CKS1B

CDC28 protein kinase regulatory subunit 1B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:154974653-154979251

Links

ENSG00000173207 ∙ NCBI:1163 ∙ OMIM:116900 ∙ HGNC:19083 ∙ Uniprot:P61024 ∙ 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 CKS1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKS1B 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in CKS1B

This is a list of pathogenic ClinVar variants found in the CKS1B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-154974775-CA-C		Breast neoplasm	Pathogenic (-)
1-154974793-GT-G		Breast neoplasm	Pathogenic (-)
1-154978084-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-154978748-C-T		not specified	Uncertain significance (Feb 22, 2025)
1-154978749-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKS1B	protein_coding	protein_coding	ENST00000308987	3	4597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.431	0.540	125068	0	1	125069	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	21	46.1	0.455	0.00000243	519
Missense in Polyphen		5	13.047	0.38323		174
Synonymous	0.694	13	16.6	0.783	8.32e-7	132
Loss of Function	1.75	1	5.36	0.187	2.31e-7	58

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);regulation of p27 phosphorylation during cell cycle progression;Cyclin D associated events in G1;G1 Phase;SCF(Skp2)-mediated degradation of p27/p21;Cyclin E associated events during G1/S transition ;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;S Phase;G1/S Transition;Cell Cycle;Cell Cycle, Mitotic;FOXM1 transcription factor network (Consensus)

Intolerance Scores

• loftool: 0.490
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.935
• hipred: Y
• hipred_score: 0.640
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cks1b
• Phenotype: immune system phenotype; hematopoietic system 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); neoplasm; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;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;nucleoplasm;SCF ubiquitin ligase complex
• Molecular function: protein binding;protein kinase binding;histone binding;ubiquitin binding;cyclin-dependent protein serine/threonine kinase activator activity