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CDKL5 cyclin dependent kinase like 5 [ Homo sapiens (human) ]

Gene ID: 6792, updated on 17-Oct-2021

Summary

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Official Symbol
CDKL5provided by HGNC
Official Full Name
cyclin dependent kinase like 5provided by HGNC
Primary source
HGNC:HGNC:11411
See related
Ensembl:ENSG00000008086 MIM:300203
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEE2; ISSX; STK9; EIEE2; CFAP247
Summary
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]
Expression
Broad expression in brain (RPKM 11.1), lung (RPKM 3.0) and 18 other tissues See more
Orthologs
mouse all
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Genomic context

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See CDKL5 in Genome Data Viewer
Location:
Xp22.13
Exon count:
23
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (18425608..18653629)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18443728..18671749)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene BEN domain containing 2 Neighboring gene Scm polycomb group protein like 2 Neighboring gene thymosin beta 10 pseudogene 2 Neighboring gene gap junction protein alpha 6, pseudogene Neighboring gene tRNA-Val (anticodon TAC) 1-2 Neighboring gene PPEF1 antisense RNA 1 Neighboring gene retinoschisin 1 Neighboring gene protein phosphatase with EF-hand domain 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. CDKL5 deficiency disorder in males: Five new variants and review of the literature. Siri B, et al. Eur J Paediatr Neurol, 2021 Jul. PMID 33989939
  2. Exploring genotype-phenotype relationships in the CDKL5 deficiency disorder using an international dataset. MacKay CI, et al. Clin Genet, 2021 Jan. PMID 33047306
  3. Gene replacement ameliorates deficits in mouse and human models of cyclin-dependent kinase-like 5 disorder. Gao Y, et al. Brain, 2020 Mar 1. PMID 32125365
  4. Novel CDKL5 mutations were found in patients in China: retrospective investigation in cases of CDKL5-related disorders. Yan Y, et al. Ital J Pediatr, 2020 Feb 28. PMID 32111237, Free PMC Article
  5. Expanding the phenotype of the CDKL5 deficiency disorder: Are seizures mandatory? MacKay CI, et al. Am J Med Genet A, 2020 May. PMID 32034940

See all (117) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CDKL5 deficiency disorder in males: Five new variants and review of the literature.
    Title: CDKL5 deficiency disorder in males: Five new variants and review of the literature.
  2. Exploring genotype-phenotype relationships in the CDKL5 deficiency disorder using an international dataset.
    Title: Exploring genotype-phenotype relationships in the CDKL5 deficiency disorder using an international dataset.
  3. Unusual double mutation in MECP2 and CDKL5 genes in Rett-like syndrome: Correlation with phenotype and genes expression.
    Title: Unusual double mutation in MECP2 and CDKL5 genes in Rett-like syndrome: Correlation with phenotype and genes expression.
  4. Dopaminergic loss of cyclin-dependent kinase-like 5 recapitulates methylphenidate-remediable hyperlocomotion in mouse model of CDKL5 deficiency disorder.
    Title: Dopaminergic loss of cyclin-dependent kinase-like 5 recapitulates methylphenidate-remediable hyperlocomotion in mouse model of CDKL5 deficiency disorder.
  5. Cyclin-dependent-like kinase 5 is required for pain signaling in human sensory neurons and mouse models.
    Title: Cyclin-dependent-like kinase 5 is required for pain signaling in human sensory neurons and mouse models.
  6. Rett Syndrome, a Neurodevelopmental Disorder, Whole-Transcriptome, and Mitochondrial Genome Multiomics Analyses Identify Novel Variations and Disease Pathways.
    Title: Rett Syndrome, a Neurodevelopmental Disorder, Whole-Transcriptome, and Mitochondrial Genome Multiomics Analyses Identify Novel Variations and Disease Pathways.
  7. Novel CDKL5 mutations were found in patients in China: retrospective investigation in cases of CDKL5-related disorders.
    Title: Novel CDKL5 mutations were found in patients in China: retrospective investigation in cases of CDKL5-related disorders.
  8. Increased DNA Damage and Apoptosis in CDKL5-Deficient Neurons.
    Title: Increased DNA Damage and Apoptosis in CDKL5-Deficient Neurons.
  9. Progressive EEG Changes in CDKL-5 Related Epileptic Encephalopathy.
    Title: Progressive EEG Changes in CDKL-5 Related Epileptic Encephalopathy.
  10. Expanding the phenotype of the CDKL5 deficiency disorder: Are seizures mandatory?
    Title: Expanding the phenotype of the CDKL5 deficiency disorder: Are seizures mandatory?
Submit: New GeneRIF Correction See all GeneRIFs (92)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Angelman syndrome-like
MedGen: CN128785 GeneReviews: Not available
Compare labs
Early infantile epileptic encephalopathy 2
MedGen: C4750718 OMIM: 300672 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2012-07-12)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-12)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cyclin-dependent protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein serine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables small GTPase binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of axon extension IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in positive regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendritic spine development IEA
Inferred from Electronic Annotation
more info
  
involved_in protein autophosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of dendrite development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of postsynapse organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary tip IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in dendrite cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in dendrite cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendritic growth cone ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in postsynaptic density, intracellular component IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with ruffle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
cyclin-dependent kinase-like 5
Names
cyclin dependent kinase 5 transcript
serine/threonine kinase 9
serine/threonine-protein kinase 9
NP_001032420.1
NP_001310218.1
NP_003150.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008475.1 RefSeqGene

    Range
    5001..233025
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037343.2 → NP_001032420.1  cyclin-dependent kinase-like 5 isoform 1

    See identical proteins and their annotated locations for NP_001032420.1

    Status: REVIEWED

    Source sequence(s)
    AI286150, AL704691, AY217744, BC036091
    Consensus CDS
    CCDS14186.1
    UniProtKB/Swiss-Prot
    O76039
    Related
    ENSP00000369325.3, ENST00000379989.6
    Conserved Domains (2) summary
    smart00220
    Location:13 → 297
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  2. NM_001323289.2 → NP_001310218.1  cyclin-dependent kinase-like 5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL109798, AW452901, HQ171445, Z92542
    Consensus CDS
    CCDS83458.1
    UniProtKB/Swiss-Prot
    O76039
    Related
    ENSP00000485244.1, ENST00000623535.2
    Conserved Domains (1) summary
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  3. NM_003159.3 → NP_003150.1  cyclin-dependent kinase-like 5 isoform 1

    See identical proteins and their annotated locations for NP_003150.1

    Status: REVIEWED

    Source sequence(s)
    AI286150, AY217744, BC010966
    Consensus CDS
    CCDS14186.1
    UniProtKB/Swiss-Prot
    O76039
    Related
    ENSP00000369332.3, ENST00000379996.7
    Conserved Domains (2) summary
    smart00220
    Location:13 → 297
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    18425608..18653629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O76039.2 GenPept UniProtKB/Swiss-Prot:O76039

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