CDK5R2

cyclin dependent kinase 5 regulatory subunit 2

Basic information

Region (hg38): 2:218959666-218962155

Links

ENSG00000171450 ∙ NCBI:8941 ∙ OMIM:603764 ∙ HGNC:1776 ∙ Uniprot:Q13319 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK5R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK5R2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in CDK5R2

This is a list of pathogenic ClinVar variants found in the CDK5R2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-218959933-G-A		not specified	Uncertain significance (Apr 06, 2023)
2-218959938-G-A		not specified	Uncertain significance (Feb 26, 2024)
2-218959938-G-C		not specified	Uncertain significance (Nov 10, 2024)
2-218960028-G-C		not specified	Uncertain significance (Jan 01, 2025)
2-218960067-G-A		not specified	Uncertain significance (Nov 08, 2021)
2-218960112-C-T			Uncertain significance (-)
2-218960150-T-A		not specified	Uncertain significance (Sep 25, 2023)
2-218960151-C-G		not specified	Uncertain significance (Sep 25, 2023)
2-218960167-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-218960176-A-G		not specified	Uncertain significance (Aug 02, 2021)
2-218960178-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-218960185-C-T		not specified	Uncertain significance (Dec 10, 2024)
2-218960196-C-A		not specified	Uncertain significance (Feb 06, 2025)
2-218960217-G-A		not specified	Uncertain significance (Sep 27, 2024)
2-218960220-A-T		not specified	Uncertain significance (Nov 03, 2023)
2-218960250-G-T		not specified	Uncertain significance (Jun 05, 2024)
2-218960265-G-A		not specified	Uncertain significance (Aug 04, 2021)
2-218960266-G-T		not specified	Uncertain significance (Mar 11, 2024)
2-218960296-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-218960302-C-T		not specified	Uncertain significance (Nov 09, 2024)
2-218960341-C-T		not specified	Uncertain significance (Jun 21, 2021)
2-218960419-G-A		not specified	Uncertain significance (Mar 16, 2024)
2-218960563-G-A		not specified	Uncertain significance (Oct 25, 2022)
2-218960601-G-T		not specified	Uncertain significance (Jun 03, 2022)
2-218960900-C-A		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK5R2	protein_coding	protein_coding	ENST00000302625	1	2500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.671	0.325	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	92	172	0.535	0.00000806	2259
Missense in Polyphen		23	57.949	0.3969		784
Synonymous	-0.193	85	82.8	1.03	0.00000408	843
Loss of Function	2.27	1	7.90	0.127	3.51e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activator of CDK5/TPKII.
• Pathway: Lissencephaly gene (LIS1) in neuronal migration and development (Consensus)

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• pHI: 0.442
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.856

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk5r2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: cdk5r2a
• Affected structure: retinal outer plexiform layer
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;neuron migration;cerebellum development;superior olivary nucleus maturation;hippocampus development;layer formation in cerebral cortex;positive regulation of calcium ion-dependent exocytosis;positive regulation of protein serine/threonine kinase activity
• Cellular component: cytoplasm;plasma membrane;membrane;protein kinase 5 complex;growth cone;neuron projection
• Molecular function: actin binding;lipid binding;cyclin-dependent protein serine/threonine kinase activator activity