CHKB

choline kinase beta

Basic information

Region (hg38): 22:50578959-50601455

Previous symbols: [ "CHKL" ]

Links

ENSG00000100288 ∙ NCBI:1120 ∙ OMIM:612395 ∙ HGNC:1938 ∙ Uniprot:Q9Y259 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• megaconial type congenital muscular dystrophy (Strong), mode of inheritance: AR
• megaconial type congenital muscular dystrophy (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, congenital, megaconial type	AR	Cardiovascular	The condition can include cardiac sequelae (eg, cardiomyopathy and arrhythmias), and surveillance (eg, with echocardiogram and electrocardiogram) can allow potentially beneficial medical interventions	Cardiovascular; Dermatologic; Musculoskeletal; Neurologic	9427222; 21665002; 22782513; 24997086

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHKB gene.

• Megaconial_type_congenital_muscular_dystrophy (348 variants)
• Inborn_genetic_diseases (51 variants)
• not_provided (43 variants)
• not_specified (20 variants)
• CHKB-related_disorder (9 variants)
• Congenital_Muscular_Dystrophy,_CHKB-related (2 variants)
• Seizure (1 variants)
• Muscular_dystrophy (1 variants)
• See_cases (1 variants)
• Severe_global_developmental_delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHKB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005198.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1	3	82	1	87
missense		2	153	11		166
nonsense	11	2				13
start loss			1			1
frameshift	13	3				16
splice donor/acceptor (+/-2bp)	4	5	1			10
Total	28	13	158	93	1

Highest pathogenic variant AF is 0.000086175

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHKB	protein_coding	protein_coding	ENST00000406938	11	22507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.78e-7	0.946	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.533	236	214	1.10	0.0000120	2526
Missense in Polyphen		77	75.957	1.0137		922
Synonymous	0.488	84	89.9	0.934	0.00000506	760
Loss of Function	1.88	14	23.9	0.586	0.00000113	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000374	0.000355
Ashkenazi Jewish	0.00	0.00
East Asian	0.000546	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.000546	0.000544
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a key role in phospholipid biosynthesis. Catalyzes the first step in phosphatidylethanolamine biosynthesis. Phosphorylates ethanolamine, and can also act on choline (in vitro). Has higher activity with ethanolamine. May not significantly contribute to in vivo phosphatidylcholine biosynthesis. {ECO:0000269|PubMed:19915674}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Fatty Acid Beta Oxidation;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Signal Transduction;mitochondrial L-carnitine shuttle;Metabolism of lipids;Import of palmitoyl-CoA into the mitochondrial matrix;phosphatidylcholine biosynthesis;Metabolism;Fatty acid metabolism;Synthesis of PC;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;Glycerophospholipid biosynthesis;Phospholipid metabolism;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.847
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.210
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chkb
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process;phosphatidylcholine biosynthetic process;CDP-choline pathway;phosphorylation
• Cellular component: cytosol
• Molecular function: choline kinase activity;ethanolamine kinase activity;ATP binding