CKS1B

protein-coding

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

Gene summary

CKS1B protein binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function. The CKS1B mRNA is found to be expressed in different patterns through the cell cycle in HeLa cells, which reflects a specialized role for the encoded protein. At least two transcript variants have been identified for this gene, and it appears that only one of them encodes a protein. [provided by RefSeq, Sep 2008]

MANE transcript

NM_001826.3

Inheritance

—

ClinVar variants

P:2U:3

Top phenotype

Breast neoplasm

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr1:154,974,653-154,979,251

External References & Databases

Ensembl (ENSG00000173207)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 kb

Loading mutation effect viewer...

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 CKS1B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 3

Breast neoplasmTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001826.3. 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						0
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)						0
Total	2	0	3	0	0	5

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001826.3	RefSeq	NP_001817.1	3	MANE Select
ENST00000308987.6	Ensembl	ENSP00000311083.5	3	MANE Select
ENST00000368436.1	Ensembl	ENSP00000357421.1	2	Standard
ENST00000368436.2	Ensembl	ENSP00000357421.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

protein binding
protein kinase binding
histone binding
ubiquitin binding
cyclin-dependent protein serine/threonine kinase activator activity

Cellular Component

cyclin-dependent protein kinase holoenzyme complex
nucleoplasm
SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308987
Coding exons: 3
Length: 4597
Individuals with no LoFs: 125068
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125069
p: 0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.31	21	46.1	0.455	0.00000243	519
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.;

Intolerance Scores

LoFtool: 0.490
RVIS EVS: 0.1
RVIS percentile EVS: 60.96

Essentials

Essential (CRISPR): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.976

Gene Damage Prediction

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