CKB

protein-coding

creatine kinase B

Gene summary

The protein encoded by this gene is a cytoplasmic enzyme involved in energy homeostasis. The encoded protein reversibly catalyzes the transfer of phosphate between ATP and various phosphogens such as creatine phosphate. It acts as a homodimer in brain as well as in other tissues, and as a heterodimer with a similar muscle isozyme in heart. The encoded protein is a member of the ATP:guanido phosphotransferase protein family. A pseudogene of this gene has been characterized. [provided by RefSeq, Jul 2008]

Previous symbols:

CKBB

MANE transcript

NM_001823.5

Inheritance

—

ClinVar variants

U:41

Top phenotype

Premature ovarian insufficiency

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr14:103,519,667-103,522,833

External References & Databases

Ensembl (ENSG00000166165)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 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 CKB variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

Premature ovarian insufficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001823.5. 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			35 clinvar			35
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	41	0	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001823.5	RefSeq	NP_001814.2	7	MANE Select
ENST00000348956.7	Ensembl	ENSP00000299198.2	7	MANE Select
NM_001362531.2	RefSeq	NP_001349460.1	6	Standard
ENST00000553610.5	Ensembl	ENSP00000451426.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Arginine and proline metabolism - Homo sapiens (human)
Abacavir Pathway, Pharmacokinetics/Pharmacodynamics
Hyperornithinemia with gyrate atrophy (HOGA)
Creatine deficiency, guanidinoacetate methyltransferase deficiency
L-arginine:glycine amidinotransferase deficiency

Biological Process

creatine metabolic process
phosphorylation
cerebellum development
substantia nigra development
cellular chloride ion homeostasis

Molecular Function

creatine kinase activity
protein binding
ATP binding
ubiquitin protein ligase binding

Cellular Component

extracellular space
nucleus
cytosol
dendrite
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000348956
Coding exons: 7
Length: 3453
Individuals with no LoFs: 125483
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125497
p: 0.0000558

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.32	131	230	0.570	0.0000122	2473
Missense (PolyPhen)		39	78.116	0.49926		932
Synonymous	-0.600	108	100	1.08	0.00000568	745
Loss of Function	2.75	4	15.8	0.253	8.45e-7	167

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate). Creatine kinase isoenzymes play a central role in energy transduction in tissues with large, fluctuating energy demands, such as skeletal muscle, heart, brain and spermatozoa.;

Recessive Scores

pRec: 0.834

Intolerance Scores

LoFtool: 0.457
RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.991

Gene Damage Prediction

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