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GeneE
50 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.
KDM1A
lysine demethylase 1A
Chromosome 1 Β· 1p36.12
NCBI Gene: 23028Ensembl: ENSG00000004487.18HGNC: HGNC:29079UniProt: A0A8I5KSH0
566PubMed Papers
22Diseases
1Drugs
16Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTranscription Factor
RESEARCH IMPACT
Highly StudiedTrending
CLINICAL
Clinical TrialsOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
enzyme bindingregulation of double-strand break repair via homologous recombinationpositive regulation of protein ubiquitinationregulation of protein localizationpalatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeneurodegenerative diseaseACTH-independent macronodular adrenal hyperplasia 3Cushing syndrome due to macronodular adrenal hyperplasia
✦AI Summary

KDM1A (lysine demethylase 1A) is a histone demethylase that functions as a key epigenetic regulator of gene transcription. The enzyme specifically demethylates histone H3 lysine 4 (H3K4me1/2) through an oxidation reaction that generates formaldehyde, leading to transcriptional repression 1. KDM1A also exhibits H3K9me2 demethylase activity through cooperation with supervillin protein, essential for neuronal differentiation [UniProt]. The protein acts as a transcriptional corepressor, with RNAi inhibition causing increased H3K4 methylation and target gene derepression 1. KDM1A plays critical roles in cancer biology, promoting tumor progression and maintaining cancer stem cell properties through activation of the Wnt/Ξ²-catenin pathway by suppressing pathway antagonists APC2 and DKK1 2. In skin homeostasis, KDM1A collaborates with ZNF750 to silence pattern recognition receptors in differentiated keratinocytes, preventing excessive inflammation 3. The enzyme is implicated in breast cancer metastasis through epigenomic remodeling that facilitates MAF/estrogen-driven gene expression programs 4. Clinically, KDM1A represents a therapeutic target, with selective inhibitors like ORY-1001 showing promise in acute leukemia treatment 5. Germline KDM1A mutations are associated with primary bilateral macronodular adrenal hyperplasia 6.

Sources cited
1
KDM1A demethylates H3K4 through oxidation reaction generating formaldehyde and functions as transcriptional corepressor
PMID: 15620353
2
KDM1A promotes cancer stem cell properties and tumor progression via Wnt/Ξ²-catenin pathway
PMID: 35198054
3
KDM1A collaborates with ZNF750 to silence pattern recognition receptors preventing skin inflammation
PMID: 39353440
4
KDM1A enables MAF/estrogen-driven metastatic gene expression through epigenomic remodeling
PMID: 37945904
5
ORY-1001 KDM1A inhibitor shows therapeutic potential in acute leukemia
PMID: 29502954
6
KDM1A mutations associated with primary bilateral macronodular adrenal hyperplasia
PMID: 36548967
Disease Associationsβ“˜22
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeOpen Targets
0.74Strong
neurodegenerative diseaseOpen Targets
0.55Moderate
ACTH-independent macronodular adrenal hyperplasia 3Open Targets
0.47Moderate
Cushing syndrome due to macronodular adrenal hyperplasiaOpen Targets
0.37Weak
developmental disabilityOpen Targets
0.37Weak
essential thrombocythemiaOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.30Weak
myelofibrosisOpen Targets
0.29Weak
polycythemia veraOpen Targets
0.29Weak
Neurodevelopmental delayOpen Targets
0.27Weak
genetic disorderOpen Targets
0.20Weak
lysosomal storage diseaseOpen Targets
0.18Weak
obesityOpen Targets
0.17Weak
overnutritionOpen Targets
0.13Weak
small cell lung carcinomaOpen Targets
0.12Weak
neoplasmOpen Targets
0.12Weak
colobomaOpen Targets
0.12Weak
breast cancerOpen Targets
0.12Weak
vein disorderOpen Targets
0.12Weak
Global developmental delayOpen Targets
0.12Weak
ACTH-independent macronodular adrenal hyperplasia 3UniProt
Cleft palate, psychomotor retardation, and distinctive facial featuresUniProt
Pathogenic Variants16
NM_001009999.3(KDM1A):c.1733A>G (p.Gln578Arg)Likely pathogenic
Neurodevelopmental delay|Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome|Squamous cell lung carcinoma
β˜…β˜…β˜†β˜†2024β†’ Residue 578
NM_001009999.3(KDM1A):c.1196A>G (p.Asp399Gly)Likely pathogenic
not provided|Intellectual disability
β˜…β˜…β˜†β˜†2021β†’ Residue 399
NM_001009999.3(KDM1A):c.532C>T (p.Leu178Phe)Likely pathogenic
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 178
NM_001009999.3(KDM1A):c.1035_1038dup (p.Ala347fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 347
NM_001009999.3(KDM1A):c.2299-2A>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001009999.3(KDM1A):c.1736A>T (p.Asp579Val)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 579
NM_001009999.3(KDM1A):c.1208A>C (p.Glu403Ala)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 403
NM_001009999.3(KDM1A):c.1736A>G (p.Asp579Gly)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 579
NM_001009999.3(KDM1A):c.1003G>T (p.Gly335Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2018β†’ Residue 335
NM_001009999.3(KDM1A):c.2353T>C (p.Tyr785His)Pathogenic
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome
β˜…β˜†β˜†β˜†2015β†’ Residue 785
NM_001009999.3(KDM1A):c.1207G>A (p.Glu403Lys)Pathogenic
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome
β˜…β˜†β˜†β˜†2015β†’ Residue 403
NM_001009999.3(KDM1A):c.1739A>G (p.Asp580Gly)Pathogenic
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome
β˜…β˜†β˜†β˜†2015β†’ Residue 580
NM_001009999.3(KDM1A):c.1849dup (p.Val617fs)Pathogenic
ACTH-independent macronodular adrenal hyperplasia 3
β˜†β˜†β˜†β˜†2024β†’ Residue 617
NM_001009999.3(KDM1A):c.352-1G>APathogenic
ACTH-independent macronodular adrenal hyperplasia 3
β˜†β˜†β˜†β˜†2024
NM_001009999.3(KDM1A):c.811C>T (p.Arg271Ter)Pathogenic
ACTH-independent macronodular adrenal hyperplasia 3
β˜†β˜†β˜†β˜†2024β†’ Residue 271
NM_001009999.3(KDM1A):c.1984C>T (p.Gln662Ter)Pathogenic
ACTH-independent macronodular adrenal hyperplasia 3
β˜†β˜†β˜†β˜†2024β†’ Residue 662
View on ClinVar β†—
Drug Targets1
BOMEDEMSTATPhase III
Lysine-specific histone demethylase 1 inhibitor
polycythemia vera
Related Genes
CTBP1Protein interaction100%CTBP2Protein interaction100%GFI1Protein interaction100%INSM1Protein interaction100%RREB1Protein interaction100%ZNF217Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
75%
Ovary
63%
Lung
39%
Heart
37%
Liver
32%
Gene Interaction Network
Click a node to explore
KDM1ACTBP1CTBP2GFI1INSM1RREB1ZNF217
PROTEIN STRUCTURE
Preparing viewer…
PDB6E1F Β· 1.16 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.64LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.47 [0.35–0.64]
RankingsWhere KDM1A stands among ~20K protein-coding genes
  • #424of 20,598
    Most Researched566 Β· top 5%
  • #2,378of 5,498
    Most Pathogenic Variants16
  • #4,545of 17,882
    Most Constrained (LOEUF)0.64
Genes detectedKDM1A
Sources retrieved50 papers
Response timeβ€”
πŸ“„ Sources
50β–Ό
1
Tanshinone IIA destabilizes SLC7A11 by regulating PIAS4-mediated SUMOylation of SLC7A11 through KDM1A, and promotes ferroptosis in breast cancer.
PMID: 38615741
J Adv Res Β· 2025
1.00
2
KDM1A promotes thyroid cancer progression and maintains stemness through the Wnt/Ξ²-catenin signaling pathway.
PMID: 35198054
Theranostics Β· 2022
0.90
3
SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry.
PMID: 36882421
Nat Commun Β· 2023
0.86
4
Lysine Demethylation in Pathogenesis.
PMID: 37751133
Adv Exp Med Biol Β· 2023
0.84
5
Targeting LSD1 in cancer: Molecular elucidation and recent advances.
PMID: 38969160
Cancer Lett Β· 2024
0.80