ENSG00000126012


Homo sapiens

Features
Gene ID: ENSG00000126012
  
Biological name :KDM5C
  
Synonyms : KDM5C / lysine demethylase 5C / P41229
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: X
Strand: -1
Band: p11.22
Gene start: 53191321
Gene end: 53225422
  
Corresponding Affymetrix probe sets: 202383_at (Human Genome U133 Plus 2.0 Array)   239207_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000445176
Ensembl peptide - ENSP00000407277
Ensembl peptide - ENSP00000409757
Ensembl peptide - ENSP00000344004
Ensembl peptide - ENSP00000364528
Ensembl peptide - ENSP00000364532
Ensembl peptide - ENSP00000364550
Ensembl peptide - ENSP00000385394
NCBI entrez gene - 8242     See in Manteia.
OMIM - 314690
RefSeq - XM_017029889
RefSeq - XM_011530824
RefSeq - XM_011530825
RefSeq - XM_011530826
RefSeq - XM_011530827
RefSeq - XM_011530828
RefSeq - XM_011530829
RefSeq - XM_011530830
RefSeq - XM_011530831
RefSeq - XM_017029886
RefSeq - XM_017029887
RefSeq - XM_017029888
RefSeq - NM_001146702
RefSeq - NM_001282622
RefSeq - NM_001353981
RefSeq - NM_001353982
RefSeq - NM_001353984
RefSeq - NM_004187
RefSeq - XM_005262035
RefSeq Peptide - NP_001340907
RefSeq Peptide - NP_001340913
RefSeq Peptide - NP_004178
RefSeq Peptide - NP_001140174
RefSeq Peptide - NP_001269551
RefSeq Peptide - NP_001340910
RefSeq Peptide - NP_001340911
swissprot - F8WF56
swissprot - F8WDK1
swissprot - P41229
swissprot - F8W7H7
Ensembl - ENSG00000126012
  
Related genetic diseases (OMIM): 300534 - Mental retardation, X-linked, syndromic, Claes-Jensen type, 300534

This gene has been taged as a transcription factor by TFT
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
 kdm5cENSDARG00000006124Danio rerio
 Kdm5cENSMUSG00000025332Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
KDM5D / Q9BY66 / lysine demethylase 5DENSG0000001281785
KDM5A / P29375 / lysine demethylase 5AENSG0000007361453
KDM5B / Q9UGL1 / lysine demethylase 5BENSG0000011713946
JARID2 / Q92833 / jumonji and AT-rich interaction domain containing 2ENSG0000000808312


Protein motifs (from Interpro)
Interpro ID Name
 IPR001606  ARID DNA-binding domain
 IPR001965  Zinc finger, PHD-type
 IPR003347  JmjC domain
 IPR003349  JmjN domain
 IPR004198  Zinc finger, C5HC2-type
 IPR011011  Zinc finger, FYVE/PHD-type
 IPR013083  Zinc finger, RING/FYVE/PHD-type
 IPR013637  Lysine-specific demethylase-like domain
 IPR019786  Zinc finger, PHD-type, conserved site
 IPR019787  Zinc finger, PHD-finger
 IPR036431  ARID DNA-binding domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0006325 chromatin organization IEA
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0009636 response to toxic substance IEA
 biological_processGO:0034720 histone H3-K4 demethylation IDA
 biological_processGO:0045892 negative regulation of transcription, DNA-templated ISS
 biological_processGO:0048511 rhythmic process IEA
 biological_processGO:0055114 oxidation-reduction process IEA
 cellular_componentGO:0005634 nucleus IDA
 cellular_componentGO:0005654 nucleoplasm TAS
 cellular_componentGO:0005829 cytosol IDA
 molecular_functionGO:0003677 DNA binding IEA
 molecular_functionGO:0005515 protein binding IPI
 molecular_functionGO:0008270 zinc ion binding IDA
 molecular_functionGO:0016491 oxidoreductase activity IEA
 molecular_functionGO:0032452 histone demethylase activity TAS
 molecular_functionGO:0032453 histone demethylase activity (H3-K4 specific) IDA
 molecular_functionGO:0046872 metal ion binding IEA
 molecular_functionGO:0051213 dioxygenase activity IEA


Pathways (from Reactome)
Pathway description
HDMs demethylate histones


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 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]
Show

 HP:0000054 Micropenis 
Show

 HP:0000218 High palate "Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective)." [pmid:19125428]
Show

 HP:0000219 Thin upper lip 
Show

 HP:0000221 Furrowed tongue "Accentuation of the grooves on the dorsal surface of the tongue." [pmid:19125428]
Show

 HP:0000252 Microcephaly "Microcephaly is a neurodevelopmental disorder in which the circumference of the head is more than two standard deviations smaller than the age- and gender-dependent norm." [HPO:curators]
Show

 HP:0000256 Macrocephaly "The presence of an abnormally large `skull` (FMA:46565)." [HPO:probinson]
Show

 HP:0000297 Facial hypotonia 
Show

 HP:0000303 Mandibular prognathia "Abnormal prominence of the chin related to an abnormally long mandible." [HPO:curators]
Show

 HP:0000319 Flat philtrum 
Show

 HP:0000327 Hypoplasia of the maxilla "Underdevelopment of the `Maxilla` (FMA:9711)." [HPO:probinson]
Show

 HP:0000347 Mandibular hypoplasia "Underdevelopment of the mandible." [HPO:curators]
Show

 HP:0000350 Small forehead "The presence of a forehead that is abnormally small." [HPO:curators]
Show

 HP:0000400 Large ears 
Show

 HP:0000411 Protruding ears 
Show

 HP:0000426 Prominent nasal bridge 
Show

 HP:0000486 Strabismus "Strabismus (also known as squint) is a condition in which the eyes are not properly aligned with each other." [HPO:curators]
Show

 HP:0000490 Deep set eyes 
Show

 HP:0000540 Hypermetropia 
Show

 HP:0000545 Myopia 
Show

 HP:0000582 Upslanting palpebral fissures 
Show

 HP:0000699 Diastema 
Show

 HP:0000711 Restlessness 
Show

 HP:0000717 Autism 
Show

 HP:0000718 Aggressive behavior "Aggressive behavior can denote verbal aggression, physical aggression against objects, physical aggression against people, and may also include aggression towards oneself." [HPO:curators]
Show

 HP:0000744 Low frustration tolerance 
Show

 HP:0000750 Impaired language development 
Show

 HP:0000767 Pectus excavatum "A defect of the chest wall characterized by a depression of the sternum, giving the chest ("pectus") a caved-in ("excavatum") appearance." [HPO:curators]
Show

 HP:0001156 Brachydactyly 
Show

 HP:0001176 Large hands 
Show

 HP:0001182 Tapered fingers 
Show

 HP:0001250 Seizures "Seizures are an intermittent `abnormality of the central nervous system` (FMA:HP:0002011) due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements." [HPO:probinson]
Show

 HP:0001257 Spasticity "A motor disorder characterized by a velocity-dependent increase in tonic stretch reflexes with increased muscle tone, exaggerated (hyperexcitable) tendon reflexes." [HPO:curators]
Show

 HP:0001347 Hyperreflexia "The presence of overactive or overresponsive reflexes." [HPO:curators]
Show

 HP:0001419 X-linked recessive inheritance "A mode of inheritance that is observed for recessive traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked recessive disorders manifest in males (who have one copy of the X chromosome and are thus hemizygotes), but generally not in female heterozygotes who have one mutant and one normal allele." [HPO:curators]
Show

 HP:0001762 Talipes equinovarus "Also called clubfoot typically has 4 main components: inversion and adduction of the forefoot; inversion of the heel and hindfoot; equinus (limitation of extension) of the ankle and subtalar joint; and internal rotation of the leg. Clubfoot is a complex, multifactorial deformity with genetic and intrauterine factors. One popular theory postulates that a clubfoot is a result of intrauterine maldevelopment of the talus that leads to adduction and plantarflexion of the foot. On radiographic projection a clubfoot can be noted as parallel axes of talus and calcaneus." [HPO:curators]
Show

 HP:0001773 Short, broad feet "Abnormally short and wide feet." [HPO:curators]
Show

 HP:0002229 Alopecia areata 
Show

 HP:0002362 Shuffling gait 
Show

 HP:0002395 Lower limb hyperreflexia 
Show

 HP:0002705 High, narrow palate "The presence of a high and narrow palate." [HPO:curators]
Show

 HP:0003487 Babinski sign "Upturning of the big toe (and sometimes fanning of the other toes) in response to stimulation of the sole of the foot. If the Babinski sign is present it can indicate damage to the corticospinal tract." [HPO:curators]
Show

 HP:0004279 Hypoplastic hand 
Show

 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]
Show

 HP:0006887 Mental retardation, progressive "Mental retardation is defined as a decreased intelligence quotient of varying degree. The term progressive mental retardation should be used if intelligence decreases/deteriorates over time." [HPO:curators]
Show

 HP:0006895 Lower limb hypertonia 
Show

 HP:0007020 Progressive spastic paraplegia 
Show

 HP:0007565 Multiple cafe-au-lait spots 
Show

 HP:0008124 Talipes calcaneovarus 
Show

 HP:0008734 Decreased testicular size 
Show

 HP:0008944 Distal lower limb muscle weakness and atrophy "Amyotrophy of distal lower leg muscles with resultant weakness." [HPO:curators]
Show

 HP:0009882 Hypoplasia of the distal phalanges of the hand 
Show

 HP:0010864 Mental retardation, severe "Moderate mental retardation is defined as an intelligence quotient (IQ) in the range of 20-34." [HPO:probinson]
Show

 HP:0030084 Clinodactyly "An angulation of a digit at an interphalangeal joint in the plane of the palm (finger) or sole (toe)." [pmid:16252026]
Show

 HP:0100490 Camptodactyly (hands) "Contractures of one ore more joints of the fingers." [HPO:sdoelken]
Show

  


Interacting proteins (from Reactome)
Interactor ID Name Interaction type
No match






 

0 s.

 
External programs and data are copyrighted by and are the property of their respective authors.
The Manteia system, data and analyses are provided "as is" with no warranties, expressed or implied as to capabilities or accuracy. User assumes the entire risk as to the results and performance of the software, data and documentation


                   


© Olivier Tassy / Olivier Pourquie 2007-2024
contact: otassy@igbmc.fr