CHKB
Basic information
Region (hg38): 22:50578959-50601455
Previous symbols: [ "CHKL" ]
Links
Phenotypes
GenCC
Source:
- megaconial type congenital muscular dystrophy (Strong), mode of inheritance: AR
- megaconial type congenital muscular dystrophy (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
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
- 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 82 | 87 | ||||
missense | 153 | 11 | 166 | |||
nonsense | 11 | 13 | ||||
start loss | 1 | 1 | ||||
frameshift | 13 | 16 | ||||
splice donor/acceptor (+/-2bp) | 10 | |||||
Total | 28 | 13 | 158 | 93 | 1 |
Highest pathogenic variant AF is 0.000086175
GnomAD
Source:
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:
- 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