CDKL3

protein-coding

cyclin dependent kinase like 3, the group of Cyclin dependent kinases

Gene summary

The protein encoded by this gene is a member of cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of Saccharomyces cerevisiae cdc28, and Schizosaccharomyces pombe cdc2, and are known to be important regulators of cell cycle progression. This gene was identified as a gene absent in leukemic patients with chromosome 5q deletion. This loss may be an important determinant of dysmyelopoiesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001113575.2

Inheritance

—

ClinVar variants

U:86B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr5:134,286,350-134,371,047

External References & Databases

Ensembl (ENSG00000006837)

Transcript & Mutation Effects

hg38 • Region Span ~84.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDKL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001113575.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		2 clinvar	4
missense			80 clinvar	3 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	86	3	2	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001113575.2	RefSeq	NP_001107047.1	12	MANE Select
ENST00000265334.9	Ensembl	ENSP00000265334.4	12	MANE Select
NM_001300853.2	RefSeq	NP_001287782.1	9	Standard
NM_001349363.2	RefSeq	NP_001336292.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular protein modification process
protein phosphorylation
negative regulation of axon extension
positive regulation of dendrite morphogenesis
regulation of cell cycle

Molecular Function

protein kinase activity
cyclin-dependent protein serine/threonine kinase activity
protein binding
ATP binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265334
Coding exons: 12
Length: 165434
Individuals with no LoFs: 124530
Homozygous LoFs: 1
Heterozygous LoFs: 117
Defined: 124648
p: 0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.388	245	263	0.933	0.0000122	3886
Missense (PolyPhen)		79	95.294	0.82901		1495
Synonymous	1.07	75	87.8	0.854	0.00000427	1043
Loss of Function	0.966	21	26.4	0.797	0.00000140	395

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00030	0.00026	rare
Latino/Admixed American	0.00026	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0031	0.0028	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00044	0.00041	rare
South Asian	0.00034	0.00026	rare
Other	0.00036	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.647
RVIS EVS: 0.33
RVIS percentile EVS: 73.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.357

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium