CKS2

protein-coding

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

Gene summary

CKS2 protein binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function. The CKS2 mRNA is found to be expressed in different patterns through the cell cycle in HeLa cells, which reflects specialized role for the encoded protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001827.3

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr9:89,311,195-89,316,703

External References & Databases

Ensembl (ENSG00000123975)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 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 CKS2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 4

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001827.3. 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			1 clinvar			1
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	8	0	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001827.3	RefSeq	NP_001818.1	3	MANE Select
ENST00000314355.7	Ensembl	ENSP00000364976.3	3	MANE Select
ENST00000940740.1	Ensembl	ENSP00000610799.1	3	Standard
ENST00000940741.1	Ensembl	ENSP00000610800.1	3	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)

Biological Process

regulation of transcription by RNA polymerase II
meiosis I
regulation of mitotic cell cycle
cell population proliferation
mitotic cell cycle phase transition

Molecular Function

chromatin binding
protein binding
protein kinase binding
histone binding
ubiquitin binding

Cellular Component

cyclin-dependent protein kinase holoenzyme complex
SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314355
Coding exons: 3
Length: 5506
Individuals with no LoFs: 124885
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124886
p: 0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.28	17	39.7	0.428	0.00000175	517
Missense (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

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.;

Recessive Scores

pRec: 0.221

Intolerance Scores

LoFtool: 0.381
RVIS EVS: 0.04
RVIS percentile EVS: 56.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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