Gene Gene information from NCBI Gene database.
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
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
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
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.
MIM HGNC e!Ensembl
609132 29079 ENSG00000004487
Protein Protein information from UniProt database.
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
PYNSDTVLVHRVHSYLERHGLINF
GIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSF
GMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKC
PLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLV
KSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFAN
ATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGC
EVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLN
KVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPI
TPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIA
DQFLGAMYTLPRQA
TPGVPAQQSPSM
Sequence length 852
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
24
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Intellectual disability Likely pathogenic rs1553130904 RCV001527312
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay Likely pathogenic rs2124523419 RCV002274347
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome Likely pathogenic; Pathogenic rs2124523419, rs864309714, rs864309715, rs864309716 RCV005869769
RCV000203273
RCV000203263
RCV000203268
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Squamous cell lung carcinoma Likely pathogenic rs2124523419 RCV005930208
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
CARCINOMA, NON-SMALL-CELL LUNG CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CLEFT PALATE, PSYCHOMOTOR RETARDATION, AND DISTINCTIVE FACIAL FEATURES CTD, Disgenet, HPO
CTD, Disgenet, HPO
CTD, Disgenet, HPO
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute Erythroblastic Leukemia Erythroblastic Leukemia BEFREE 27903753, 31676828
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 29502954, 30568590
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 30679800, 30992567
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 28722470, 31576004
★☆☆☆☆
Found in Text Mining only
Acute Undifferentiated Leukemia Leukemia BEFREE 22464800, 26837761
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of prostate Prostate adenocarcinoma BEFREE 30828079
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 31040714
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 24252778, 30659187
★☆☆☆☆
Found in Text Mining only
Anemia, Sickle Cell Anemia BEFREE 28238805, 30067082
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 32908449 Associate
★☆☆☆☆
Found in Text Mining only