6A Gene

Proteins for KDM6A Gene

  • Protein details for KDM6A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15550-KDM6A_HUMAN
    Recommended name:
    Lysine-specific demethylase 6A
    Protein Accession:
    O15550
    Secondary Accessions:
    • Q52LL9
    • Q5JVQ7

    Protein attributes for KDM6A Gene

    Size:
    1401 amino acids
    Molecular mass:
    154177 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Interacts with TLE1 (By similarity). Component of the MLL2/3 complex (also named ASCOM complex), at least composed of KMT2D/MLL2 or KMT2C/MLL3, ASH2L, RBBP5, WDR5, NCOA6, DPY30, KDM6A (or KDM6B), PAXIP1/PTIP, PAGR1 and alpha- and beta-tubulin. Interacts with SUPT6H (By similarity).
    Miscellaneous:
    • Escapes X chromosome inactivation.

    Three dimensional structures from OCA and Proteopedia for KDM6A Gene

neXtProt entry for KDM6A Gene

Selected DME Specific Peptides for KDM6A Gene

O15550:
  • GTCDKVNNIHP
  • ASSPSSAIST
  • DYWKNAAFLYGLGLVYF
  • QRPGDLVWINAGTVHWVQA
  • IGKVQDAF
  • GWCNNIAWNVGPLTA
  • DPNSGQSWYFLGRCYS
  • YQRYYSLQ
  • KLNPPTPSIYLE
  • SEASADTWCSIGVLYQQQNQP
  • FCRAKEIHLRLG
  • IKFGTNIDLSD
  • SFQESLREENE
  • SHTTIAKYAQYQA
  • VEVRTQLLQPADENWDP
  • EIQFHIAHLYETQRKYHSAK

Post-translational modifications for KDM6A Gene

  • Ubiquitination at posLast=225225
  • Modification sites at PhosphoSitePlus

Domains & Families for KDM6A Gene

Graphical View of Domain Structure for InterPro Entry

O15550

UniProtKB/Swiss-Prot:

KDM6A_HUMAN :
  • Belongs to the UTX family.
Family:
  • Belongs to the UTX family.
genes like me logo Genes that share domains with KDM6A: view

Function for KDM6A Gene

Molecular function for KDM6A Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-27 of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-27 (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of Lys-27 of histone H3 is concomitant with methylation of Lys-4 of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849).

Enzyme Numbers (IUBMB) for KDM6A Gene

Gene Ontology (GO) - Molecular Function for KDM6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0031490 chromatin DNA binding IEA --
GO:0032452 histone demethylase activity TAS --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with KDM6A: view
genes like me logo Genes that share phenotypes with KDM6A: view

Human Phenotype Ontology for KDM6A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for KDM6A Gene

MGI Knock Outs for KDM6A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM6A

No data available for Transcription Factor Targets and HOMER Transcription for KDM6A Gene

Localization for KDM6A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM6A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM6A gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for KDM6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 17500065
GO:0005654 nucleoplasm TAS --
GO:0035097 histone methyltransferase complex IDA 17500065
GO:0044666 MLL3/4 complex IDA 17500065
genes like me logo Genes that share ontologies with KDM6A: view

Pathways & Interactions for KDM6A Gene

genes like me logo Genes that share pathways with KDM6A: view

Gene Ontology (GO) - Biological Process for KDM6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001843 neural tube closure IEA --
GO:0003007 heart morphogenesis IEA --
GO:0003016 respiratory system process IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with KDM6A: view

No data available for SIGNOR curated interactions for KDM6A Gene

Drugs & Compounds for KDM6A Gene

No Compound Related Data Available

Transcripts for KDM6A Gene

Unigene Clusters for KDM6A Gene

Lysine (K)-specific demethylase 6A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM6A

Alternative Splicing Database (ASD) splice patterns (SP) for KDM6A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23a ·
SP1: -
SP2:
SP3:
SP4:
SP5:

ExUns: 23b ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32 ^ 33
SP1: -
SP2: -
SP3:
SP4:
SP5:

Relevant External Links for KDM6A Gene

GeneLoc Exon Structure for
KDM6A
ECgene alternative splicing isoforms for
KDM6A

Expression for KDM6A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM6A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KDM6A Gene

This gene is overexpressed in Plasma (41.1), Placenta (12.0), CD8 Tcells (7.5), and Blymphocyte (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for KDM6A Gene



Protein tissue co-expression partners for KDM6A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KDM6A Gene:

KDM6A

SOURCE GeneReport for Unigene cluster for KDM6A Gene:

Hs.522616

Evidence on tissue expression from TISSUES for KDM6A Gene

  • Nervous system(4.5)
  • Bone marrow(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM6A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • pituitary gland
  • skull
  • thyroid
  • tooth
Thorax:
  • aorta
  • breast
  • bronchus
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • rectum
  • testicle
  • ureter
  • urinary bladder
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • digit
  • elbow
  • femur
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • thigh
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with KDM6A: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for KDM6A Gene

Orthologs for KDM6A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM6A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM6A 34 35
  • 99.88 (n)
dog
(Canis familiaris)
Mammalia KDM6A 34 35
  • 97.59 (n)
cow
(Bos Taurus)
Mammalia KDM6A 34 35
  • 97.14 (n)
rat
(Rattus norvegicus)
Mammalia Kdm6a 34
  • 95.49 (n)
mouse
(Mus musculus)
Mammalia Kdm6a 34 16 35
  • 95.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 93 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 90 (a)
OneToMany
chicken
(Gallus gallus)
Aves KDM6A 34
  • 90.4 (n)
-- 35
  • 89 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 85 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm6a 34
  • 84.54 (n)
Str.3199 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.34704 34
zebrafish
(Danio rerio)
Actinopterygii kdm6a 34 35
  • 75.21 (n)
kdm6al 35
  • 66 (a)
ManyToMany
Dr.7106 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10250 34
fruit fly
(Drosophila melanogaster)
Insecta Utx 34 35
  • 59.12 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008509 34
  • 56.29 (n)
worm
(Caenorhabditis elegans)
Secernentea utx-1 34 35
  • 50.13 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CYC8 35
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8580 35
  • 45 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3634 34
Species where no ortholog for KDM6A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM6A Gene

ENSEMBL:
Gene Tree for KDM6A (if available)
TreeFam:
Gene Tree for KDM6A (if available)

Paralogs for KDM6A Gene

Paralogs for KDM6A Gene

genes like me logo Genes that share paralogs with KDM6A: view

Variants for KDM6A Gene

Sequence variations from dbSNP and Humsavar for KDM6A Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
VAR_035871 A colorectal cancer sample
VAR_067225 A patient with chronic myelomonocytic leukemia
VAR_067226 A patient with chronic myelomonocytic leukemia
VAR_067227 A patient with chronic myelomonocytic leukemia
rs397514628 Pathogenic 45,063,449(+) AGGTA(C/T)GATCT nc-transcript-variant, reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for KDM6A Gene

Variant ID Type Subtype PubMed ID
esv2740127 CNV deletion 23290073
esv2740129 CNV deletion 23290073
nsv1153309 CNV insertion 26484159

Variation tolerance for KDM6A Gene

Residual Variation Intolerance Score: 4.59% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.71; 73.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM6A Gene

Human Gene Mutation Database (HGMD)
KDM6A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM6A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM6A Gene

Disorders for KDM6A Gene

MalaCards: The human disease database

(6) MalaCards diseases for KDM6A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
kabuki syndrome 2
  • kabuk2
kabuki syndrome 1
  • kabuki syndrome
kdm6a-related kabuki syndrome
  • kabuki syndrome 2
chronic myelomonocytic leukemia
  • leukemia, myelomonocytic, chronic
tanycytic ependymoma
- elite association - COSMIC cancer census association via MalaCards
Search KDM6A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

KDM6A_HUMAN
  • Kabuki syndrome 2 (KABUK2) [MIM:300867]: A congenital mental retardation syndrome with additional features, including postnatal dwarfism, a peculiar facies characterized by long palpebral fissures with eversion of the lateral third of the lower eyelids, a broad and depressed nasal tip, large prominent earlobes, a cleft or high-arched palate, scoliosis, short fifth finger, persistence of fingerpads, radiographic abnormalities of the vertebrae, hands, and hip joints, and recurrent otitis media in infancy. {ECO:0000269 PubMed:22197486}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for KDM6A

Genetic Association Database (GAD)
KDM6A
Human Genome Epidemiology (HuGE) Navigator
KDM6A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM6A
genes like me logo Genes that share disorders with KDM6A: view

No data available for Genatlas for KDM6A Gene

Publications for KDM6A Gene

  1. Functional coherence of the human Y chromosome. (PMID: 9381176) Lahn B.T. … Page D.C. (Science 1997) 2 3 4 64
  2. Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. (PMID: 22197486) Lederer D. … Verellen-Dumoulin C. (Am. J. Hum. Genet. 2012) 3 4 64
  3. Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. (PMID: 21828135) Jankowska A.M. … Maciejewski J.P. (Blood 2011) 3 4 64
  4. Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. (PMID: 22002947) Sengoku T. … Yokoyama S. (Genes Dev. 2011) 3 4 64
  5. Follow-up of potential novel Graves' disease susceptibility loci, identified in the UK WTCCC genome-wide nonsynonymous SNP study. (PMID: 20442750) Newby P.R. … Gough S.C. (Eur. J. Hum. Genet. 2010) 3 46 64

Products for KDM6A Gene

  • Addgene plasmids for KDM6A

Sources for KDM6A Gene

Content
Loading form....