Human Gene CDKL5 (ENST00000623535.2)
  Description: Homo sapiens cyclin dependent kinase like 5 (CDKL5), transcript variant III, mRNA. (from RefSeq NM_001323289)
RefSeq Summary (NM_001323289): This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Mutations in this gene have been associated with X-linked infantile spasm syndrome (ISSX), also known as X-linked West syndrome, and Rett syndrome (RTT). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000623535.2
Gencode Gene: ENSG00000008086.13
Transcript (Including UTRs)
   Position: hg38 chrX:18,425,608-18,640,196 Size: 214,589 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg38 chrX:18,507,097-18,628,757 Size: 121,661 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:18,425,608-18,640,196)mRNA (may differ from genome)Protein (960 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cyclin-dependent kinase-like 5; EC=; AltName: Full=Serine/threonine-protein kinase 9;
FUNCTION: Mediates phosphorylation of MECP2.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SUBUNIT: Interacts with MECP2.
TISSUE SPECIFICITY: Expressed in brain, lung, kidney, prostate, ovary, placenta, pancreas and testis.
PTM: Autophosphorylated.
DISEASE: Note=Chromosomal aberrations involving CDKL5 are found in patients manifesting early-onset seizures and spams and psychomotor impairment. Translocation t(X;6)(p22.3;q14); translocation t(X;7)(p22.3;p15).
DISEASE: Defects in CDKL5 are a cause of epileptic encephalopathy early infantile type 2 (EIEE2) [MIM:300672]; also known as atypical CDKL5-related Rett syndrome. EIEE2 is a severe form of epilepsy characterized by seizures or spasms beginning in infancy. Patients manifest features resembling Rett syndrome such as microcephaly, lack of speech development, stereotypic hand movements.
SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
SIMILARITY: Contains 1 protein kinase domain.
CAUTION: It is uncertain whether Met-1 or Met-10 is the initiator.
SEQUENCE CAUTION: Sequence=CAA61445.1; Type=Frameshift; Positions=415;
WEB RESOURCE: Name=GeneReviews; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: CDKL5
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 2* (1331), rett syndrome* (573), autistic disorder* (406), focal epilepsy* (285), angelman syndrome* (234), west syndrome* (122), epileptic encephalopathy, early infantile, 15* (116), cdkl5-related angelman-like syndrome* (100), infantile epileptic encephalopathy (21), encephalopathy (18), gait apraxia (9), early myoclonic encephalopathy (8), mental retardation, x-linked syndromic, christianson type (8), aicardi syndrome (7), pitt-hopkins syndrome (6), infancy electroclinical syndrome (5), epileptic encephalopathy, early infantile, 9 (5), seizure disorder (3), pervasive developmental disorder (2), microcephaly (1), epileptic encephalopathy, early infantile, 6 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.99 RPKM in Testis
Total median expression: 33.62 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -91.60250-0.366 Picture PostScript Text
3' UTR -3134.3011439-0.274 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain

ModBase Predicted Comparative 3D Structure on O76039
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0048365 Rac GTPase binding
GO:0004693 cyclin-dependent protein serine/threonine kinase activity

Biological Process:
GO:0001764 neuron migration
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0043547 positive regulation of GTPase activity
GO:0045773 positive regulation of axon extension
GO:0046777 protein autophosphorylation
GO:0050773 regulation of dendrite development
GO:0050775 positive regulation of dendrite morphogenesis
GO:0060999 positive regulation of dendritic spine development
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0032587 ruffle membrane
GO:0032839 dendrite cytoplasm
GO:0036064 ciliary basal body
GO:0044294 dendritic growth cone
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0097542 ciliary tip

-  Descriptions from all associated GenBank mRNAs
  BC010966 - Homo sapiens cyclin-dependent kinase-like 5, mRNA (cDNA clone IMAGE:4294753), with apparent retained intron.
AK307444 - Homo sapiens cDNA, FLJ97392.
AY217744 - Homo sapiens serine/threonine kinase 9 (CDKL5) mRNA, complete cds.
Y15057 - Homo sapiens mRNA for STK9 protein.
BC036091 - Homo sapiens cyclin-dependent kinase-like 5, mRNA (cDNA clone IMAGE:5295038), containing frame-shift errors.
AB527333 - Synthetic construct DNA, clone: pF1KE0065, Homo sapiens CDKL5 gene for cyclin-dependent kinase-like protein 5, without stop codon, in Flexi system.
BC152846 - Synthetic construct Homo sapiens clone IMAGE:100016109, MGC:184200 cyclin-dependent kinase-like 5 (CDKL5) mRNA, encodes complete protein.
HQ171445 - Homo sapiens cyclin dependent kinase 5 transcript variant (CDKL5) mRNA, complete cds, alternatively spliced.
X89059 - H.sapiens mRNA for unknown protein expressed in macrophages.
JD053527 - Sequence 34551 from Patent EP1572962.
JD534307 - Sequence 515331 from Patent EP1572962.
AK056879 - Homo sapiens cDNA FLJ32317 fis, clone PROST2003340, weakly similar to SERINE/THREONINE-PROTEIN KINASE 9 (EC 2.7.1.-).
DQ574677 - Homo sapiens piRNA piR-42789, complete sequence.
JD222883 - Sequence 203907 from Patent EP1572962.
JD497722 - Sequence 478746 from Patent EP1572962.
JD047202 - Sequence 28226 from Patent EP1572962.
JD238290 - Sequence 219314 from Patent EP1572962.
JD047202 - Sequence 28226 from Patent EP1572962.
AK094443 - Homo sapiens cDNA FLJ37124 fis, clone BRACE2022633.

-  Other Names for This Gene
  Alternate Gene Symbols: CDKL5_HUMAN, ENST00000623535.1, G9B9X4, NM_001323289, O76039, Q14198, Q5H985, Q8IYC7, Q9UJL6, STK9, uc064yfi.1, uc064yfi.2
UCSC ID: ENST00000623535.2
RefSeq Accession: NM_001323289
Protein: O76039 (aka CDKL5_HUMAN or STK9_HUMAN)
CCDS: CCDS83458.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.