KDM1A (lysine demethylase 1A)

Gene
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
23028
Gene name Gene Name - the full gene name approved by the HGNC.
Lysine demethylase 1A
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
KDM1A
Synonyms (NCBI Gene) Gene synonyms aliases
AIMAH3, AOF2, BHC110, CPRF, KDM1, LSD1
Chromosome Chromosome number
1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
1p36.12
Summary Summary of gene provided in NCBI Entrez 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. Altern
SNPs SNP information provided by dbSNP.
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.
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 assay, Microarray, qRT-PCR, Western blot 20682795
MIRT004579 hsa-miR-137 Luciferase reporter assay, Microarray, qRT-PCR, Western 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 information of associated ontologies with gene provided by GO database.
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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
609132 29079 ENSG00000004487
Protein
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID 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
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (2)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Cleft Palate, Psychomotor Retardation, And Distinctive Facial Features palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome rs864309714, rs864309715, rs864309716 N/A
Mental retardation intellectual disability rs1553130904 N/A
Show/Hide Unknown Diseases (1)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Developmental Delay global developmental delay N/A N/A ClinVar
Show/Hide Text Mining Associations (101)
Associations from Text Mining Disease 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