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    KDM6A lysine demethylase 6A [ Homo sapiens (human) ]

    Gene ID: 7403, updated on 5-May-2024

    Summary

    Official Symbol
    KDM6Aprovided by HGNC
    Official Full Name
    lysine demethylase 6Aprovided by HGNC
    Primary source
    HGNC:HGNC:12637
    See related
    Ensembl:ENSG00000147050 MIM:300128; AllianceGenome:HGNC:12637
    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
    UTX; KABUK2; bA386N14.2
    Summary
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 10.3), thyroid (RPKM 7.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KDM6A in Genome Data Viewer
    Location:
    Xp11.3
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (44873188..45112779)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (44280009..44519820)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (44732434..44972024)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20786 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:44738216-44738357 Neighboring gene dual specificity phosphatase 21 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:44811731-44812256 Neighboring gene Sharpr-MPRA regulatory region 12888 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:44834497-44835696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29568 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:44900925-44901669 Neighboring gene divergent protein kinase domain 2B Neighboring gene uncharacterized LOC105373191

    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
    Kabuki syndrome 2
    MedGen: C3275495 OMIM: 300867 GeneReviews: Kabuki Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2013-07-18)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2013-07-18)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat upregulates expression of KDM6A (UTX1) in 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

    • MGC141941, DKFZp686A03225

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K27me2/H3K27me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    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 chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of MLL3/4 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of MLL3/4 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    lysine-specific demethylase 6A
    Names
    [histone H3]-trimethyl-L-lysine(27) demethylase 6A
    bA386N14.2 (ubiquitously transcribed X chromosome tetratricopeptide repeat protein (UTX))
    histone demethylase UTX
    lysine (K)-specific demethylase 6A
    ubiquitously transcribed tetratricopeptide repeat protein X-linked
    ubiquitously-transcribed TPR gene on the X chromosome
    NP_001278344.1
    NP_001278345.1
    NP_001278346.1
    NP_001278347.1
    NP_001278350.1
    NP_001397671.1
    NP_001406738.1
    NP_001406739.1
    NP_001406740.1
    NP_001406741.1
    NP_001406742.1
    NP_001406743.1
    NP_001406744.1
    NP_066963.2
    XP_011542271.1
    XP_011542274.1
    XP_011542276.1
    XP_016885272.1
    XP_024308207.1
    XP_047298384.1
    XP_047298385.1
    XP_047298386.1
    XP_047298387.1
    XP_054183677.1
    XP_054183679.1
    XP_054183680.1
    XP_054183682.1
    XP_054183683.1
    XP_054183684.1
    XP_054183685.1
    XP_054183686.1

    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_016260.1 RefSeqGene

      Range
      4999..244435
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_616

    mRNA and Protein(s)

    1. NM_001291415.2NP_001278344.1  lysine-specific demethylase 6A isoform 1

      See identical proteins and their annotated locations for NP_001278344.1

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
      Consensus CDS
      CCDS94599.1
      UniProtKB/TrEMBL
      A0A087X0R0, B7ZKN5
      Related
      ENSP00000483595.2, ENST00000611820.5
      Conserved Domains (6) summary
      pfam02373
      Location:11851293
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:11511215
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106399
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    2. NM_001291416.2NP_001278345.1  lysine-specific demethylase 6A isoform 2

      See identical proteins and their annotated locations for NP_001278345.1

      Status: REVIEWED

      Source sequence(s)
      AC136488, AI364446, AL041377, AL831996, BC143272, BC143278, DC381812
      Consensus CDS
      CCDS94601.1
      UniProtKB/TrEMBL
      B7ZKN1, F8W8R6
      Related
      ENSP00000372355.6, ENST00000382899.9
      Conserved Domains (6) summary
      pfam02373
      Location:11401248
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:11061170
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    3. NM_001291417.2NP_001278346.1  lysine-specific demethylase 6A isoform 4

      See identical proteins and their annotated locations for NP_001278346.1

      Status: REVIEWED

      Source sequence(s)
      AC136488, AI364446, AK303430, AL041377, AL831996, BC143278, DC381812
      Consensus CDS
      CCDS94603.1
      UniProtKB/TrEMBL
      B7ZKN6, F5H6S1
      Related
      ENSP00000437405.3, ENST00000536777.6
      Conserved Domains (7) summary
      pfam02373
      Location:10881196
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10541118
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:317378
      TPR_11; TPR repeat
      pfam13424
      Location:205282
      TPR_12; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    4. NM_001291418.2NP_001278347.1  lysine-specific demethylase 6A isoform 5

      See identical proteins and their annotated locations for NP_001278347.1

      Status: REVIEWED

      Source sequence(s)
      AB208795, AC136488, AI364446, AL041377, BC143278, DC381812, DQ062677
      Consensus CDS
      CCDS94604.1
      UniProtKB/TrEMBL
      E1U0S6, F5H5V6
      Related
      ENSP00000443078.3, ENST00000543216.6
      Conserved Domains (7) summary
      pfam02373
      Location:10541162
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10201084
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:317378
      TPR_11; TPR repeat
      pfam13424
      Location:205282
      TPR_12; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    5. NM_001291421.2NP_001278350.1  lysine-specific demethylase 6A isoform 6

      See identical proteins and their annotated locations for NP_001278350.1

      Status: REVIEWED

      Source sequence(s)
      AC136488, AI364446, AL041377, AL831996, BC143275, BC143278, DC381812
      UniProtKB/TrEMBL
      A0A6Q8PG32
      Related
      ENST00000675157.1
      Conserved Domains (4) summary
      smart00558
      Location:803867
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG4235
      Location:18121
      NrfG; Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]
      sd00006
      Location:3461
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:837945
      JmjC; JmjC domain, hydroxylase
    6. NM_001410742.1NP_001397671.1  lysine-specific demethylase 6A isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
      Consensus CDS
      CCDS94600.1
      UniProtKB/TrEMBL
      A0A6Q8PFK0
      Related
      ENSP00000501855.1, ENST00000675577.1
    7. NM_001419809.1NP_001406738.1  lysine-specific demethylase 6A isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    8. NM_001419810.1NP_001406739.1  lysine-specific demethylase 6A isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    9. NM_001419811.1NP_001406740.1  lysine-specific demethylase 6A isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
      Related
      ENSP00000502311.1, ENST00000676062.1
    10. NM_001419812.1NP_001406741.1  lysine-specific demethylase 6A isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    11. NM_001419813.1NP_001406742.1  lysine-specific demethylase 6A isoform 12

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    12. NM_001419814.1NP_001406743.1  lysine-specific demethylase 6A isoform 13

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    13. NM_001419815.1NP_001406744.1  lysine-specific demethylase 6A isoform 14

      Status: REVIEWED

      Source sequence(s)
      AC136488, AL133545, AL138744
    14. NM_021140.4NP_066963.2  lysine-specific demethylase 6A isoform 3

      See identical proteins and their annotated locations for NP_066963.2

      Status: REVIEWED

      Source sequence(s)
      AB208795, AC136488, AI364446, AL041377, DC381812
      Consensus CDS
      CCDS14265.1
      UniProtKB/Swiss-Prot
      O15550, Q52LL9, Q5JVQ7
      UniProtKB/TrEMBL
      Q59HG3
      Related
      ENSP00000367203.4, ENST00000377967.9
      Conserved Domains (4) summary
      pfam02373
      Location:11331241
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10991163
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106399
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]

    RNA

    1. NR_111960.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AB208795, AC136488, AI364446, AK303430, AL041377, BC143272, DC381812, EU026291
      Related
      ENST00000674564.1

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      44873188..45112779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543969.4XP_011542271.1  lysine-specific demethylase 6A isoform X6

      UniProtKB/TrEMBL
      B7ZKN1
      Conserved Domains (6) summary
      pfam02373
      Location:11061214
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10721136
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    2. XM_017029783.3XP_016885272.1  lysine-specific demethylase 6A isoform X9

      UniProtKB/TrEMBL
      A0A804HJA2, B7ZKN1
      Related
      ENSP00000507416.1, ENST00000683021.1
      Conserved Domains (6) summary
      pfam02373
      Location:11061214
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10721136
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    3. XM_011543972.4XP_011542274.1  lysine-specific demethylase 6A isoform X8

      UniProtKB/TrEMBL
      B7ZKN6
      Conserved Domains (7) summary
      pfam02373
      Location:10881196
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10541118
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:317378
      TPR_11; TPR repeat
      pfam13424
      Location:205282
      TPR_12; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    4. XM_011543974.3XP_011542276.1  lysine-specific demethylase 6A isoform X12

      UniProtKB/TrEMBL
      A0A6Q8PGN0
      Conserved Domains (6) summary
      pfam02373
      Location:11331241
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10991163
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106399
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272303
      TPR_17; Tetratricopeptide repeat
    5. XM_047442430.1XP_047298386.1  lysine-specific demethylase 6A isoform X14

    6. XM_047442431.1XP_047298387.1  lysine-specific demethylase 6A isoform X15

    7. XM_024452439.2XP_024308207.1  lysine-specific demethylase 6A isoform X11

      UniProtKB/TrEMBL
      A0A6Q8PG32
      Conserved Domains (4) summary
      pfam02373
      Location:10101118
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:9761040
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:7224
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:110137
      TPR; TPR repeat [structural motif]
    8. XM_047442429.1XP_047298385.1  lysine-specific demethylase 6A isoform X13

    9. XM_047442428.1XP_047298384.1  lysine-specific demethylase 6A isoform X11

      Related
      ENST00000676389.1

    RNA

    1. XR_007068200.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      44280009..44519820
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327702.1XP_054183677.1  lysine-specific demethylase 6A isoform X6

    2. XM_054327705.1XP_054183680.1  lysine-specific demethylase 6A isoform X9

      UniProtKB/TrEMBL
      A0A804HJA2
    3. XM_054327704.1XP_054183679.1  lysine-specific demethylase 6A isoform X8

    4. XM_054327708.1XP_054183683.1  lysine-specific demethylase 6A isoform X12

    5. XM_054327710.1XP_054183685.1  lysine-specific demethylase 6A isoform X14

    6. XM_054327711.1XP_054183686.1  lysine-specific demethylase 6A isoform X15

    7. XM_054327707.1XP_054183682.1  lysine-specific demethylase 6A isoform X11

    8. XM_054327709.1XP_054183684.1  lysine-specific demethylase 6A isoform X13

    RNA

    1. XR_008485506.1 RNA Sequence