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CDKL5 Gene(Protein Coding)

Cyclin Dependent Kinase Like 5

GCID:
GC0XP018443
GIFtS:
59
Genes Participants
UDN Logo

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 2.7.11.22 4 61
  • STK9 3 4
  • Cyclin Dependent Kinase 5 Transcript 3
  • EC 2.7.11 61
  • 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. 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

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

Genomics for CDKL5 Gene

Products:

  1. Regulatory Element

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
GH0XG018674 1.4 FANTOM5 ENCODE 1.7 +249.5 249464 1.7 ATF1 BRCA1 GTF3C2 GLIS2 ELK1 ZNF207 ZNF143 FOS DEK SP3 CDKL5 PHKA2 PPEF1 TRV-TAC1-2
GH0XG018424 1 ENCODE 0.7 -0.2 -170 2.1 SIN3A YY1 ZNF766 GLIS2 ELK1 ZNF143 KLF7 FOS SP3 SP5 CDKL5 GC0XP018417
GH0XG018421 0.6 ENCODE 0.7 -3.1 -3128 1.1 ATF1 JUN JUNB BRCA1 ATF2 JUND EED CREB1 FOS CREM CDKL5 GC0XP018417
- 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 SIN3A ZNF766 GLIS2 ELK1 ZNF143 KLF7 FOS SP3 SP5 NFYC

Transcription factor binding sites by QIAGEN in the CDKL5 gene promoter:

Genomic Location for CDKL5 Gene

Chromosome:
X
Start:
18,425,583 bp from pter
End:
18,660,858 bp from pter
Size:
235,276 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for CDKL5 Gene

Proteins for CDKL5 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    O76039-CDKL5_HUMAN
    Recommended name:
    Cyclin-dependent kinase-like 5
    Protein Accession:
    O76039
    Secondary Accessions:
    • G9B9X4
    • Q14198
    • Q5H985
    • Q8IYC7
    • Q9UJL6

    Protein attributes for CDKL5 Gene

    Size:
    1030 amino acids
    Molecular mass:
    115538 Da
    Quaternary structure:
    • Interacts with MECP2.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for CDKL5 Gene

Protein Expression for CDKL5 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for CDKL5 Gene

O76039:
  • YVATRWYR
  • SEIDQLF
  • PYGKSVD
  • WSVGCIL
  • HRDIKPEN
  • KLYLVFE

Post-translational modifications for CDKL5 Gene

Other Protein References for CDKL5 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for CDKL5

Domains & Families for CDKL5 Gene

Gene Families for CDKL5 Gene

HGNC:
IUPHAR :

Protein Domains for CDKL5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CDKL5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O76039

UniProtKB/Swiss-Prot:

CDKL5_HUMAN :
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
Family:
  • 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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:

Animal Model Products

  • Taconic Biosciences Mouse Models for CDKL5

CRISPR Products

miRNA for CDKL5 Gene

miRTarBase miRNAs that target CDKL5

Inhibitory RNA Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for CDKL5 Gene

Localization for CDKL5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKL5 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
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

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 IBA,ISS --
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

Products:

  1. Drug

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0
Anesthetics Pharma 9596
Central Nervous System Depressants Pharma 13403
Pregnanolone Pharma 20

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

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:

CRISPR Products

Inhibitory RNA Products

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: -
SP4:
SP5:

Relevant External Links for CDKL5 Gene

GeneLoc Exon Structure for
CDKL5
ECgene alternative splicing isoforms for
CDKL5

Expression for CDKL5 Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for CDKL5 Gene
mRNA expression by BioGPS for CDKL5 GenemRNA expression by GTEx 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:

CDKL5

SOURCE GeneReport for Unigene cluster for CDKL5 Gene:

Hs.659851

mRNA Expression by UniProt/SwissProt for CDKL5 Gene:

O76039-CDKL5_HUMAN
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
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
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
Thorax:
  • chest wall
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • arm
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • 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

Primer Products

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
chimpanzee
(Pan troglodytes)
 Mammalia CDKL5 34 35
  • 98.7 (n)
dog
(Canis familiaris)
 Mammalia CDKL5 34 35
  • 92.51 (n)
cow
(Bos Taurus)
 Mammalia CDKL5 34 35
  • 92.07 (n)
mouse
(Mus musculus)
 Mammalia Cdkl5 34 16 35
  • 89.38 (n)
rat
(Rattus norvegicus)
 Mammalia Cdkl5 34
  • 89.12 (n)
oppossum
(Monodelphis domestica)
 Mammalia CDKL5 35
  • 81 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia CDKL5 35
  • 81 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CDKL5 34 35
  • 79.68 (n)
lizard
(Anolis carolinensis)
 Reptilia CDKL5 35
  • 75 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia cdkl5 34
  • 72.62 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.22826 34
zebrafish
(Danio rerio)
 Actinopterygii cdkl5 34 35
  • 65.86 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG6800 35
  • 32 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea dyf-18 35
  • 31 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes KIN28 35
  • 31 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 71 (a)
 OneToOne
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

ENSEMBL:
Gene Tree for CDKL5 (if available)
TreeFam:
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)
CDKL5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDKL5

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

Disorders for CDKL5 Gene

MalaCards: The human disease database

(16) MalaCards diseases for CDKL5 Gene - From: 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
west syndrome
  • epileptic encephalopathy, early infantile, 1
angelman syndrome
  • happy puppet syndrome
cdkl5-related angelman-like syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CDKL5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CDKL5_HUMAN
  • 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:24564546}. 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)
CDKL5
Human Genome Epidemiology (HuGE) Navigator
CDKL5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CDKL5
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. (J. Biol. Chem. 2006) 2 3 4 22 64
  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 46 64
  3. [Methyl-CpG-binding protein 2 gene and CDKL5 gene mutation in patients with Rett syndrome: analysis of 177 Chinese pediatric patients]. (PMID: 19552836) Li M.R. … Wu X.R. (Zhonghua Yi Xue Za Zhi 2009) 3 22 46 64
  4. 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. (Clin. Genet. 2009) 3 22 46 64
  5. Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes. (PMID: 19241098) Russo S. … Larizza L. (Neurogenetics 2009) 3 4 22 64

Products for CDKL5 Gene

Sources for CDKL5 Gene

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