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GeneE
26 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.
KMT2D
lysine methyltransferase 2D
Chromosome 12 Β· 12q13.12
NCBI Gene: 8085Ensembl: ENSG00000167548.18HGNC: HGNC:7133UniProt: O14686
280PubMed Papers
22Diseases
0Drugs
1,026Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingresponse to estrogenpositive regulation of cell population proliferationtranscription cis-regulatory region bindingKabuki syndromeKabuki syndrome 1choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndromediffuse large B-cell lymphoma
✦AI Summary

KMT2D (lysine methyltransferase 2D) is a histone methyltransferase that catalyzes monomethylation of histone H3 at lysine 4 (H3K4me1) 1, a chr12 mark associated with active gene enhancers and transcriptional regulation sites 21. KMT2D functions within chr12 remodeling complexes, including phase-separated liquid condensates that concentrate its enzymatic activity 3. It acts as a coactivator for estrogen receptor-driven transcription by priming gene enhancer regions 45. Pathogenic KMT2D variants cause Kabuki syndrome, a developmental disorder characterized by hypotonia, developmental delay, distinctive facial dysmorphism, cardiac and renal anomalies, occurring in ~75% of cases 67. Beyond developmental disease, KMT2D functions as a tumor suppressor, with frequent mutations in multiple cancers: 10-20% of breast cancers 5, >20% of lung squamous cell carcinomas 8, and acute myeloid leukemias 9. KMT2D loss drives tumorigenesis through chr12 reprogramming; in lung cancer, deficiency increases RTK-RAS signaling and renders tumors vulnerable to RTK pathway inhibition 8. In AML, KMT2D loss activates mTOR signaling and enhances ribosome biogenesis, creating vulnerability to RNA polymerase I inhibitors 9.

Sources cited
1
KMT2D catalyzes H3K4 methylation and is part of chromatin remodeling machinery
PMID: 25561738
2
KMT2D forms H3K4me1 marks at active chromatin sites for transcription and DNA repair
PMID: 17500065
3
KMT2D acts as coactivator for estrogen receptor-driven transcription
PMID: 16603732
4
KMT2D pathogenic variants cause Kabuki syndrome in up to 75% of cases
PMID: 33805950
5
Diagnostic criteria for Kabuki syndrome with KMT2D mutations established
PMID: 30514738
6
KMT2D functions in phase-separated condensates for tumor suppression and chromatin regulation
PMID: 34526716
7
KMT2D is most frequently mutated histone methyltransferase in breast cancer (10-20%)
PMID: 38453563
8
KMT2D loss drives lung squamous cell carcinoma through RTK-RAS signaling activation
PMID: 36525973
9
KMT2D deficiency promotes AML through mTOR pathway activation and ribosome biogenesis
PMID: 37142882
Disease Associationsβ“˜22
Kabuki syndromeOpen Targets
0.84Strong
Kabuki syndrome 1Open Targets
0.81Strong
choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndromeOpen Targets
0.79Strong
diffuse large B-cell lymphomaOpen Targets
0.63Moderate
head and neck squamous cell carcinomaOpen Targets
0.63Moderate
prostate adenocarcinomaOpen Targets
0.63Moderate
squamous cell lung carcinomaOpen Targets
0.62Moderate
medulloblastomaOpen Targets
0.61Moderate
genetic disorderOpen Targets
0.55Moderate
urinary bladder cancerOpen Targets
0.54Moderate
cervical squamous cell carcinomaOpen Targets
0.52Moderate
Intellectual disabilityOpen Targets
0.48Moderate
gastric adenocarcinomaOpen Targets
0.47Moderate
microphthalmiaOpen Targets
0.46Moderate
esophageal cancerOpen Targets
0.46Moderate
lymphomaOpen Targets
0.45Moderate
small cell lung carcinomaOpen Targets
0.45Moderate
pancreatic adenocarcinomaOpen Targets
0.44Moderate
Anal Squamous Cell CarcinomaOpen Targets
0.44Moderate
non-small cell lung carcinomaOpen Targets
0.42Moderate
Branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndromeUniProt
Kabuki syndrome 1UniProt
Pathogenic Variants1,026
NM_003482.4(KMT2D):c.6595del (p.Tyr2199fs)Pathogenic
Kabuki syndrome 1|not provided|Kabuki syndrome|Kabuki syndrome 1;Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 2199
NM_003482.4(KMT2D):c.8200C>T (p.Arg2734Ter)Pathogenic
Kabuki syndrome|Kabuki syndrome 1
β˜…β˜…β˜†β˜†2026β†’ Residue 2734
NM_003482.4(KMT2D):c.6295C>T (p.Arg2099Ter)Pathogenic
Inborn genetic diseases|Kabuki syndrome 1|not provided|Intellectual disability|KMT2D-related disorder|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 2099
NM_003482.4(KMT2D):c.3754C>T (p.Arg1252Ter)Pathogenic
Kabuki syndrome 1|not provided|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1252
NM_003482.4(KMT2D):c.16019G>A (p.Arg5340Gln)Pathogenic
Kabuki syndrome 1|Kabuki syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 5340
NM_003482.4(KMT2D):c.15061C>T (p.Arg5021Ter)Pathogenic
Kabuki syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 5021
NM_003482.4(KMT2D):c.15079C>T (p.Arg5027Ter)Pathogenic
Kabuki syndrome 1|not provided|Inborn genetic diseases|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 5027
NM_003482.4(KMT2D):c.12844C>T (p.Arg4282Ter)Pathogenic
not provided|Kabuki syndrome 1|Multiple myeloma|Kabuki syndrome|KMT2D-related disorder|Neoplasm
β˜…β˜…β˜†β˜†2025β†’ Residue 4282
NM_003482.4(KMT2D):c.508C>T (p.Gln170Ter)Pathogenic
not provided|Kabuki syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 170
NM_003482.4(KMT2D):c.12811_12814del (p.Thr4271fs)Pathogenic
Kabuki syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 4271
NM_003482.4(KMT2D):c.8059C>T (p.Arg2687Ter)Pathogenic
not provided|Kabuki syndrome 1|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 2687
NM_003482.4(KMT2D):c.2533del (p.Arg845fs)Pathogenic
Kabuki syndrome|Kabuki syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 845
NM_003482.4(KMT2D):c.15535C>T (p.Arg5179Cys)Pathogenic
not provided|Inborn genetic diseases|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 5179
NM_003482.4(KMT2D):c.15629A>G (p.Tyr5210Cys)Pathogenic
Kabuki syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 5210
NM_003482.4(KMT2D):c.12592C>T (p.Arg4198Ter)Pathogenic
Kabuki syndrome 1|Inborn genetic diseases|Kabuki syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 4198
NM_003482.4(KMT2D):c.5467G>T (p.Gly1823Ter)Pathogenic
Kabuki syndrome 1|Kabuki syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1823
NM_003482.4(KMT2D):c.9265dup (p.Val3089fs)Pathogenic
not provided|Kabuki syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 3089
NM_003482.4(KMT2D):c.13450C>T (p.Arg4484Ter)Pathogenic
Kabuki syndrome 1|Inborn genetic diseases|Kabuki syndrome|Neoplasm|Cervical cancer
β˜…β˜…β˜†β˜†2025β†’ Residue 4484
NM_003482.4(KMT2D):c.16342C>T (p.Arg5448Ter)Pathogenic
Kabuki syndrome|Kabuki syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 5448
NM_003482.4(KMT2D):c.12730C>T (p.Gln4244Ter)Pathogenic
not provided|Autism
β˜…β˜…β˜†β˜†2025β†’ Residue 4244
View on ClinVar β†—
Related Genes
H3-4Protein interaction100%H3-3BProtein interaction100%H3C13Protein interaction100%H3C12Protein interaction100%EP300Protein interaction100%H2AC18Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
46%
Ovary
40%
Liver
25%
Heart
24%
Brain
24%
Gene Interaction Network
Click a node to explore
KMT2DH3-4H3-3BH3C13H3C12EP300H2AC18
PROTEIN STRUCTURE
Preparing viewer…
PDB3UVK Β· 1.40 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.14Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.11 [0.09–0.14]
RankingsWhere KMT2D stands among ~20K protein-coding genes
  • #1,288of 20,598
    Most Researched280 Β· top 10%
  • #33of 5,498
    Most Pathogenic Variants1,026 Β· top 1%
  • #172of 17,882
    Most Constrained (LOEUF)0.14 Β· top 1%
Genes detectedKMT2D
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Kabuki Syndrome-Clinical Review with Molecular Aspects.
PMID: 33805950
Genes (Basel) Β· 2021
1.00
2
KMT2C and KMT2D aberrations in breast cancer.
PMID: 38453563
Trends Cancer Β· 2024
0.90
3
KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition.
PMID: 36525973
Cancer Cell Β· 2023
0.80
4
Targeting Excessive EZH1 and EZH2 Activities for Abnormal Histone Methylation and Transcription Network in Malignant Lymphomas.
PMID: 31747604
Cell Rep Β· 2019
0.76
5
Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3.
PMID: 38926506
Nat Cell Biol Β· 2024
0.72