CKS2

CDC28 protein kinase regulatory subunit 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 9:89311195-89316703

Links

ENSG00000123975

∙ NCBI:1164 ∙ OMIM:116901 ∙ HGNC:2000 ∙ Uniprot:P33552 ∙ 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 CKS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKS2 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in CKS2

This is a list of pathogenic ClinVar variants found in the CKS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-89315245-A-C		not specified	Uncertain significance (Aug 14, 2023)	2594457

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKS2	protein_coding	protein_coding	ENST00000314355	3	5506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.419	0.550	124885	0	1	124886	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	17	39.7	0.428	0.00000175	517
Missense in Polyphen		2	7.3282	0.27292		112
Synonymous	-0.539	15	12.6	1.19	5.61e-7	126
Loss of Function	1.71	1	5.23	0.191	2.24e-7	61

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)	0.00000884	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.;
Pathway: Small cell lung cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.221

Intolerance Scores

loftool: 0.381
rvis_EVS: 0.04
rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

pHI: 0.952
hipred: Y
hipred_score: 0.800
ghis: 0.722

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Cks2
Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;meiosis I;regulation of mitotic cell cycle;cell population proliferation;mitotic cell cycle phase transition;positive regulation of cyclin-dependent protein serine/threonine kinase activity;cell division
Cellular component: cyclin-dependent protein kinase holoenzyme complex;SCF ubiquitin ligase complex
Molecular function: chromatin binding;protein binding;protein kinase binding;histone binding;ubiquitin binding;cyclin-dependent protein serine/threonine kinase activator activity