NBEA
Basic information
Region (hg38): 13:34942270-35673022
Links
Phenotypes
GenCC
Source:
- syndromic intellectual disability (Strong), mode of inheritance: AD
- neurodevelopmental disorder with or without early-onset generalized epilepsy (Strong), mode of inheritance: AD
- complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
- neurodevelopmental disorder with or without early-onset generalized epilepsy (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Neurodevelopmental disorder with or without early-onset generalized epilepsy | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 28554332; 30269351 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (376 variants)
- Inborn_genetic_diseases (229 variants)
- Neurodevelopmental_disorder_with_or_without_early-onset_generalized_epilepsy (138 variants)
- NBEA-related_disorder (73 variants)
- not_specified (43 variants)
- See_cases (13 variants)
- Cerebellar,_ocular,_craniofacial,_and_genital_syndrome (6 variants)
- Neurodevelopmental_disorder (2 variants)
- Autism_spectrum_disorder (2 variants)
- Intellectual_disability (2 variants)
- MAB21L1-related_disorder (2 variants)
- NBEA-related_intellectual_disability (2 variants)
- Developmental_disorder (2 variants)
- Epilepsy (1 variants)
- NBEA-related_developmental_delay_and_generalized_epilepsy (1 variants)
- NBEA-related_complex_neurodevelopmental_disorder (1 variants)
- Neurodevelopmental_delay (1 variants)
- Intellectual_disability_and_seizures (1 variants)
- Hypoplasia_of_scrotum (1 variants)
- typical_paroxysmal_kinesigenic_dyskinesia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBEA gene is commonly pathogenic or not. These statistics are base on transcript: NM_001385012.1. 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 | 92 | 98 | ||||
missense | 10 | 472 | 75 | 563 | ||
nonsense | 14 | 24 | ||||
start loss | 0 | |||||
frameshift | 18 | |||||
splice donor/acceptor (+/-2bp) | 19 | |||||
Total | 28 | 38 | 483 | 167 | 6 |
Highest pathogenic variant AF is 0.00000410674
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NBEA | protein_coding | protein_coding | ENST00000400445 | 58 | 730736 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 5.55e-20 | 124615 | 0 | 11 | 124626 | 0.0000441 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 5.51 | 875 | 1.47e+3 | 0.595 | 0.0000746 | 19241 |
Missense in Polyphen | 194 | 540.22 | 0.35911 | 7330 | ||
Synonymous | 0.344 | 505 | 515 | 0.981 | 0.0000264 | 5628 |
Loss of Function | 10.7 | 5 | 142 | 0.0352 | 0.00000778 | 1798 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000192 | 0.000192 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000116 | 0.0000556 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000381 | 0.0000354 |
Middle Eastern | 0.000116 | 0.0000556 |
South Asian | 0.0000351 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the membrane. May anchor the kinase to cytoskeletal and/or organelle-associated proteins (By similarity). {ECO:0000250}.;
Intolerance Scores
- loftool
- 0.362
- rvis_EVS
- -1.89
- rvis_percentile_EVS
- 1.98
Haploinsufficiency Scores
- pHI
- 0.506
- hipred
- Y
- hipred_score
- 0.761
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.836
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nbea
- Phenotype
- embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- nbeaa
- Affected structure
- Mauthner neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein localization
- Cellular component
- trans-Golgi network;cytosol;plasma membrane;endomembrane system
- Molecular function
- protein kinase binding