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

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: mouse all
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Genomic context

Location:: Xp22.13

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (18425608..18653629)
110	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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Analysis of electrocardiograms in individuals with CDKL5 deficiency disorder.
Title: Analysis of electrocardiograms in individuals with CDKL5 deficiency disorder.
CDKL5 deficiency causes epileptic seizures independent of cellular mosaicism.
Title: CDKL5 deficiency causes epileptic seizures independent of cellular mosaicism.
Neuronal hyperexcitability and ion channel dysfunction in CDKL5-deficiency patient iPSC-derived cortical organoids.
Title: Neuronal hyperexcitability and ion channel dysfunction in CDKL5-deficiency patient iPSC-derived cortical organoids.
CDKL5 deficiency disorder: clinical features, diagnosis, and management.
Title: CDKL5 deficiency disorder: clinical features, diagnosis, and management.
Clinical manifestation of CDKL5 deficiency disorder and identified mutations in a cohort of Slovak patients.
Title: Clinical manifestation of CDKL5 deficiency disorder and identified mutations in a cohort of Slovak patients.
Phenotypes in adult patients with Rett syndrome: results of a 13-year experience and insights into healthcare transition.
Title: Phenotypes in adult patients with Rett syndrome: results of a 13-year experience and insights into healthcare transition.
CDKL5 promotes proliferation, migration, and chemotherapeutic drug resistance of glioma cells via activation of the PI3K/AKT signaling pathway.
Title: CDKL5 promotes proliferation, migration, and chemotherapeutic drug resistance of glioma cells via activation of the PI3K/AKT signaling pathway.
Exploring quality of life in individuals with a severe developmental and epileptic encephalopathy, CDKL5 Deficiency Disorder.
Title: Exploring quality of life in individuals with a severe developmental and epileptic encephalopathy, CDKL5 Deficiency Disorder.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (100)

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
Developmental and 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-32426 (e-PCR)
- UniSTS:41486

SHGC-170800 (e-PCR)
- UniSTS:185119

L77289 (e-PCR)
- UniSTS:30783

STS-H55764 (e-PCR)
- UniSTS:13137

DXS7038E (e-PCR)
- UniSTS:25961

A009V26 (e-PCR)
- UniSTS:58997

A003B18 (e-PCR)
- UniSTS:4987

DXS8000 (e-PCR)
- UniSTS:99718

L77279 (e-PCR)
- UniSTS:40629

CHLC.GGAT18G07 (e-PCR)
- UniSTS:8377

RH11240 (e-PCR)
- UniSTS:25789

G32881 (e-PCR)
- UniSTS:117460

SGC35640 (e-PCR)
- UniSTS:2268

DXS8368 (e-PCR)
- UniSTS:68086

Homology

Homologs of the CDKL5 gene: The CDKL5 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 468 organisms have orthologs with human gene CDKL5
Orthologs

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 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	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 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
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	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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

EC 2.7.11.22

NP_001310218.1

EC 2.7.11.22

NP_003150.1

EC 2.7.11.22

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

NG_008475.1 RefSeqGene

Range

5004..219592

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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, Q9UJL6

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
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