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KDM1A Gene(Protein Coding)

Lysine Demethylase 1A

GCID:
GC01P023019
GIFtS:
53
Genes Participants
UDN Logo

Aliases for KDM1A Gene

Aliases for KDM1A Gene

  • Lysine Demethylase 1A 2 3 5
  • Flavin-Containing Amine Oxidase Domain-Containing Protein 2 3 4
  • Amine Oxidase (Flavin Containing) Domain 2 2 3
  • Lysine-Specific Histone Demethylase 1A 2 3
  • BRAF35-HDAC Complex Protein BHC110 3 4
  • AOF2 3 4
  • KDM1 3 4
  • LSD1 3 4
  • FAD-Binding Protein BRAF35-HDAC Complex, 110 KDa Subunit 3
  • Lysine-Specific Histone Demethylase 1 3
  • Lysine (K)-Specific Demethylase 1A 3
  • Lysine (K)-Specific Demethylase 1 2
  • EC 1.-.-.- 4
  • KIAA0601 4
  • BHC110 3
  • CPRF 3

External Ids for KDM1A Gene

Previous HGNC Symbols for KDM1A Gene

  • AOF2
  • KDM1

Previous GeneCards Identifiers for KDM1A Gene

  • GC01P023220
  • GC01P023347
  • GC01P021590

Summaries for KDM1A Gene

Entrez Gene Summary for KDM1A Gene

  • 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]

GeneCards Summary for KDM1A Gene

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 Signaling by Rho GTPases and Coregulation of Androgen receptor activity. 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.

UniProtKB/Swiss-Prot for KDM1A Gene

  • Histone demethylase that demethylates both Lys-4 (H3K4me) and Lys-9 (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of Thr-6 of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated Lys-370 of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.

Tocris Summary for KDM1A Gene

  • 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.

Additional gene information for KDM1A Gene

No data available for CIViC summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM1A Gene

Genomics for KDM1A Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for KDM1A Gene

Promoters and enhancers for KDM1A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J023018 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 683.7 +0.6 580 3.2 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 KDM1A SRSF10 ZBTB40 HNRNPR LINC01355 CDC42-IT1 LACTBL1 ELOA CDC42 ENSG00000271428
GH01J022051 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 54.7 -966.1 -966136 3.1 MLX DMAP1 IRF4 YY1 ZNF213 E2F8 SP3 NFYC MEF2D ZNF610 CDC42 ZBTB40 KDM1A USP48 LINC00339 CDC42-IT1 NBPF3 ENSG00000271428 NBPF2P LINC01635
GH01J023691 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 39.1 +673.2 673180 3.1 HDGF FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 RPL11 SRSF10 SRRM1 LINC01355 HNRNPR PNRC2 KDM1A ELOA ASAP3 GC01M023708
GH01J023521 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.4 +509.2 509241 13.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 GC01P023526 E2F2 SRSF10 LINC01355 KDM1A HNRNPR ASAP3 ID3 ZNF436 ELOA
GH01J022023 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 41.3 -993.7 -993705 3.8 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 MEF2D LINC00339 LINC01635 ZBTB40 CDC42-IT1 KDM1A USP48 ENSG00000271428 NBPF3 HSPG2 CDC42
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM1A on UCSC Golden Path with GeneCards custom track

Genomic Locations for KDM1A Gene

Genomic Locations for KDM1A Gene
chr1:23,019,443-23,083,691
(GRCh38/hg38)
Size:
64,249 bases
Orientation:
Plus strand
chr1:23,345,941-23,410,184
(GRCh37/hg19)
Size:
64,244 bases
Orientation:
Plus strand

Genomic View for KDM1A Gene

Genes around KDM1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM1A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for KDM1A Gene

Proteins for KDM1A Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for KDM1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60341-KDM1A_HUMAN
    Recommended name:
    Lysine-specific histone demethylase 1A
    Protein Accession:
    O60341
    Secondary Accessions:
    • A8MWP9
    • Q5TH94
    • Q5TH95
    • Q86VT7
    • Q8IXK4
    • Q8NDP6
    • Q8TAZ3
    • Q96AW4

    Protein attributes for KDM1A Gene

    Size:
    852 amino acids
    Molecular mass:
    92903 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Component of a RCOR/GFI/KDM1A/HDAC complex (PubMed:12032298, PubMed:11102443). Interacts directly with GFI1 and GFI1B. Interacts with INSM1 (By similarity). Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I (PubMed:12493763, PubMed:16140033, PubMed:16885027). In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it from the proteasome while PHF21A/BHC80 inhibits the demethylase activity (PubMed:16079794, PubMed:16956976). Interacts with the androgen receptor (AR) (PubMed:16079795). Interacts with ASXL1 (PubMed:19880879). Interacts with SNAI1 (via SNAG domain) (PubMed:20562920). Interacts (via AOD/Tower domain) with JADE2 (via C-terminus) (PubMed:25018020). Interacts with ESRRB; co-occupes the core set of ESRRB targets (By similarity).
    SequenceCaution:
    • Sequence=BAA25527.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM1A Gene

    Alternative splice isoforms for KDM1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM1A Gene

Protein Expression for KDM1A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for KDM1A Gene

  • Polyubiquitinated by JADE2; which leads to its proteasomal degradation.
  • Ubiquitination at isoforms=2744, Lys732, isoforms=2647, Lys492, isoforms=2374, isoforms=2355, Lys322, and isoforms=2280
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM1A Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for KDM1A Gene

Domains & Families for KDM1A Gene

Gene Families for KDM1A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for KDM1A Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for KDM1A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O60341

UniProtKB/Swiss-Prot:

KDM1A_HUMAN :
  • The SWIRM domain may act as an anchor site for a histone tail.
  • Belongs to the flavin monoamine oxidase family.
Domain:
  • The SWIRM domain may act as an anchor site for a histone tail.
Family:
  • Belongs to the flavin monoamine oxidase family.
genes like me logo Genes that share domains with KDM1A: view

Function for KDM1A Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for KDM1A Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that demethylates both Lys-4 (H3K4me) and Lys-9 (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of Thr-6 of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated Lys-370 of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.0 uM for H3 monomethyl-K4 {ECO:0000269 PubMed:16223729}; KM=4.2 uM for H3 dimethyl-K4 {ECO:0000269 PubMed:16223729}; KM=3.9 uM for H3 monomethyl-K4-monomethyl-K9 {ECO:0000269 PubMed:16223729}; KM=17.5 uM for monomethyl-K4-acetyl-K9 {ECO:0000269 PubMed:16223729};
UniProtKB/Swiss-Prot Induction:
Down-regulated during neural differentiation in neuroblastoma cancer.

Enzyme Numbers (IUBMB) for KDM1A Gene

Phenotypes From GWAS Catalog for KDM1A Gene

Gene Ontology (GO) - Molecular Function for KDM1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002039 p53 binding IPI 17805299
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA,IDA 16079795
GO:0004407 histone deacetylase activity TAS --
GO:0005515 protein binding IPI 16169070
genes like me logo Genes that share ontologies with KDM1A: view
genes like me logo Genes that share phenotypes with KDM1A: view

Human Phenotype Ontology for KDM1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for KDM1A Gene

MGI Knock Outs for KDM1A:

Animal Model Products

  • Taconic Biosciences Mouse Models for KDM1A

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM1A

Clone Products

  • Addgene plasmids for KDM1A

No data available for Transcription Factor Targets and HOMER Transcription for KDM1A Gene

Localization for KDM1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM1A Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM1A gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM1A Gene

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 IDA 16079795
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex ISS --
genes like me logo Genes that share ontologies with KDM1A: view

Pathways & Interactions for KDM1A Gene

genes like me logo Genes that share pathways with KDM1A: view

Gene Ontology (GO) - Biological Process for KDM1A Gene

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:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with KDM1A: view

No data available for SIGNOR curated interactions for KDM1A Gene

Drugs & Compounds for KDM1A Gene

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(19) Drugs for KDM1A Gene - From: ApexBio, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Tranylcypromine Approved, Investigational Pharma inhibitor 25
FAD Approved Pharma 0
OG-L002 Pharma LSD1 inhibitor,potent and specific 0
2,4-Pyridinedicarboxylic Acid Pharma Histone LSD inhibitor 0
CBB1003 Pharma 0

(4) Additional Compounds for KDM1A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(12) ApexBio Compounds for KDM1A Gene

Compound Action Cas Number
2,4-Pyridinedicarboxylic Acid Histone LSD inhibitor 499-80-9
CBB1003 1379573-88-2
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
genes like me logo Genes that share compounds with KDM1A: view

Drug Products

Transcripts for KDM1A Gene

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  3. Inhibitory RNA
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mRNA/cDNA for KDM1A Gene

(8) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(350) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for KDM1A Gene

Lysine (K)-specific demethylase 1A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM1A

Clone Products

  • Addgene plasmids for KDM1A

Alternative Splicing Database (ASD) splice patterns (SP) for KDM1A Gene

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:

Relevant External Links for KDM1A Gene

GeneLoc Exon Structure for
KDM1A
ECgene alternative splicing isoforms for
KDM1A

Expression for KDM1A Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM1A Gene

mRNA expression in normal human tissues for KDM1A Gene
mRNA expression by BioGPS for KDM1A GenemRNA expression by GTEx for KDM1A Gene

Protein differential expression in normal tissues from HIPED for KDM1A Gene

This gene is overexpressed in Serum (32.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for KDM1A Gene



Protein tissue co-expression partners for KDM1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KDM1A Gene:

KDM1A

SOURCE GeneReport for Unigene cluster for KDM1A Gene:

Hs.591518

mRNA Expression by UniProt/SwissProt for KDM1A Gene:

O60341-KDM1A_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for KDM1A Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Skin(4.3)
  • Blood(2.1)
  • Lung(2.1)
  • Eye(2)
  • Intestine(2)
genes like me logo Genes that share expression patterns with KDM1A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM1A Gene

Orthologs for KDM1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDM1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia KDM1A 34 33
  • 98.49 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia KDM1A 34 33
  • 94.13 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia KDM1A 34 33
  • 93.61 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia KDM1A 34
  • 93 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia AOF2 34
  • 91 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Kdm1a 33
  • 90.37 (n)
mouse
(Mus musculus)
 Mammalia Kdm1a 16 34 33
  • 88.97 (n)
chicken
(Gallus gallus)
 Aves KDM1A 34 33
  • 83.12 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia KDM1A 34
  • 91 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia kdm1a 33
  • 75.5 (n)
Str.3510 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.24726 33
zebrafish
(Danio rerio)
 Actinopterygii kdm1a 34 33
  • 73.94 (n)
 OneToOne
wufc51a02 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011661 33
  • 59.91 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Su(var)3-3 34 33
  • 56.59 (n)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea spr-5 33
  • 43.04 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons LDL2 33
  • 50.07 (n)
rice
(Oryza sativa)
 Liliopsida Os08g0143400 33
  • 49.2 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.9877 34
  • 52 (a)
 OneToOne
bread mold
(Neurospora crassa)
 Ascomycetes NCU09120 33
  • 45 (n)
Species where no ortholog for KDM1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM1A Gene

ENSEMBL:
Gene Tree for KDM1A (if available)
TreeFam:
Gene Tree for KDM1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDM1A: view image

Paralogs for KDM1A Gene

Paralogs for KDM1A Gene

(2) SIMAP similar genes for KDM1A Gene using alignment to 4 proteins:

  • KDM1A_HUMAN
  • F6S0T5_HUMAN
  • R4GMP9_HUMAN
  • R4GMQ1_HUMAN
genes like me logo Genes that share paralogs with KDM1A: view

Variants for KDM1A Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for KDM1A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs864309714 pathogenic, Cleft palate, psychomotor retardation, and distinctive facial features, Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728] 23,082,274(+) T/C coding_sequence_variant, missense_variant
rs864309715 pathogenic, Cleft palate, psychomotor retardation, and distinctive facial features, Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728] 23,068,566(+) G/A coding_sequence_variant, missense_variant
rs864309716 conflicting-interpretations-of-pathogenicity, Cleft palate, psychomotor retardation, and distinctive facial features, Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728] 23,077,232(+) A/G coding_sequence_variant, missense_variant
rs1000019170 -- 23,038,723(+) A/G intron_variant
rs1000026842 -- 23,025,365(+) TTTT/TT genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KDM1A Gene

Variant ID Type Subtype PubMed ID
esv3425192 CNV insertion 20981092
nsv6520 CNV insertion 18451855

Variation tolerance for KDM1A Gene

Residual Variation Intolerance Score: 7.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 15.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM1A Gene

Human Gene Mutation Database (HGMD)
KDM1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM1A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM1A Gene

Disorders for KDM1A Gene

MalaCards: The human disease database

(4) MalaCards diseases for KDM1A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cleft palate, psychomotor retardation, and distinctive facial features
  • cprf
kbg syndrome
  • kbgs
neuroblastoma
  • neuroblastoma, susceptibility to
ewing sarcoma
  • es
- elite association - COSMIC cancer census association via MalaCards
Search KDM1A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

KDM1A_HUMAN
  • Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]: A syndrome characterized by cleft palate, developmental delay, psychomotor retardation, and facial dysmorphic features including a prominent forehead, slightly arched eyebrows, elongated palpebral fissures, a wide nasal bridge, thin lips, and widely spaced teeth. Cleft palate is a congenital fissure of the soft and/or hard palate, due to faulty fusion. {ECO:0000269 PubMed:23020937, ECO:0000269 PubMed:24838796, ECO:0000269 PubMed:26656649}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for KDM1A

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with KDM1A: view

No data available for Genatlas for KDM1A Gene

Publications for KDM1A Gene

  1. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PMID: 12493763) Hakimi MA … Shiekhattar R (The Journal of biological chemistry 2003) 2 3 4 22 58
  2. p53 is regulated by the lysine demethylase LSD1. (PMID: 17805299) Huang J … Berger SL (Nature 2007) 3 4 22 58
  3. Solution structure of the SWIRM domain of human histone demethylase LSD1. (PMID: 16531230) Tochio N … Yokoyama S (Structure (London, England : 1993) 2006) 3 4 22 58
  4. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. (PMID: 16885027) Yang M … Yu H (Molecular cell 2006) 3 4 22 58
  5. Crystal structure of human histone lysine-specific demethylase 1 (LSD1). (PMID: 16956976) Chen Y … Lei M (Proceedings of the National Academy of Sciences of the United States of America 2006) 3 4 22 58

Products for KDM1A Gene

  • Addgene plasmids for KDM1A

Sources for KDM1A Gene