NBEA

neurobeachin, the group of BEACH domain containing |WD repeat domain containing|A-kinase anchoring proteins|Armadillo like helical domain containing

Basic information

Region (hg38): 13:34942270-35673022

Links

ENSG00000172915NCBI:26960OMIM:604889HGNC:7648Uniprot:Q8NFP9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with or without early-onset generalized epilepsyADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic28554332; 30269351

ClinVar

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

  • 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
92
clinvar
3
clinvar
98
missense
3
clinvar
10
clinvar
472
clinvar
75
clinvar
3
clinvar
563
nonsense
9
clinvar
14
clinvar
1
clinvar
24
start loss
0
frameshift
8
clinvar
7
clinvar
3
clinvar
18
splice donor/acceptor (+/-2bp)
8
clinvar
7
clinvar
4
clinvar
19
Total 28 38 483 167 6

Highest pathogenic variant AF is 0.00000410674

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NBEAprotein_codingprotein_codingENST00000400445 58730736
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.005.55e-201246150111246260.0000441
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense5.518751.47e+30.5950.000074619241
Missense in Polyphen194540.220.359117330
Synonymous0.3445055150.9810.00002645628
Loss of Function10.751420.03520.000007781798

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001920.000192
Ashkenazi Jewish0.000.00
East Asian0.0001160.0000556
Finnish0.000.00
European (Non-Finnish)0.00003810.0000354
Middle Eastern0.0001160.0000556
South Asian0.00003510.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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