U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 7403, updated on 17-Jun-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, Q59HG3
    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
    UniProtKB/TrEMBL
    B7ZKN5
  8. NM_001419810.1NP_001406739.1  lysine-specific demethylase 6A isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC136488, AL133545, AL138744
    UniProtKB/TrEMBL
    B7ZKN5
  9. NM_001419811.1NP_001406740.1  lysine-specific demethylase 6A isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC136488, AL133545, AL138744
    UniProtKB/TrEMBL
    B7ZKN1
    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
    UniProtKB/TrEMBL
    Q59HG3
  11. NM_001419813.1NP_001406742.1  lysine-specific demethylase 6A isoform 12

    Status: REVIEWED

    Source sequence(s)
    AC136488, AL133545, AL138744
    UniProtKB/TrEMBL
    B7ZKN5
  12. NM_001419814.1NP_001406743.1  lysine-specific demethylase 6A isoform 13

    Status: REVIEWED

    Source sequence(s)
    AC136488, AL133545, AL138744
    UniProtKB/TrEMBL
    Q59HG3
  13. NM_001419815.1NP_001406744.1  lysine-specific demethylase 6A isoform 14

    Status: REVIEWED

    Source sequence(s)
    AC136488, AL133545, AL138744
    UniProtKB/TrEMBL
    E1U0S6
  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

    UniProtKB/TrEMBL
    A0A6Q8PHJ0
  6. XM_047442431.1XP_047298387.1  lysine-specific demethylase 6A isoform X15

    UniProtKB/TrEMBL
    A0A6Q8PHJ0
  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

    UniProtKB/TrEMBL
    A0A6Q8PG32
  9. XM_047442428.1XP_047298384.1  lysine-specific demethylase 6A isoform X11

    UniProtKB/TrEMBL
    A0A6Q8PG32
    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

    UniProtKB/TrEMBL
    B7ZKN1
  2. XM_054327705.1XP_054183680.1  lysine-specific demethylase 6A isoform X9

    UniProtKB/TrEMBL
    A0A804HJA2, B7ZKN1
  3. XM_054327704.1XP_054183679.1  lysine-specific demethylase 6A isoform X8

    UniProtKB/TrEMBL
    B7ZKN6
  4. XM_054327708.1XP_054183683.1  lysine-specific demethylase 6A isoform X12

    UniProtKB/TrEMBL
    A0A6Q8PGN0
  5. XM_054327710.1XP_054183685.1  lysine-specific demethylase 6A isoform X14

    UniProtKB/TrEMBL
    A0A6Q8PHJ0
  6. XM_054327711.1XP_054183686.1  lysine-specific demethylase 6A isoform X15

    UniProtKB/TrEMBL
    A0A6Q8PHJ0
  7. XM_054327707.1XP_054183682.1  lysine-specific demethylase 6A isoform X11

    UniProtKB/TrEMBL
    A0A6Q8PG32
  8. XM_054327709.1XP_054183684.1  lysine-specific demethylase 6A isoform X13

    UniProtKB/TrEMBL
    A0A6Q8PG32

RNA

  1. XR_008485506.1 RNA Sequence