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Aliases for NBEA Gene

Aliases for NBEA Gene

  • Neurobeachin 2 3 3 5
  • Lysosomal-Trafficking Regulator 2 3 4
  • BCL8B 3 4
  • LYST2 3 4
  • Protein BCL8B 4
  • EC 1.14.14.5 56
  • EC 6.1.1.11 56
  • KIAA1544 4

External Ids for NBEA Gene

Previous GeneCards Identifiers for NBEA Gene

  • GC13P033850
  • GC13P029502
  • GC13P034453
  • GC13P033314
  • GC13P034414
  • GC13P035516
  • GC13P016329

Summaries for NBEA Gene

Entrez Gene Summary for NBEA Gene

  • This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011]

GeneCards Summary for NBEA Gene

NBEA (Neurobeachin) is a Protein Coding gene. Diseases associated with NBEA include Atrial Septal Defect 1 and Chediak-Higashi Syndrome. Gene Ontology (GO) annotations related to this gene include binding and phospholipid binding. An important paralog of this gene is LRBA.

UniProtKB/Swiss-Prot for NBEA Gene

  • 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).

Additional gene information for NBEA Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NBEA Gene

Genomics for NBEA Gene

GeneHancer (GH) Regulatory Elements for NBEA Gene

Promoters and enhancers for NBEA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13I035469 Promoter/Enhancer 2.6 UCNEbase EPDnew Ensembl ENCODE dbSUPER 550 +532.4 532367 9.9 PKNOX1 MZF1 SIN3A GLI4 ZNF2 ZNF335 GLIS2 ZNF366 ZSCAN5C SCRT2 MAB21L1 NBEA ENSG00000261728 GC13P035361
GH13I034941 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 557 +0.2 214 2.2 CLOCK ARID4B SIN3A ZNF2 ZNF48 YY1 GLIS2 ZNF143 SP3 YY2 NBEA SCAND3P1
GH13I035198 Enhancer 0.9 VISTA UCNEbase 10.4 +256.9 256922 2.1 POLR2A NBEA SCAND3P1 PHBP13
GH13I034155 Enhancer 1.3 Ensembl ENCODE dbSUPER 6 -785.6 -785648 3.2 SIN3A IRF4 ATF7 FOS RUNX3 JUNB SMARCB1 GLIS1 SP7 ZBTB21 ENSG00000199196 NBEA GC13M034101 ENSG00000278477
GH13I034968 Enhancer 0.6 ENCODE 11.3 +26.0 26026 0.1 ZNF189 ZFP37 ZNF335 OSR2 ZNF366 ZNF341 PRDM1 PRDM4 SP7 NBEA SCAND3P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NBEA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NBEA gene promoter:

Genomic Locations for NBEA Gene

Genomic Locations for NBEA Gene
chr13:34,942,287-35,673,022
(GRCh38/hg38)
Size:
730,736 bases
Orientation:
Plus strand
chr13:35,516,424-36,247,159
(GRCh37/hg19)

Genomic View for NBEA Gene

Genes around NBEA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBEA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBEA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NBEA Gene

Proteins for NBEA Gene

  • Protein details for NBEA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NFP9-NBEA_HUMAN
    Recommended name:
    Neurobeachin
    Protein Accession:
    Q8NFP9
    Secondary Accessions:
    • B7Z2H9
    • Q5T320
    • Q9HCM8
    • Q9NSU1
    • Q9NW98
    • Q9Y6J1

    Protein attributes for NBEA Gene

    Size:
    2946 amino acids
    Molecular mass:
    327822 Da
    Quaternary structure:
    • Interacts with RII subunit of PKA.
    SequenceCaution:
    • Sequence=AAD41633.1; Type=Frameshift; Positions=2900; Evidence={ECO:0000305}; Sequence=BAA91485.1; Type=Erroneous termination; Positions=762; Note=Translated as Trp.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NBEA Gene

    Alternative splice isoforms for NBEA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NBEA Gene

Selected DME Specific Peptides for NBEA Gene

Q8NFP9:
  • NLVTGGD
  • AKLERAL

Post-translational modifications for NBEA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for NBEA Gene

Gene Families for NBEA Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Graphical View of Domain Structure for InterPro Entry

Q8NFP9

UniProtKB/Swiss-Prot:

NBEA_HUMAN :
  • RII-alpha binding site, predicted to form an amphipathic helix, could participate in protein-protein interactions with a complementary surface on the R-subunit dimer.
  • Belongs to the WD repeat neurobeachin family.
Domain:
  • RII-alpha binding site, predicted to form an amphipathic helix, could participate in protein-protein interactions with a complementary surface on the R-subunit dimer.
Family:
  • Belongs to the WD repeat neurobeachin family.
genes like me logo Genes that share domains with NBEA: view

Function for NBEA Gene

Molecular function for NBEA Gene

GENATLAS Biochemistry:
neurobeachin,cytosolic protein,specifically expressed in brain,peripherally associated with several membrane compartments including trans-Golgi network and endosome-like structures,may be involved in membrane trafficking events
UniProtKB/Swiss-Prot 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).

Enzyme Numbers (IUBMB) for NBEA Gene

Phenotypes From GWAS Catalog for NBEA Gene

Gene Ontology (GO) - Molecular Function for NBEA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019901 protein kinase binding IEA --
genes like me logo Genes that share ontologies with NBEA: view
genes like me logo Genes that share phenotypes with NBEA: view

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NBEA Gene

Localization for NBEA Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBEA Gene

Cytoplasm. Membrane; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NBEA gene
Compartment Confidence
plasma membrane 5
cytosol 5
golgi apparatus 5
endoplasmic reticulum 1
lysosome 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Golgi apparatus (3)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NBEA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005802 trans-Golgi network ISS --
GO:0005829 cytosol ISS --
GO:0005886 plasma membrane ISS --
GO:0012505 endomembrane system ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with NBEA: view

Pathways & Interactions for NBEA Gene

No Data Available

Gene Ontology (GO) - Biological Process for NBEA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008104 protein localization IEA --
genes like me logo Genes that share ontologies with NBEA: view

No data available for Pathways by source and SIGNOR curated interactions for NBEA Gene

Drugs & Compounds for NBEA Gene

(1) Drugs for NBEA Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
antidepressants Pharma 0
genes like me logo Genes that share compounds with NBEA: view

Transcripts for NBEA Gene

Unigene Clusters for NBEA Gene

Neurobeachin:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NBEA Gene

No ASD Table

Relevant External Links for NBEA Gene

GeneLoc Exon Structure for
NBEA
ECgene alternative splicing isoforms for
NBEA

Expression for NBEA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NBEA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NBEA Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.0).

Protein differential expression in normal tissues from HIPED for NBEA Gene

This gene is overexpressed in Fetal Brain (24.9), Urine (16.9), and Heart (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NBEA Gene



Protein tissue co-expression partners for NBEA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NBEA Gene:

NBEA

SOURCE GeneReport for Unigene cluster for NBEA Gene:

Hs.491172

mRNA Expression by UniProt/SwissProt for NBEA Gene:

Q8NFP9-NBEA_HUMAN
Tissue specificity: Predominant in many brain structures. Also expressed at medium levels in spleen, thymus, prostate, testis and ovary. Low level expression is seen in heart, kidney, pancreas, skeletal muscle and intestine.

Evidence on tissue expression from TISSUES for NBEA Gene

  • Nervous system(4.9)
  • Pancreas(2.2)
genes like me logo Genes that share expression patterns with NBEA: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NBEA Gene

Orthologs for NBEA Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NBEA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NBEA 34
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NBEA 34
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NBEA 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NBEA 34 33
  • 94.91 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NBEA 33 34
  • 93.47 (n)
mouse
(Mus musculus)
Mammalia Nbea 33 16 34
  • 89.83 (n)
rat
(Rattus norvegicus)
Mammalia RGD1562629 33
  • 89.54 (n)
chicken
(Gallus gallus)
Aves NBEA 34 33
  • 85.44 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 96 (a)
OneToMany
-- 34
  • 90 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia nbea 33
  • 80.53 (n)
zebrafish
(Danio rerio)
Actinopterygii nbeaa 34
  • 85 (a)
OneToMany
nbeab 34
  • 84 (a)
OneToMany
LOC565885 33
  • 73.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta rg 33 34
  • 59.3 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000017 33
  • 58.34 (n)
worm
(Caenorhabditis elegans)
Secernentea sel-2 34 33
  • 53.07 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BPH1 34
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9799 34
  • 43 (a)
OneToMany
Species where no ortholog for NBEA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NBEA Gene

ENSEMBL:
Gene Tree for NBEA (if available)
TreeFam:
Gene Tree for NBEA (if available)

Paralogs for NBEA Gene

Paralogs for NBEA Gene

(5) SIMAP similar genes for NBEA Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with NBEA: view

Variants for NBEA Gene

Sequence variations from dbSNP and Humsavar for NBEA Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs869312667 uncertain-significance, not specified 35,157,262(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs878853169 uncertain-significance, not specified 35,550,528(+) C/T coding_sequence_variant, stop_gained
rs879255409 uncertain-significance, not specified 35,161,787(+) A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000000968 -- 35,169,102(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000008327 -- 35,371,053(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NBEA Gene

Variant ID Type Subtype PubMed ID
dgv3112n54 CNV loss 21841781
dgv3113n54 CNV loss 21841781
dgv3114n54 CNV loss 21841781
dgv3115n54 CNV loss 21841781
dgv321n67 CNV gain 20364138
dgv947n106 CNV deletion 24896259
esv2026049 CNV deletion 18987734
esv22371 CNV gain 19812545
esv22696 CNV gain+loss 19812545
esv23864 CNV loss 19812545
esv2558098 CNV deletion 19546169
esv2661190 CNV deletion 23128226
esv2668233 CNV deletion 23128226
esv2747257 CNV deletion 23290073
esv2747258 CNV deletion 23290073
esv2747259 CNV deletion 23290073
esv2760284 CNV loss 21179565
esv3304752 CNV mobile element insertion 20981092
esv33135 CNV loss 17666407
esv3389246 CNV insertion 20981092
esv3417506 CNV insertion 20981092
esv3433109 CNV insertion 20981092
esv3550301 CNV deletion 23714750
esv3550302 CNV deletion 23714750
esv3550305 CNV deletion 23714750
esv3580599 CNV loss 25503493
esv3580600 CNV loss 25503493
esv3580601 CNV loss 25503493
esv3580602 CNV loss 25503493
esv3580603 CNV loss 25503493
esv3580604 CNV loss 25503493
esv3580606 CNV loss 25503493
esv3631757 CNV loss 21293372
esv3631758 CNV loss 21293372
esv3631759 CNV loss 21293372
esv3631762 CNV loss 21293372
esv3631764 CNV loss 21293372
esv3631765 CNV loss 21293372
esv3631766 CNV loss 21293372
nsv1001 CNV insertion 18451855
nsv1002 CNV deletion 18451855
nsv1045569 CNV loss 25217958
nsv1071092 CNV deletion 25765185
nsv1122803 CNV deletion 24896259
nsv1138212 CNV deletion 24896259
nsv471126 CNV loss 18288195
nsv510329 OTHER sequence alteration 20534489
nsv510600 CNV deletion 20534489
nsv561464 CNV loss 21841781
nsv561465 CNV loss 21841781
nsv561481 CNV loss 21841781
nsv561482 CNV gain 21841781
nsv561483 CNV gain 21841781
nsv64727 CNV deletion 16902084
nsv826611 CNV loss 20364138
nsv832579 CNV loss 17160897
nsv832580 CNV loss 17160897
nsv957456 CNV deletion 24416366
nsv974080 CNV duplication 23825009
nsv976102 CNV duplication 23825009
nsv983574 CNV duplication 23825009
nsv983575 CNV duplication 23825009
nsv983739 CNV duplication 23825009

Variation tolerance for NBEA Gene

Residual Variation Intolerance Score: 0.747% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.97; 74.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NBEA Gene

Human Gene Mutation Database (HGMD)
NBEA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NBEA

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NBEA Gene

Disorders for NBEA Gene

MalaCards: The human disease database

(3) MalaCards diseases for NBEA Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
atrial septal defect 1
  • asd1
chediak-higashi syndrome
  • chs
autism
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards
Search NBEA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NBEA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NBEA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBEA Gene

Publications for NBEA Gene

  1. Crystal structure of the BEACH domain reveals an unusual fold and extensive association with a novel PH domain. (PMID: 12234919) Jogl G … Tong L (The EMBO journal 2002) 3 4 22 58
  2. The neurobeachin gene (Nbea) identifies a new region of homology between mouse central chromosome 3 and human chromosome 13q13. (PMID: 10501977) Gilbert DJ … Kilimann MW (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 22 58
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58
  5. Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma. (PMID: 19135901) O'Neal J … Tomasson MH (Experimental hematology 2009) 3 22 58

Products for NBEA Gene

Sources for NBEA Gene

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