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

    Gene ID: 6792, updated on 20-Apr-2024

    Summary

    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; AllianceGenome:HGNC:11411
    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
    NEW
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    Genomic context

    Location:
    Xp22.13
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18425608..18653629)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (18008223..18236232)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18443728..18671749)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Scm polycomb group protein like 2 Neighboring gene uncharacterized LOC124905253 Neighboring gene thymosin beta 10 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 2020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460197-18460698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460699-18461198 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18487190-18487391 Neighboring gene uncharacterized LOC124905289 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:18583809-18584371 Neighboring gene gap junction protein alpha 6, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18658784-18658953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18667451-18668199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18679457-18680008 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18693026-18693212 Neighboring gene tRNA-Val (anticodon TAC) 1-2 Neighboring gene retinoschisin 1 Neighboring gene PPEF1 antisense RNA 1 Neighboring gene protein phosphatase with EF-hand domain 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Angelman syndrome-like
    MedGen: CN128785 GeneReviews: Not available
    Compare labs
    Developmental and epileptic encephalopathy, 2
    MedGen: C4750718 OMIM: 300672 GeneReviews: CDKL5 Deficiency Disorder
    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 modulation of chemical synaptic transmission IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in modulation of chemical synaptic transmission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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
     
    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
     
    involved_in protein phosphorylation TAS
    Traceable Author Statement
    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
     
    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
     
    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 
    is_active_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
     
    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

    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)

    NEW Try the new Transcript table

    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
      5004..219592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001037343.2NP_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/TrEMBL
      A0A669KBC2
      Related
      ENSP00000369325.3, ENST00000379989.6
      Conserved Domains (2) summary
      smart00220
      Location:13297
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd07848
      Location:11297
      STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5
    2. NM_001323289.2NP_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
      G9B9X4, O76039, Q14198, Q5H985, Q8IYC7, Q9UJL6
      UniProtKB/TrEMBL
      A0A669KBC2
      Related
      ENSP00000485244.1, ENST00000623535.2
      Conserved Domains (1) summary
      cd07848
      Location:11297
      STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5
    3. NM_003159.3NP_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/TrEMBL
      A0A669KBC2
      Related
      ENSP00000369332.3, ENST00000379996.7
      Conserved Domains (2) summary
      smart00220
      Location:13297
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd07848
      Location:11297
      STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      18425608..18653629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      18008223..18236232
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)