Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CDKL5 Gene

Aliases for CDKL5 Gene

  • Cyclin Dependent Kinase Like 5 2 3 5
  • Serine/Threonine-Protein Kinase 9 3 4
  • Cyclin-Dependent Kinase-Like 5 2 3
  • Serine/Threonine Kinase 9 2 3
  • STK9 3 4
  • Cyclin Dependent Kinase 5 Transcript 3
  • EC 4
  • CFAP247 3
  • EIEE2 3
  • ISSX 3

External Ids for CDKL5 Gene

Previous HGNC Symbols for CDKL5 Gene

  • STK9

Previous GeneCards Identifiers for CDKL5 Gene

  • GC0XP017109
  • GC0XP017645
  • GC0XP017805
  • GC0XP018203
  • GC0XP018353
  • GC0XP016199

Summaries for CDKL5 Gene

Entrez Gene Summary for CDKL5 Gene

  • 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]

GeneCards Summary for CDKL5 Gene

CDKL5 (Cyclin Dependent Kinase Like 5) is a Protein Coding gene. Diseases associated with CDKL5 include Epileptic Encephalopathy, Early Infantile, 2 and Rett Syndrome. Among its related pathways are Sweet Taste Signaling and Brain-Derived Neurotrophic Factor (BDNF) signaling pathway. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is CDKL2.

UniProtKB/Swiss-Prot for CDKL5 Gene

  • Mediates phosphorylation of MECP2 (PubMed:15917271, PubMed:16935860). May regulate ciliogenesis (PubMed:29420175).

Gene Wiki entry for CDKL5 Gene

Additional gene information for CDKL5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDKL5 Gene

Genomics for CDKL5 Gene

GeneHancer (GH) Regulatory Elements for CDKL5 Gene

Promoters and enhancers for CDKL5 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ018424 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.7 +0.3 290 3.1 SIN3A YY1 ZNF766 GLIS2 E2F8 ELK1 ZNF143 ATF7 KLF7 FOS CDKL5 GC0XP018417 PIR56944
GH0XJ018501 Promoter 0.5 EPDnew 650.2 +76.0 75968 0.1 CDKL5 GJA6P PIR56944
GH0XJ018674 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE 1.7 +249.5 249463 1.7 ATF1 SIN3A BRCA1 NCOA2 YY1 GTF3C2 GLIS2 ZNF213 ELK1 ZNF207 TRV-TAC1-2 PPEF1 CDKL5 PHKA2
GH0XJ018421 Enhancer 0.6 ENCODE 0.7 -3.1 -3127 1.1 ATF1 JUN JUNB SIN3A BRCA1 ATF2 SP1 JUND EED CREB1 CDKL5 GC0XP018417
GH0XJ018616 Enhancer 0.8 Ensembl ENCODE 0.1 +191.9 191892 1.4 SOX5 SOX13 NFIA HLF SIN3A TEAD3 TGIF2 SP1 JUND HNF1A PIR35788 GC0XP018534 CDKL5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDKL5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDKL5 gene promoter:
  • FOXL1
  • FOXD3
  • Cart-1
  • Sox5
  • Hlf
  • HFH-1

Genomic Locations for CDKL5 Gene

Genomic Locations for CDKL5 Gene
235,276 bases
Plus strand
228,047 bases
Plus strand

Genomic View for CDKL5 Gene

Genes around CDKL5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKL5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKL5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDKL5 Gene

Proteins for CDKL5 Gene

  • Protein details for CDKL5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cyclin-dependent kinase-like 5
    Protein Accession:
    Secondary Accessions:
    • G9B9X4
    • Q14198
    • Q5H985
    • Q8IYC7
    • Q9UJL6

    Protein attributes for CDKL5 Gene

    1030 amino acids
    Molecular mass:
    115538 Da
    Quaternary structure:
    • Interacts with MECP2.
    • Sequence=CAA61445.1; Type=Frameshift; Positions=415; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CDKL5 Gene

    Alternative splice isoforms for CDKL5 Gene


neXtProt entry for CDKL5 Gene

Post-translational modifications for CDKL5 Gene

No data available for DME Specific Peptides for CDKL5 Gene

Domains & Families for CDKL5 Gene

Gene Families for CDKL5 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for CDKL5 Gene

Suggested Antigen Peptide Sequences for CDKL5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
genes like me logo Genes that share domains with CDKL5: view

Function for CDKL5 Gene

Molecular function for CDKL5 Gene

UniProtKB/Swiss-Prot Function:
Mediates phosphorylation of MECP2 (PubMed:15917271, PubMed:16935860). May regulate ciliogenesis (PubMed:29420175).
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.

Enzyme Numbers (IUBMB) for CDKL5 Gene

Gene Ontology (GO) - Molecular Function for CDKL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IDA 16935860
GO:0004674 protein serine/threonine kinase activity TAS 9721213
GO:0004693 NOT cyclin-dependent protein serine/threonine kinase activity IBA --
GO:0005524 ATP binding IDA 16935860
GO:0016301 kinase activity IDA 15917271
genes like me logo Genes that share ontologies with CDKL5: view
genes like me logo Genes that share phenotypes with CDKL5: view

Human Phenotype Ontology for CDKL5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CDKL5 Gene

MGI Knock Outs for CDKL5:

Animal Model Products

  • Taconic Biosciences Mouse Models for CDKL5

miRNA for CDKL5 Gene

miRTarBase miRNAs that target CDKL5

Clone Products

No data available for Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for CDKL5 Gene

Localization for CDKL5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKL5 Gene

Nucleus. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDKL5 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDKL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 16935860
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0032587 colocalizes_with ruffle membrane ISS --
GO:0032839 dendrite cytoplasm ISS,IBA --
genes like me logo Genes that share ontologies with CDKL5: view

Pathways & Interactions for CDKL5 Gene

genes like me logo Genes that share pathways with CDKL5: view

Pathways by source for CDKL5 Gene

1 GeneTex pathway for CDKL5 Gene
1 Qiagen pathway for CDKL5 Gene

SIGNOR curated interactions for CDKL5 Gene

Other effect:

Gene Ontology (GO) - Biological Process for CDKL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration ISS --
GO:0006468 protein phosphorylation TAS 9721213
GO:0016310 phosphorylation IEA --
GO:0043547 positive regulation of GTPase activity ISS --
GO:0045773 positive regulation of axon extension ISS,IBA --
genes like me logo Genes that share ontologies with CDKL5: view

Drugs & Compounds for CDKL5 Gene

(4) Drugs for CDKL5 Gene - From: ClinicalTrials and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0
Anesthetics Pharma 10650
Central Nervous System Depressants Pharma 14508
Pregnanolone Pharma 23

(1) Additional Compounds for CDKL5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with CDKL5: view

Transcripts for CDKL5 Gene

mRNA/cDNA for CDKL5 Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(22) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CDKL5 Gene

Cyclin-dependent kinase-like 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDKL5 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2: - - - - -
SP3: -

Relevant External Links for CDKL5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDKL5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDKL5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CDKL5 Gene

This gene is overexpressed in Nasal epithelium (55.5) and Plasma (11.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CDKL5 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDKL5 Gene:


SOURCE GeneReport for Unigene cluster for CDKL5 Gene:


mRNA Expression by UniProt/SwissProt for CDKL5 Gene:

Tissue specificity: Expressed in brain, lung, kidney, prostate, ovary, placenta, pancreas and testis.

Evidence on tissue expression from TISSUES for CDKL5 Gene

  • Nervous system(3.1)
  • Lung(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKL5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • salivary gland
  • skull
  • tongue
  • tooth
  • vocal cord
  • chest wall
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • abdominal wall
  • intestine
  • large intestine
  • stomach
  • pelvis
  • rectum
  • arm
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with CDKL5: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CDKL5 Gene

Orthologs for CDKL5 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CDKL5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDKL5 34 33
  • 98.7 (n)
(Canis familiaris)
Mammalia CDKL5 34 33
  • 92.51 (n)
(Bos Taurus)
Mammalia CDKL5 34 33
  • 92.07 (n)
(Mus musculus)
Mammalia Cdkl5 16 34 33
  • 89.38 (n)
(Rattus norvegicus)
Mammalia Cdkl5 33
  • 89.12 (n)
(Monodelphis domestica)
Mammalia CDKL5 34
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia CDKL5 34
  • 81 (a)
(Gallus gallus)
Aves CDKL5 34 33
  • 79.68 (n)
(Anolis carolinensis)
Reptilia CDKL5 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cdkl5 33
  • 72.62 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.22826 33
(Danio rerio)
Actinopterygii cdkl5 34 33
  • 65.86 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6800 34
  • 32 (a)
(Caenorhabditis elegans)
Secernentea dyf-18 34
  • 31 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes KIN28 34
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 71 (a)
Species where no ortholog for CDKL5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CDKL5 Gene

Gene Tree for CDKL5 (if available)
Gene Tree for CDKL5 (if available)
Evolutionary constrained regions (ECRs) for CDKL5: view image

Paralogs for CDKL5 Gene

Paralogs for CDKL5 Gene

(17) SIMAP similar genes for CDKL5 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CDKL5: view

Variants for CDKL5 Gene

Sequence variations from dbSNP and Humsavar for CDKL5 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs104894928 not-provided, pathogenic, not provided, Juvenile retinoschisis 18,647,303(+) C/G/T genic_downstream_transcript_variant, intron_variant
rs104894929 pathogenic, Juvenile retinoschisis 18,642,012(+) A/G genic_downstream_transcript_variant, intron_variant
rs104894930 pathogenic, not-provided, Juvenile retinoschisis, not provided 18,642,071(+) G/A genic_downstream_transcript_variant, intron_variant
rs104894932 pathogenic, not-provided, Juvenile retinoschisis, not provided 18,647,301(+) C/G/T genic_downstream_transcript_variant, intron_variant
rs104894933 pathogenic, not-provided, Juvenile retinoschisis, not provided 18,647,296(+) C/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDKL5 Gene

Variant ID Type Subtype PubMed ID
esv3359808 CNV insertion 20981092
esv3573625 CNV loss 25503493
esv3573626 CNV loss 25503493
esv3576792 CNV gain 25503493
nsv476338 CNV novel sequence insertion 20440878
nsv528654 CNV gain 19592680
nsv6821 CNV insertion 18451855

Variation tolerance for CDKL5 Gene

Residual Variation Intolerance Score: 2.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.59; 44.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDKL5 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDKL5 Gene

Disorders for CDKL5 Gene

MalaCards: The human disease database

(27) MalaCards diseases for CDKL5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 2
  • eiee2
rett syndrome
  • rtt
cdkl5 deficiency disorder
  • cdkl5
west syndrome
  • epileptic encephalopathy, early infantile, 1
epileptic encephalopathy, early infantile, 15
  • eiee15
- elite association - COSMIC cancer census association via MalaCards
Search CDKL5 in MalaCards View complete list of genes associated with diseases


  • 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).
  • Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672]: A severe form of epilepsy characterized by seizures or spasms beginning in infancy. Patients with epileptic encephalopathy early infantile type 2 manifest features resembling Rett syndrome such as microcephaly, lack of speech development, stereotypic hand movements. However, EIEE2 and Rett syndrome are considered two distinct entities. {ECO:0000269 PubMed:12736870, ECO:0000269 PubMed:15492925, ECO:0000269 PubMed:15499549, ECO:0000269 PubMed:15689447, ECO:0000269 PubMed:15917271, ECO:0000269 PubMed:16015284, ECO:0000269 PubMed:16611748, ECO:0000269 PubMed:16935860, ECO:0000269 PubMed:17993579, ECO:0000269 PubMed:18790821, ECO:0000269 PubMed:18809835, ECO:0000269 PubMed:19241098, ECO:0000269 PubMed:19253388, ECO:0000269 PubMed:23662938, ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:24564546, ECO:0000269 PubMed:26993267, ECO:0000269 PubMed:27864847}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CDKL5

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDKL5: view

No data available for Genatlas for CDKL5 Gene

Publications for CDKL5 Gene

  1. Functional consequences of mutations in CDKL5, an X-linked gene involved in infantile spasms and mental retardation. (PMID: 16935860) Bertani I … Kilstrup-Nielsen C (The Journal of biological chemistry 2006) 2 3 4 22 58
  2. Xp22.3 genomic deletions involving the CDKL5 gene in girls with early onset epileptic encephalopathy. (PMID: 19780792) Mei D … Guerrini R (Epilepsia 2010) 3 22 44 58
  3. Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes. (PMID: 19241098) Russo S … Larizza L (Neurogenetics 2009) 3 4 22 58
  4. [Methyl-CpG-binding protein 2 gene and CDKL5 gene mutation in patients with Rett syndrome: analysis of 177 Chinese pediatric patients]. (PMID: 19552836) Li MR … Wu XR (Zhonghua yi xue za zhi 2009) 3 22 44 58
  5. Mutational spectrum of CDKL5 in early-onset encephalopathies: a study of a large collection of French patients and review of the literature. (PMID: 19793311) Nemos C … Philippe C (Clinical genetics 2009) 3 22 44 58

Products for CDKL5 Gene

Sources for CDKL5 Gene

Loading form....