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

ENSG00000172915

∙ NCBI:26960 ∙ OMIM:604889 ∙ HGNC:7648 ∙ Uniprot:Q8NFP9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the NBEA gene.

not_provided (428 variants)
Inborn_genetic_diseases (264 variants)
Neurodevelopmental_disorder_with_or_without_early-onset_generalized_epilepsy (153 variants)
NBEA-related_disorder (73 variants)
not_specified (58 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			7 clinvar	101 clinvar	2 clinvar	110
missense	3 clinvar	11 clinvar	540 clinvar	82 clinvar	2 clinvar	638
nonsense	11 clinvar	14 clinvar	3 clinvar			28
start loss						0
frameshift	9 clinvar	7 clinvar	4 clinvar			20
splice donor/acceptor (+/-2bp)	9 clinvar	7 clinvar	10 clinvar			26
Total	32	39	564	183	4

Highest pathogenic variant AF is 0.0000041067424

Loading clinvar variants...

GnomAD

Source: gnomAD

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
		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: 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

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

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