ENSG00000004487


Homo sapiens

Features
Gene ID: ENSG00000004487
  
Biological name :KDM1A
  
Synonyms : KDM1A / lysine demethylase 1A / O60341
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 1
Strand: 1
Band: p36.12
Gene start: 23019443
Gene end: 23083689
  
Corresponding Affymetrix probe sets: 212348_s_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000349049
Ensembl peptide - ENSP00000383042
Ensembl peptide - ENSP00000473294
Ensembl peptide - ENSP00000473297
NCBI entrez gene - 23028     See in Manteia.
OMIM - 609132
RefSeq - XM_017000720
RefSeq - NM_001009999
RefSeq - NM_015013
RefSeq - XM_006710474
RefSeq - XM_017000716
RefSeq - XM_017000717
RefSeq - XM_017000718
RefSeq - XM_017000719
RefSeq - XM_005245786
RefSeq - XM_006710472
RefSeq - XM_006710473
RefSeq Peptide - NP_055828
RefSeq Peptide - NP_001009999
swissprot - O60341
swissprot - R4GMP9
swissprot - R4GMQ1
Ensembl - ENSG00000004487
  
Related genetic diseases (OMIM): 616728 - Cleft palate, psychomotor retardation, and distinctive facial features, 616728
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 kdm1aENSDARG00000060679Danio rerio
 KDM1AENSGALG00000033469Gallus gallus
 Kdm1aENSMUSG00000036940Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
KDM1B / Q8NB78 / lysine demethylase 1BENSG0000016509721
SMOX / Q9NWM0 / spermine oxidaseENSG0000008882616
PAOX / Q6QHF9 / polyamine oxidaseENSG0000014883216


Protein motifs (from Interpro)
Interpro ID Name
 IPR002937  Amine oxidase
 IPR007526  SWIRM domain
 IPR009057  Homeobox-like domain superfamily
 IPR017366  Histone lysine-specific demethylase
 IPR036188  FAD/NAD(P)-binding domain superfamily
 IPR036388  Winged helix-like DNA-binding domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000122 negative regulation of transcription by RNA polymerase II ISS
 biological_processGO:0000380 alternative mRNA splicing, via spliceosome IEA
 biological_processGO:0006325 chromatin organization IEA
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0006357 regulation of transcription by RNA polymerase II IMP
 biological_processGO:0006482 protein demethylation IMP
 biological_processGO:0007275 multicellular organism development IEA
 biological_processGO:0007596 blood coagulation TAS
 biological_processGO:0010569 regulation of double-strand break repair via homologous recombination IMP
 biological_processGO:0010976 positive regulation of neuron projection development IEA
 biological_processGO:0014070 response to organic cyclic compound IEA
 biological_processGO:0016575 histone deacetylation IEA
 biological_processGO:0021987 cerebral cortex development IEA
 biological_processGO:0032091 negative regulation of protein binding IMP
 biological_processGO:0033169 histone H3-K9 demethylation IDA
 biological_processGO:0033184 positive regulation of histone ubiquitination IMP
 biological_processGO:0034644 cellular response to UV IDA
 biological_processGO:0034720 histone H3-K4 demethylation IDA
 biological_processGO:0035563 positive regulation of chromatin binding IEA
 biological_processGO:0042551 neuron maturation IEA
 biological_processGO:0043392 negative regulation of DNA binding IC
 biological_processGO:0043433 negative regulation of DNA-binding transcription factor activity IMP
 biological_processGO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator IMP
 biological_processGO:0045793 positive regulation of cell size IEA
 biological_processGO:0045892 negative regulation of transcription, DNA-templated IDA
 biological_processGO:0045944 positive regulation of transcription by RNA polymerase II IEA
 biological_processGO:0046098 guanine metabolic process IEA
 biological_processGO:0051091 positive regulation of DNA-binding transcription factor activity IDA
 biological_processGO:0055001 muscle cell development ISS
 biological_processGO:0055114 oxidation-reduction process IEA
 biological_processGO:0060992 response to fungicide IEA
 biological_processGO:0071320 cellular response to cAMP IEA
 biological_processGO:0071480 cellular response to gamma radiation IMP
 biological_processGO:1902166 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
 biological_processGO:1903827 regulation of cellular protein localization IMP
 cellular_componentGO:0000784 nuclear chromosome, telomeric region IDA
 cellular_componentGO:0000790 nuclear chromatin IEA
 cellular_componentGO:0005634 nucleus IDA
 cellular_componentGO:0005654 nucleoplasm TAS
 cellular_componentGO:0005667 transcription factor complex ISS
 cellular_componentGO:0032991 protein-containing complex IDA
 cellular_componentGO:1990391 DNA repair complex IDA
 molecular_functionGO:0002039 p53 binding IPI
 molecular_functionGO:0003677 DNA binding IEA
 molecular_functionGO:0003682 chromatin binding IEA
 molecular_functionGO:0004407 histone deacetylase activity TAS
 molecular_functionGO:0005515 protein binding IPI
 molecular_functionGO:0008134 transcription factor binding IDA
 molecular_functionGO:0016491 oxidoreductase activity IEA
 molecular_functionGO:0019899 enzyme binding IPI
 molecular_functionGO:0030374 nuclear receptor transcription coactivator activity IMP
 molecular_functionGO:0032451 demethylase activity IMP
 molecular_functionGO:0032452 histone demethylase activity IDA
 molecular_functionGO:0032453 histone demethylase activity (H3-K4 specific) IDA
 molecular_functionGO:0032454 histone demethylase activity (H3-K9 specific) IDA
 molecular_functionGO:0034648 histone demethylase activity (H3-dimethyl-K4 specific) IDA
 molecular_functionGO:0042162 telomeric DNA binding IMP
 molecular_functionGO:0043426 MRF binding IDA
 molecular_functionGO:0044212 transcription regulatory region DNA binding ISS
 molecular_functionGO:0050660 flavin adenine dinucleotide binding IDA
 molecular_functionGO:0050681 androgen receptor binding IDA
 molecular_functionGO:0061752 telomeric repeat-containing RNA binding IDA


Pathways (from Reactome)
Pathway description
HDACs deacetylate histones
HDMs demethylate histones
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
Regulation of PTEN gene transcription
Estrogen-dependent gene expression
Factors involved in megakaryocyte development and platelet production


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000006 Autosomal dominant inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele." [HPO:curators]
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 HP:0000028 Cryptorchidism "Absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the testis." [HPO:curators]
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 HP:0000041 Chordee "A condition in which the head of the penis curves downward." [HPO:curators]
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 HP:0000219 Thin upper lip 
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 HP:0000248 Brachycephaly "Brachycephaly refers to a short, wide head, which is often caused by premature closure of both coronal sutures." [HPO:curators]
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 HP:0000256 Macrocephaly "The presence of an abnormally large `skull` (FMA:46565)." [HPO:probinson]
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 HP:0000431 Broad nasal bridge "Increased horizontal dimension of the upper, bony part of the nose." [HPO:curators]
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 HP:0000463 Nares, anteverted "Anteriorly-facing nostrils viewed with the head in the Frankfurt horizontal and the eyes of the observer level with the eyes of the subject." [pmid:19152422]
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 HP:0000494 Downward slanting palpebral fissures 
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 HP:0000508 Ptosis "Drooping of the eyelid." [HPO:curators]
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 HP:0000577 Exotropia 
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 HP:0000592 Blue sclerae 
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 HP:0000657 Oculomotor apraxia 
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 HP:0000664 Synophrys "Fusion of the left and right `eyebrow` (FMA:54237)." [HPO:probinson]
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 HP:0000687 Widely spaced teeth 
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 HP:0000750 Impaired language development 
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 HP:0001182 Tapered fingers 
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 HP:0001263 Developmental retardation "A delay in the achievement of motor or mental milestones manifested prior to age 18 and generally associated with lifelong mental and/or physical impairments." [HPO:curators]
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 HP:0001270 Motor retardation 
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 HP:0001290 Generalized hypotonia "Generalized muscular hypotonia (abnormally low muscle tone)." [HPO:curators]
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 HP:0001382 Joint hypermobility "The ability of a joint to move beyond its normal range of motion." [HPO:curators]
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 HP:0001800 Hypoplastic toenails "Underdeveloped toenails." [HPO:curators]
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 HP:0002007 Frontal bossing "The presence of an unusually prominent forehead." [HPO:curators]
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 HP:0002019 Constipation 
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 HP:0002079 Hypoplasia of the corpus callosum "Underdevelopment of the corpus callosum." [HPO:curators]
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 HP:0002144 Tethered cord "During normal embryological development, the spinal cord first occupies the entire length of the vertebral column but goes on to assume a position at the level of L1 due to differential growth of the conus medullaris and the vertebral column. The filum terminale is a slender, threadlike structure that remains after the normal regression of the distal embryonic spinal cord and attaches the spinal cord to the coccyx. A tethered cord results if there is a thickened rope-like filum terminale which anchors the cord at the level of L2 or below, potentially causing neurologic signs owing to abnormal tension on the spinal cord." [HPO:curators]
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 HP:0002188 Delayed myelination 
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 HP:0002553 Arched eyebrows 
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 HP:0002558 Supernumerary nipples 
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 HP:0002714 Downturned corners of mouth "A morphological `abnormality of the mouth` (HP:0000153) in which the `angle of the mouth` (FMA:77269) is downturned." [HPO:probinson]
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 HP:0003396 Syringomyelia 
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 HP:0003468 Abnormalities of the vertebrae 
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 HP:0004209 Clinodactyly of the 5th finger "Clinodactyly refers to a bending or curvature of the `fifth finger` (FMA:24949) in the radial direction (i.e., towards the 4th finger)." [HPO:curators]
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 HP:0004322 Decreased body height "A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms)." [HPO:curators]
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 HP:0006895 Lower limb hypertonia 
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 HP:0009778 Hypoplastic/small thumb 
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 HP:0011220 Prominent forehead "Forward prominence of the entire forehead, due to protrusion of the frontal bone." [pmid:19125436]
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 HP:0011968 Feeding difficulties "Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it." [ISCA:eriggs]
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 HP:0012430 Cerebral white matter hypoplasia "Underdevelopment of the `cerebral white matter` (FMA:241998)." [HPO:probinson]
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000091831 ESR1 / P03372 / estrogen receptor 1  / reaction / complex
 ENSG00000136997 MYC / P01106 / MYC proto-oncogene, bHLH transcription factor  / complex / reaction
 ENSG00000132475 H3F3B / P84243 / H3 histone family member 3B  / complex / reaction
 ENSG00000084093 REST / Q13127 / RE1 silencing transcription factor  / complex
 ENSG00000180573 Q93077 / HIST1H2AC / histone cluster 1 H2A family member c  / reaction / complex
 ENSG00000183598 Q71DI3 / HIST2H3D / histone cluster 2 H3 family member d  / reaction / complex
 ENSG00000276180 P62805 / HIST1H4I / histone cluster 1 H4 family member i  / complex / reaction
 ENSG00000169083 AR / P10275 / androgen receptor  / complex / reaction
 ENSG00000123143 PKN1 / Q16512 / protein kinase N1  / reaction / complex
 ENSG00000275714 P68431 / HIST1H3A / histone cluster 1 H3 family member a  / complex / reaction
 ENSG00000089902 RCOR1 / Q9UKL0 / REST corepressor 1  / complex
 ENSG00000196591 HDAC2 / Q92769 / histone deacetylase 2  / complex
 ENSG00000116478 HDAC1 / Q13547 / histone deacetylase 1  / complex






 

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