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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
  • EC 4 58
  • STK9 3 4
  • Cyclin Dependent Kinase 5 Transcript 3
  • EC 2.7.11 58
  • 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 Brain-Derived Neurotrophic Factor (BDNF) signaling pathway and Sweet Taste Signaling. 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.

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

Regulatory Elements for CDKL5 Gene

Enhancers for CDKL5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH018674 1.4 FANTOM5 ENCODE 1.7 +249.5 249464 1.7 ATF1 BRCA1 GTF3C2 GLIS2 ELK1 ZNF207 ZNF143 FOS RUNX3 DEK CDKL5 PHKA2 TRV-TAC1-2 PPEF1
GH0XH018424 1 ENCODE 0.7 -0.2 -170 2.1 SIN3A YY1 ZNF766 GLIS2 ELK1 ZNF143 ATF7 KLF7 FOS RUNX3 CDKL5 GC0XP018417
GH0XH018421 0.7 ENCODE 0.7 -3.1 -3128 1.1 ATF1 JUN JUNB BRCA1 ATF2 JUND EED CREB1 FOS ATF7 GC0XP018417 CDKL5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CDKL5 on UCSC Golden Path with GeneCards custom track

Promoters for CDKL5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000244982 317 3001 ZNF766 GLIS2 ELK1 ZNF143 ATF7 KLF7 FOS RUNX3 SP3 SP5

Genomic Locations for CDKL5 Gene

Genomic Locations for CDKL5 Gene
235,276 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

Selected DME Specific Peptides for CDKL5 Gene


Post-translational modifications 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 CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot Function:
Mediates phosphorylation of MECP2.

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:

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

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 IBA,ISS --
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
Anesthetics Pharma 10074
Central Nervous System Depressants Pharma 13909
Pregnanolone Pharma 21
ATP Nutra Agonist 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with CDKL5: view

Transcripts for CDKL5 Gene

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, PaxDb, 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 33 34
  • 98.7 (n)
(Canis familiaris)
Mammalia CDKL5 33 34
  • 92.51 (n)
(Bos Taurus)
Mammalia CDKL5 33 34
  • 92.07 (n)
(Mus musculus)
Mammalia Cdkl5 33 16 34
  • 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 33 34
  • 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 33 34
  • 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)

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 Sequence Context AA Info Type
rs122460157 Pathogenic, Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672] 18,581,942(+) ACTGT(G/T)TGACT reference, missense
rs122460159 Pathogenic, Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672] 18,564,496(+) TGTGG(C/T)GATCA reference, missense
rs267606713 Pathogenic, Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672] 18,598,499(+) CTTGA(C/T)AGAAC reference, missense
rs267606714 other, Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672] 18,598,508(+) ACAGT(A/G)TTTGA reference, missense
rs267606715 Pathogenic, Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672], Epileptic encephalopathy, early infantile, 2 (EIEE2) [MIM:300672] 18,584,332(+) GTATC(A/C/G)GTCCC reference, missense

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)

Relevant External Links for CDKL5 Gene

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

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

Disorders for CDKL5 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 2
  • eiee2
rett syndrome
  • rett syndrome, preserved speech variant
autistic disorder
  • autism
focal epilepsy
  • localisation-related epilepsy
angelman syndrome
  • happy puppet syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CDKL5 in MalaCards View complete list of genes associated with diseases


  • 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.
  • 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).

Relevant External Links for CDKL5

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 60
  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 45 60
  3. Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes. (PMID: 19241098) Russo S … Larizza L (Neurogenetics 2009) 3 4 22 60
  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 45 60
  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 45 60

Products for CDKL5 Gene

Sources for CDKL5 Gene

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