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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KDM6A
lysine demethylase 6A
Chromosome X Β· Xp11.3
NCBI Gene: 7403Ensembl: ENSG00000147050.18HGNC: HGNC:12637UniProt: A0A087X0R0
221PubMed Papers
21Diseases
0Drugs
172Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingMLL3/4 complexnucleushistone methyltransferase complexKabuki syndrome 2urinary bladder cancerurinary bladder carcinomaprostate adenocarcinoma
✦AI Summary

KDM6A encodes a histone H3K27 demethylase that plays crucial roles in chrX regulation and tumor suppression. The protein specifically removes di- and trimethyl marks from histone H3 lysine 27 (H3K27me2/3), leading to chrX activation and gene expression changes 12. Beyond its enzymatic activity, KDM6A functions through phase separation, forming liquid condensates via its intrinsically disordered region that are essential for tumor suppression and recruitment of the histone methyltransferase MLL4 3. KDM6A acts as a tumor suppressor in multiple cancers, including bladder cancer where it inhibits metastasis through the ARHGDIB-Rac1 pathway 1, and small cell lung cancer where it regulates subtype plasticity between ASCL1 and NEUROD1 states 4. The gene also mediates oxygen-independent regulation of ferroptosis by controlling lipid metabolic enzymes ACSL4 and ETNK1 2. Clinically, KDM6A mutations cause Kabuki syndrome 2, a rare developmental disorder characterized by intellectual disability, hypotonia, and distinctive facial features 56. KDM6A is frequently mutated across various cancer types, making it an important therapeutic target 7.

Sources cited
1
KDM6A demethylates H3K27me2/3 and inhibits bladder cancer metastasis through ARHGDIB-Rac1 pathway
PMID: 34006303
2
KDM6A regulates ferroptosis by controlling ACSL4 and ETNK1 expression through H3K27 demethylation
PMID: 40712585
3
KDM6A functions through phase separation and liquid condensate formation for tumor suppression and MLL4 recruitment
PMID: 34526716
4
KDM6A regulates SCLC subtype plasticity between ASCL1 and NEUROD1 states
PMID: 37591951
5
KDM6A mutations cause Kabuki syndrome 2 with developmental delay and distinctive features
PMID: 33805950
6
KDM6A pathogenic variants are diagnostic criteria for Kabuki syndrome
PMID: 30514738
7
KDM6A is frequently mutated in pancreatic cancer squamous subtype
PMID: 26909576
Disease Associationsβ“˜21
Kabuki syndrome 2Open Targets
0.80Strong
urinary bladder cancerOpen Targets
0.69Moderate
urinary bladder carcinomaOpen Targets
0.61Moderate
prostate adenocarcinomaOpen Targets
0.58Moderate
genetic disorderOpen Targets
0.52Moderate
Kabuki syndromeOpen Targets
0.50Moderate
Kabuki syndrome 1Open Targets
0.49Moderate
squamous cell lung carcinomaOpen Targets
0.48Moderate
Neurodevelopmental disorderOpen Targets
0.41Moderate
bladder transitional cell carcinomaOpen Targets
0.38Weak
urothelial carcinomaOpen Targets
0.38Weak
AutoimmunityOpen Targets
0.37Weak
breast ductal adenocarcinomaOpen Targets
0.37Weak
lymphoid neoplasmOpen Targets
0.37Weak
pancreatic carcinomaOpen Targets
0.37Weak
Angiomatous MeningiomaOpen Targets
0.37Weak
Atypical MeningiomaOpen Targets
0.37Weak
hemangioblastomaOpen Targets
0.37Weak
lung carcinomaOpen Targets
0.37Weak
Meningothelial MeningiomaOpen Targets
0.37Weak
Kabuki syndrome 2UniProt
Pathogenic Variants172
NM_001291415.2(KDM6A):c.385-6049_385-6047delLikely pathogenic
Kabuki syndrome 2
β˜…β˜…β˜†β˜†2026
NM_001291415.2(KDM6A):c.608_615del (p.Leu202_Ser203insTer)Pathogenic
Kabuki syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 202
NM_001291415.2(KDM6A):c.4243C>T (p.Arg1415Ter)Pathogenic
Kabuki syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 1415
NM_001291415.2(KDM6A):c.1990C>T (p.Arg664Ter)Pathogenic
Inborn genetic diseases|Kabuki syndrome 2|not provided|Kabuki syndrome 2;Kabuki syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 664
NM_001291415.2(KDM6A):c.514C>T (p.Arg172Ter)Pathogenic
Kabuki syndrome 2|Medulloblastoma non-WNT/non-SHH group 4
β˜…β˜…β˜†β˜†2025β†’ Residue 172
NM_001291415.2(KDM6A):c.3341_3344del (p.Asp1114fs)Pathogenic
not provided|Kabuki syndrome 2
β˜…β˜…β˜†β˜†2024β†’ Residue 1114
NM_001291415.2(KDM6A):c.4034+3_4034+6delPathogenic
not provided|Kabuki syndrome 2
β˜…β˜…β˜†β˜†2024
NM_001291415.2(KDM6A):c.2128C>T (p.Arg710Ter)Pathogenic
not provided|Neurodevelopmental disorder|Kabuki syndrome 2
β˜…β˜…β˜†β˜†2024β†’ Residue 710
NM_001291415.2(KDM6A):c.1581+1G>TLikely pathogenic
Kabuki syndrome 2|not provided
β˜…β˜…β˜†β˜†2024
NM_001291415.2(KDM6A):c.1711C>T (p.Arg571Ter)Pathogenic
Kabuki syndrome 2|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 571
NM_001291415.2(KDM6A):c.4207C>T (p.Arg1403Ter)Pathogenic
Kabuki syndrome 2|Anemia
β˜…β˜…β˜†β˜†2024β†’ Residue 1403
NM_001291415.2(KDM6A):c.3919C>T (p.Arg1307Trp)Pathogenic
Kabuki syndrome 2|Kabuki syndrome 1
β˜…β˜…β˜†β˜†2023β†’ Residue 1307
NM_001291415.2(KDM6A):c.3793C>T (p.Arg1265Ter)Pathogenic
Kabuki syndrome 2|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 1265
NM_001291415.2(KDM6A):c.493C>T (p.Arg165Ter)Pathogenic
Kabuki syndrome 2|not provided|Malignant tumor of urinary bladder
β˜…β˜…β˜†β˜†2023β†’ Residue 165
NM_001291415.2(KDM6A):c.3991C>T (p.Arg1331Ter)Pathogenic
Kabuki syndrome 2|not provided|Medulloblastoma WNT activated
β˜…β˜…β˜†β˜†2022β†’ Residue 1331
NM_001291415.2(KDM6A):c.2988+1G>APathogenic
not provided|Kabuki syndrome 2|Nonpapillary renal cell carcinoma|Neoplasm
β˜…β˜…β˜†β˜†2022
NM_001291415.2(KDM6A):c.2597_2598del (p.Ser866fs)Pathogenic
Kabuki syndrome 2
β˜…β˜…β˜†β˜†2022β†’ Residue 866
NM_001291415.2(KDM6A):c.2482_2485del (p.Asp828fs)Pathogenic
not provided|Kabuki syndrome 2
β˜…β˜…β˜†β˜†2019β†’ Residue 828
NM_001291415.2(KDM6A):c.3172C>T (p.Gln1058Ter)Pathogenic
Kabuki syndrome 2
β˜…β˜…β˜†β˜†2017β†’ Residue 1058
NM_001291415.2(KDM6A):c.3791A>G (p.Gln1264Arg)Likely pathogenic
Kabuki syndrome 2|not provided
β˜…β˜…β˜†β˜†2015β†’ Residue 1264
View on ClinVar β†—
Related Genes
ATP5F1AProtein interaction100%ATP5PDProtein interaction100%ATP5PBProtein interaction100%ATP5F1CProtein interaction100%H3-4Protein interaction100%EP300Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
40%
Lung
27%
Heart
27%
Brain
25%
Liver
20%
Gene Interaction Network
Click a node to explore
KDM6AATP5F1AATP5PDATP5PBATP5F1CH3-4EP300
PROTEIN STRUCTURE
Preparing viewer…
PDB6FUL Β· 1.65 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.15Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.09 [0.06–0.15]
RankingsWhere KDM6A stands among ~20K protein-coding genes
  • #1,860of 20,598
    Most Researched221 Β· top 10%
  • #427of 5,498
    Most Pathogenic Variants172 Β· top 10%
  • #227of 17,882
    Most Constrained (LOEUF)0.15 Β· top 5%
Genes detectedKDM6A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
Genomic analyses identify molecular subtypes of pancreatic cancer.
PMID: 26909576
Nature Β· 2016
1.00
2
Kabuki Syndrome-Clinical Review with Molecular Aspects.
PMID: 33805950
Genes (Basel) Β· 2021
0.90
3
Kabuki syndrome: international consensus diagnostic criteria.
PMID: 30514738
J Med Genet Β· 2019
0.80
4
Failure of human rhombic lip differentiation underlies medulloblastoma formation.
PMID: 36131014
Nature Β· 2022
0.72
5
KDM6A-ARHGDIB axis blocks metastasis of bladder cancer by inhibiting Rac1.
PMID: 34006303
Mol Cancer Β· 2021
0.70