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This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
KDM1A (Lysine Demethylase 1A) is a Protein Coding gene. Diseases associated with KDM1A include Cleft Palate, Psychomotor Retardation, And Distinctive Facial Features and Kbg Syndrome. Among its related pathways are Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and enzyme binding. An important paralog of this gene is KDM1B.
Histone demethylases (KDMs) are a family of enzymes that catalyze the removal of methyl groups from lysine and arginine residues on histone tails. They reverse the methylation of lysine and arginine residues that is catalyzed by histone methyltransferases.
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0001085 | RNA polymerase II transcription factor binding | ISS | -- |
GO:0002039 | p53 binding | IPI | 17805299 |
GO:0003677 | DNA binding | IEA | -- |
GO:0003682 | chromatin binding | IEA,IDA | 16079795 |
GO:0005515 | protein binding | IPI | 16169070 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000784 | nuclear chromosome, telomeric region | IDA | 24529708 |
GO:0000790 | nuclear chromatin | IEA,ISS | 20833138 |
GO:0005634 | nucleus | IBA,IDA | 16079795 |
GO:0005654 | nucleoplasm | TAS | -- |
GO:0005667 | transcription factor complex | ISS | -- |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000122 | negative regulation of transcription by RNA polymerase II | ISS | -- |
GO:0000380 | alternative mRNA splicing, via spliceosome | IEA | -- |
GO:0002052 | positive regulation of neuroblast proliferation | IMP | 23400681 |
GO:0006325 | chromatin organization | IEA | -- |
GO:0006355 | regulation of transcription, DNA-templated | IEA | -- |
Name | Status | Disease Links | Group | Role | Mechanism of Action | Clinical Trials |
---|---|---|---|---|---|---|
Tranylcypromine | Approved, Investigational | Pharma | inhibitor | 26 | ||
FAD | Approved | Pharma | 0 | |||
OG-L002 | Pharma | LSD1 inhibitor,potent and specific | 0 | |||
2,4-Pyridinedicarboxylic Acid | Pharma | Histone LSD inhibitor | 0 | |||
CBB1007 | Pharma | LSD1 inhibitor,potent and selective | 0 |
Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs |
---|
Compound | Action | Cas Number |
---|---|---|
2,4-Pyridinedicarboxylic Acid | Histone LSD inhibitor | 499-80-9 |
CBB1007 | LSD1 inhibitor,potent and selective | 1379573-92-8 |
GSK J2 | 1394854-52-4 | |
GSK J4 HCl | Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable | 1373423-53-0 |
GSK J5 | 1394854-51-3 | |
GSK2879552 | Novel and irreversible LSD1 inhibitor | 1401966-69-5 |
GSK-LSD1 2HCl | 1431368-48-7 | |
OG-L002 | LSD1 inhibitor,potent and specific | 1357302-64-7 |
ORY-1001 | Selective inhibitor of KDM1A. | |
RN 1 dihydrochloride | LSD1 inhibitor, potent and selective | |
SP2509 | Demethylase 1 (LSD1) antagonist, novel Lysine-specific | 1423715-09-6 |
ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14a | · | 14b | ^ | 15 | ^ | 16a | · | 16b | · | 16c | ^ | 17a | · | 17b | · | 17c | ^ | 18 | ^ | 19a | · | 19b | ^ | 20 | ^ |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
SP2: | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||
SP3: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
SP4: | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||||
SP5: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
SP6: |
ExUns: | 21 |
---|---|
SP1: | |
SP2: | |
SP3: | |
SP4: | |
SP5: | |
SP6: |
This gene was present in the common ancestor of eukaryotes.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | KDM1A 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | KDM1A 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | KDM1A 30 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | KDM1A 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | AOF2 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Kdm1a 30 |
|
||
Mouse (Mus musculus) |
Mammalia | Kdm1a 30 17 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | KDM1A 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | KDM1A 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | kdm1a 30 |
|
||
Str.3510 30 |
|
||||
African clawed frog (Xenopus laevis) |
Amphibia | Xl.24726 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | kdm1a 30 31 |
|
OneToOne | |
wufc51a02 30 |
|
||||
African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP011661 30 |
|
||
Fruit Fly (Drosophila melanogaster) |
Insecta | Su(var)3-3 30 31 |
|
OneToOne | |
Worm (Caenorhabditis elegans) |
Secernentea | spr-5 30 |
|
||
Thale Cress (Arabidopsis thaliana) |
eudicotyledons | LDL2 30 |
|
||
Rice (Oryza sativa) |
Liliopsida | Os08g0143400 30 |
|
||
Sea Squirt (Ciona savignyi) |
Ascidiacea | CSA.9877 31 |
|
OneToOne | |
Bread mold (Neurospora crassa) |
Ascomycetes | NCU09120 30 |
|
SNP ID | Clinical significance and condition | Chr 01 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
672345 | Likely Benign: not provided | 23,082,291(+) | A/C | SYNONYMOUS_VARIANT | |
689578 | Uncertain Significance: Global developmental delay | 23,082,266(+) | G/A | MISSENSE_VARIANT | |
691433 | Uncertain Significance: Pyloric stenosis; Esophageal atresia | 23,055,114(+) | A/C | MISSENSE_VARIANT | |
720857 | Benign: not provided | 23,068,544(+) | T/C | SYNONYMOUS_VARIANT | |
720858 | Benign: not provided | 23,083,310(+) | G/A | SYNONYMOUS_VARIANT |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
esv3425192 | CNV | insertion | 20981092 |
nsv6520 | CNV | insertion | 18451855 |
Disorder | Aliases | PubMed IDs |
---|---|---|
cleft palate, psychomotor retardation, and distinctive facial features |
|
|
kbg syndrome |
|
|
loeys-dietz syndrome 1 |
|
|
neuroblastoma |
|
|
ewing sarcoma |
|
|