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GeneE
50 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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KMT2A
lysine methyltransferase 2A
Chromosome 11 Β· 11q23.3
NCBI Gene: 4297Ensembl: ENSG00000118058.25HGNC: HGNC:7132UniProt: A0AA34QVI8
720PubMed Papers
21Diseases
2Drugs
521Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneOncogeneTranscription Factor
RESEARCH IMPACT
Highly StudiedTrendingVariant-Rich
CLINICAL
Clinical TrialsOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of DNA-templated transcriptionunmethylated CpG bindingprotein-cysteine methyltransferase activityprotein-containing complex assemblyWiedemann-Steiner syndromegenetic disorderIntellectual disabilityacute lymphoblastic leukemia
✦AI Summary

KMT2A (lysine methyltransferase 2A) is a histone methyltransferase that serves as the catalytic subunit of the MLL1/MLL complex, playing essential roles in early development and hematopoiesis 123. The protein catalyzes methyl group transfer from S-adenosyl-L-methionine to lysine-4 of histone H3 (H3K4), establishing H3K4me1 and H3K4me2 marks at active chr11 sites to facilitate transcription and DNA repair 1234. KMT2A requires other MLL complex components for full methyltransferase activity and also mediates histone H4 acetylation at lysine-16 356. The protein binds unmethylated CpG elements in target gene promoters, maintaining their unmethylated state, and is required for transcriptional activation of HOXA9 71. KMT2A also regulates circadian gene expression by directing rhythmic H3K4 methylation that permits circadian acetylation and CLOCK-BMAL1 recruitment 5. Clinically, KMT2A is a major disease driver in acute leukemias. Chr11 translocations involving KMT2A occur in approximately 10% of acute leukemias, particularly in infants and young children, and are associated with aggressive disease, chemotherapy resistance, and poor outcomes (30-40% progression-free survival, <25% overall survival) 89. Novel menin inhibitors like revumenib, which block the menin-KMT2A interaction, have recently been approved and demonstrate 70-90% MRD-negative response rates in KMT2A-rearranged leukemias 1011. Emerging bispecific T-cell engagers and CAR-T therapies offer additional therapeutic options for KMT2A-rearranged acute lymphoblastic leukemia 12.

Sources cited
1
KMT2A requires other MLL complex components for full methyltransferase activity and also mediates histone H4 acetylation at lysine-16 ,26886794,24235145].
PMID: 26886794
2
Emerging bispecific T-cell engagers and CAR-T therapies offer additional therapeutic options for KMT2A-rearranged acute lymphoblastic leukemia .
PMID: 38905593
⚠Limited data available β€” This gene has 2 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
Wiedemann-Steiner syndromeOpen Targets
0.80Strong
genetic disorderOpen Targets
0.56Moderate
Intellectual disabilityOpen Targets
0.54Moderate
acute lymphoblastic leukemiaOpen Targets
0.43Moderate
Kabuki syndrome 1Open Targets
0.43Moderate
acute myeloid leukemiaOpen Targets
0.40Weak
microcephalyOpen Targets
0.40Weak
Rare genetic intellectual disabilityOpen Targets
0.40Weak
melanomaOpen Targets
0.39Weak
urinary bladder cancerOpen Targets
0.39Weak
Neurodevelopmental disorderOpen Targets
0.38Weak
B-cell acute lymphoblastic leukemiaOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.37Weak
skin basal cell carcinomaOpen Targets
0.37Weak
skin squamous cell carcinomaOpen Targets
0.37Weak
Atypical MeningiomaOpen Targets
0.37Weak
bile duct carcinomaOpen Targets
0.37Weak
cutaneous melanomaOpen Targets
0.37Weak
desmoplastic melanomaOpen Targets
0.37Weak
hemangioblastomaOpen Targets
0.37Weak
Wiedemann-Steiner syndromeUniProt
Pathogenic Variants521
NM_001197104.2(KMT2A):c.5251A>T (p.Lys1751Ter)Pathogenic
not provided|Inborn genetic diseases|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 1751
NM_001197104.2(KMT2A):c.1142dup (p.Ala383fs)Pathogenic
Intellectual disability|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 383
NM_001197104.2(KMT2A):c.173dup (p.Ala59fs)Pathogenic
Wiedemann-Steiner syndrome|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 59
NM_001197104.2(KMT2A):c.9910_9911del (p.Leu3304fs)Pathogenic
not provided|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 3304
NM_001197104.2(KMT2A):c.11071+1G>APathogenic
Wiedemann-Steiner syndrome|not provided
β˜…β˜…β˜†β˜†2025
NM_001197104.2(KMT2A):c.2214_2218del (p.Arg738fs)Pathogenic
not provided|Wiedemann-Steiner syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 738
NM_001197104.2(KMT2A):c.478C>T (p.Arg160Ter)Pathogenic
not provided|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 160
NM_001197104.2(KMT2A):c.4504C>T (p.Arg1502Ter)Pathogenic
not provided|Inborn genetic diseases|KMT2A-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 1502
NM_001197104.2(KMT2A):c.8270dup (p.Ile2758fs)Pathogenic
Wiedemann-Steiner syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2758
NM_001197104.2(KMT2A):c.6487C>T (p.Arg2163Ter)Pathogenic
not provided|Inborn genetic diseases|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 2163
NM_001197104.2(KMT2A):c.5887C>T (p.Arg1963Ter)Pathogenic
not provided|Inborn genetic diseases|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1963
NM_001197104.2(KMT2A):c.11230C>T (p.Arg3744Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 3744
NM_001197104.2(KMT2A):c.5572C>T (p.Arg1858Ter)Pathogenic
not provided|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1858
NM_001197104.2(KMT2A):c.6571C>T (p.Arg2191Ter)Pathogenic
not provided|See cases|Wiedemann-Steiner syndrome|Neoplasm
β˜…β˜…β˜†β˜†2025β†’ Residue 2191
NM_001197104.2(KMT2A):c.2318del (p.Pro773fs)Pathogenic
Inborn genetic diseases|Wiedemann-Steiner syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 773
NM_001197104.2(KMT2A):c.10676_10677del (p.Lys3559fs)Likely pathogenic
Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 3559
NM_001197104.2(KMT2A):c.8407C>T (p.Gln2803Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2803
NM_001197104.2(KMT2A):c.2318dup (p.Ser774fs)Pathogenic
Wiedemann-Steiner syndrome|not provided|Inborn genetic diseases|Adrenal cortex carcinoma
β˜…β˜…β˜†β˜†2025β†’ Residue 774
NM_001197104.2(KMT2A):c.3241C>T (p.Arg1081Ter)Pathogenic
Wiedemann-Steiner syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1081
NM_001197104.2(KMT2A):c.839_843del (p.Pro280fs)Pathogenic
not provided|Wiedemann-Steiner syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 280
View on ClinVar β†—
Drug Targets2
REVUMENIBPhase III
Menin inhibitor
adult acute myeloid leukemia
REVUMENIB SESQUIFUMARATEPhase I/II
Menin/Histone-lysine N-methyltransferase MLL inhibitor
Related Genes
H3-4Protein interaction100%H3C13Protein interaction100%H3C12Protein interaction100%H3-5Protein interaction100%AFF4Protein interaction100%TAF1Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Ovary
88%
Bone Marrow
71%
Lung
50%
Heart
41%
Liver
35%
Gene Interaction Network
Click a node to explore
KMT2AH3-4H3C13H3C12H3-5AFF4TAF1
PROTEIN STRUCTURE
Preparing viewer…
PDB3EMH Β· 1.37 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.07Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.04 [0.03–0.07]
RankingsWhere KMT2A stands among ~20K protein-coding genes
  • #293of 20,598
    Most Researched720 Β· top 5%
  • #103of 5,498
    Most Pathogenic Variants521 Β· top 5%
  • #13of 17,882
    Most Constrained (LOEUF)0.07 Β· top 1%
Genes detectedKMT2A
Sources retrieved50 papers
Response timeβ€”
πŸ“„ Sources
50β–Ό
1
Neonatal leukaemia.
PMID: 29806701
Br J Haematol Β· 2018
1.00
2
Revumenib: First Approval.
PMID: 40072775
Drugs Β· 2025
0.90
3
Ziftomenib: First Approval.
PMID: 41653248
Drugs Β· 2026
0.88
4
PMID: 39201709
Int J Mol Sci Β· 2024
0.80
5
Recent Developments and Evolving Therapeutic Strategies in KMT2A-Rearranged Acute Leukemia.
PMID: 39428967
Cancer Med Β· 2024
0.80