KDM1A (lysine demethylase 1A)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID 23028
Gene name Lysine demethylase 1A
Gene symbol KDM1A
Synonyms (NCBI Gene)
AIMAH3AOF2BHC110CPRFKDM1LSD1
Chromosome 1
Chromosome location 1p36.12
Summary 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. Altern
SNPs SNP information provided by dbSNP.
5
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (5)
SNP ID Visualize variation Clinical significance Consequence
rs864309714 T>C Pathogenic Missense variant, coding sequence variant
rs864309715 G>A Pathogenic Missense variant, coding sequence variant
rs864309716 A>G Pathogenic Missense variant, coding sequence variant
rs1553129293 G>T Likely-pathogenic Coding sequence variant, stop gained
rs1553130904 A>G Likely-pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
36
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (36)
miRTarBase ID miRNA Experiments Reference
MIRT004579 hsa-miR-137 Luciferase reporter assayMicroarrayqRT-PCRWestern blot 20682795
MIRT004579 hsa-miR-137 Luciferase reporter assayMicroarrayqRT-PCRWestern blot 20682795
MIRT004579 hsa-miR-137 Luciferase reporter assay 23400681
MIRT020665 hsa-miR-155-5p Proteomics 18668040
MIRT046281 hsa-miR-23b-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
99
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (99)
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 19497860
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IMP 17805299, 35013237
GO:0000122 Process Negative regulation of transcription by RNA polymerase II ISS
GO:0000781 Component Chromosome, telomeric region IDA 24529708
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
609132 29079 ENSG00000004487
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O60341
Protein name Lysine-specific histone demethylase 1A (EC 1.14.99.66) (BRAF35-HDAC complex protein BHC110) (Flavin-containing amine oxidase domain-containing protein 2) ([histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A)
Protein function Histone demethylase that can demethylate both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context (PubMed:15620353, PubMed:15811342, PubMed:16079794, PubMed:16079795, Pu
PDB 2COM , 2DW4 , 2EJR , 2H94 , 2HKO , 2IW5 , 2L3D , 2UXN , 2UXX , 2V1D , 2X0L , 2XAF , 2XAG , 2XAH , 2XAJ , 2XAQ , 2XAS , 2Y48 , 2Z3Y , 2Z5U , 3ABT , 3ABU , 3ZMS , 3ZMT , 3ZMU , 3ZMV , 3ZMZ , 3ZN0 , 3ZN1 , 4BAY , 4CZZ , 4KUM , 4UV8 , 4UV9 , 4UVA , 4UVB , 4UVC , 4UXN , 4XBF , 5AFW , 5H6Q , 5H6R , 5IT3 , 5L3B , 5L3C , 5L3D , 5L3E , 5L3F , 5L3G , 5LBQ , 5LGN
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF04433 SWIRM 177 → 264 SWIRM domain Domain
PF01593 Amino_oxidase 288 → 826 Flavin containing amine oxidoreductase Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:16079795}.
Sequence 
MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTP
RKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEY
REMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQ
SRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEA
PYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSF
GMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKC
PLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLV
KSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFAN
ATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGC
EVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLN
KVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPI
TPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQA
TPGVPAQQSPSM
Sequence length 852
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG  Reactome
  Thermogenesis   HDACs deacetylate histones
HDMs demethylate histones
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
Estrogen-dependent gene expression
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
Factors involved in megakaryocyte development and platelet production
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
67
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (4)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual disability Likely pathogenic rs1553130904 RCV001527312
Neurodevelopmental delay Likely pathogenic rs2124523419 RCV002274347
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome Likely pathogenic; Pathogenic rs2124523419, rs864309714, rs864309715, rs864309716 RCV005869769
RCV000203273
RCV000203263
RCV000203268
Squamous cell lung carcinoma Likely pathogenic rs2124523419 RCV005930208
Show/Hide Unknown Diseases (12)
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Cervical cancer Benign rs149897862 RCV005928436
Cholangiocarcinoma Benign rs12078443 RCV005915803
Familial cancer of breast Benign rs149897862 RCV005928435
Gastric cancer Benign rs149897862 RCV005928437
Show/Hide Text Mining Associations (101)
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Acth Independent Macronodular Adrenal Hyperplasia Associate 34906447
Adenocarcinoma Associate 30828079, 32403054
Adenocarcinoma of Lung Associate 28860622, 30760542
Arthritis Rheumatoid Associate 32908449
Ataxia Telangiectasia Associate 34980595
Autism Spectrum Disorder Associate 33712455
Brain Neoplasms Associate 23612572, 23928305
Breast Neoplasms Associate 21452019, 21805138, 22533360, 23354309, 23699411, 24075993, 25139823, 25679396, 26833707, 27212032, 27325688, 28931919, 28947780, 29190800, 29311580
View all (7 more)
Calcinosis Cutis Associate 28346812
Carcinogenesis Associate 23900215, 23922913, 25674267, 25956476, 26062444, 26166558, 28121627, 36368958, 37540490