CHKB

choline kinase beta

Basic information

Region (hg38): 22:50578959-50601455

Previous symbols: [ "CHKL" ]

Links

ENSG00000100288NCBI:1120OMIM:612395HGNC:1938Uniprot:Q9Y259AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Muscular dystrophy, congenital, megaconial typeARCardiovascularThe condition can include cardiac sequelae (eg, cardiomyopathy and arrhythmias), and surveillance (eg, with echocardiogram and electrocardiogram) can allow potentially beneficial medical interventionsCardiovascular; Dermatologic; Musculoskeletal; Neurologic9427222; 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
82
clinvar
1
clinvar
87
missense
2
clinvar
153
clinvar
11
clinvar
166
nonsense
11
clinvar
2
clinvar
13
start loss
1
1
frameshift
13
clinvar
3
clinvar
16
splice donor/acceptor (+/-2bp)
4
clinvar
5
clinvar
1
clinvar
10
Total 28 13 158 93 1

Highest pathogenic variant AF is 0.000086175

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHKBprotein_codingprotein_codingENST00000406938 1122507
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.78e-70.9461257090391257480.000155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5332362141.100.00001202526
Missense in Polyphen7775.9571.0137922
Synonymous0.4888489.90.9340.00000506760
Loss of Function1.881423.90.5860.00000113266

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003740.000355
Ashkenazi Jewish0.000.00
East Asian0.0005460.000544
Finnish0.000.00
European (Non-Finnish)0.0001350.000132
Middle Eastern0.0005460.000544
South Asian0.00009810.0000980
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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