NBEA neurobeachin [Homo sapiens (human)] - Gene

Summary

Official Symbol: NBEAprovided by HGNC
Official Full Name: neurobeachinprovided by HGNC
Primary source: HGNC:HGNC:7648
See related: Ensembl:ENSG00000172915 MIM:604889; AllianceGenome:HGNC:7648
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BCL8B; LYST2; NEDEGE
Summary: 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]
Expression: Broad expression in brain (RPKM 8.2), thyroid (RPKM 2.8) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q13.3

Exon count:: 64

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (34942270..35672736)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (34160609..34891073)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (35516407..36246873)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Familial paroxysmal kinesigenic dyskinesia with a novel missense variant (Arg2866Trp) in NBEA.
Title: Familial paroxysmal kinesigenic dyskinesia with a novel missense variant (Arg2866Trp) in NBEA.
Our study suggests that rs180940944 (NBEA) is associated with an increased Non-muscle-invasive Bladder Cancer tumour size at the time of diagnosis
Title: Genome-wide Association Study for Tumour Stage, Grade, Size, and Age at Diagnosis of Non-muscle-invasive Bladder Cancer.
We identified 24 de novo NBEA variants in patients with neurodevelopmental disease, establishing NBEA as an neurodevelopmental disease gene
Title: NBEA: Developmental disease gene with early generalized epilepsy phenotypes.
NBEA encodes neurobeachin: we found no evidence of association in data from the GWAS migraine meta-analysis consortium (n=118,710 participants) suggesting that the association might be specific to migraine co-morbid with bipolar disorder.
Title: Genome wide association study identifies variants in NBEA associated with migraine in bipolar disorder.
Data indicate that the PVT1-NBEA and the PVT1-WWOX chimeric genes were associated with the expression of abnormal NBEA and WWOX.
Title: Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality.
Synapse associated protein 102 (SAP102) binds the C-terminal part of the scaffolding protein neurobeachin.
Title: Synapse associated protein 102 (SAP102) binds the C-terminal part of the scaffolding protein neurobeachin.
data obtained in mice and humans suggest that variation of Nbea abundance or activity critically affects body weight, presumably by influencing the activity of feeding-related neural circuits
Title: Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans.
The NBEA gene at 13q13, and its expression are frequently disrupted in MM.
Title: Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma.
Observational study of gene-disease association. (HuGE Navigator)
Title: 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.
neurobeachin encoding gene is disrupted in a patient with a de novo translocation t(5;13) (q12.1;q13.2), idiopathic autism, and no family history of autism
Title: The neurobeachin gene is disrupted by a translocation in a patient with idiopathic autism.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with or without early-onset generalized epilepsy MedGen: C5436914 OMIM: 619157 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-06-26) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-06-26) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Common genetic variation and the control of HIV-1 in humans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies new susceptibility loci for migraine. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80830 (e-PCR)
- UniSTS:84240

D13S758 (e-PCR)
- UniSTS:1557

G09543 (e-PCR)
- UniSTS:64799

G19728 (e-PCR)
- UniSTS:35634

A001W40 (e-PCR)
- UniSTS:35635

Nbea (e-PCR), detects polymorphism
- UniSTS:507956

RH120191 (e-PCR)
- UniSTS:133183

T03409 (e-PCR)
- UniSTS:71038

RH118650 (e-PCR)
- UniSTS:138143

SHGC-81512 (e-PCR)
- UniSTS:182755

D13S127 (e-PCR)
- UniSTS:147195

AU151351 (e-PCR)
- UniSTS:278013

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein kinase binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in protein localization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in endomembrane system	ISS Inferred from Sequence or Structural Similarity more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: neurobeachin

Names: lysosomal-trafficking regulator 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_028156.1 RefSeqGene

Range

4984..735450

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_602

mRNA and Protein(s)

NM_001204197.3 → NP_001191126.1 neurobeachin isoform 2

See identical proteins and their annotated locations for NP_001191126.1

Status: REVIEWED

Source sequence(s)

AL139083, AL390071

Consensus CDS

CCDS55894.1

UniProtKB/TrEMBL

A0A8I5KWL1

Related

ENSP00000440233.1, ENST00000537702.6

Conserved Domains (4) summary

sd00039
Location:517 → 571

7WD40; WD40 repeat [structural motif]

pfam02138
Location:80 → 356

Beach; Beige/BEACH domain

cl17171
Location:1 → 48

PH-like; Pleckstrin homology-like domain

cl29593
Location:470 → 727

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001379245.1 → NP_001366174.1 neurobeachin isoform 3

Status: REVIEWED

Source sequence(s)

AL138690, AL139083, AL161718, AL161902, AL356430, AL357083, AL390071

Conserved Domains (7) summary

sd00039
Location:2742 → 2796

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2284 → 2581

Beach; Beige/BEACH domain

pfam06469
Location:1963 → 2129

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2155 → 2252

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:477 → 737

DUF4704; Domain of unknown function (DUF4704)

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

cl29593
Location:2695 → 2952

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001385012.1 → NP_001371941.1 neurobeachin isoform 4

Status: REVIEWED

Source sequence(s)

AL138690, AL139083, AL161718, AL161902, AL356430, AL357083, AL390071

Consensus CDS

CCDS91801.1

UniProtKB/TrEMBL

Q5T321

Related

ENSP00000369271.2, ENST00000379939.7

Conserved Domains (7) summary

sd00039
Location:2745 → 2799

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2287 → 2584

Beach; Beige/BEACH domain

pfam06469
Location:1966 → 2132

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2158 → 2255

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:477 → 737

DUF4704; Domain of unknown function (DUF4704)

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

cl29593
Location:2698 → 2955

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_015678.5 → NP_056493.3 neurobeachin isoform 1

See identical proteins and their annotated locations for NP_056493.3

Status: REVIEWED

Source sequence(s)

AF467288, AK001059, AK127791, AL137748, AL138690, DA248291

Consensus CDS

CCDS45026.1

UniProtKB/Swiss-Prot

B7Z2H9, Q5T320, Q8NFP9, Q9HCM8, Q9NSU1, Q9NW98, Q9Y6J1

Related

ENSP00000383295.3, ENST00000400445.8

Conserved Domains (7) summary

sd00039
Location:2724 → 2778

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2287 → 2563

Beach; Beige/BEACH domain

pfam06469
Location:1966 → 2132

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2158 → 2255

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

cl25539
Location:2677 → 2934

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

34942270..35672736

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430271.1 → XP_047286227.1 neurobeachin isoform X8
XM_006719803.4 → XP_006719866.1 neurobeachin isoform X1

Conserved Domains (8) summary

COG2319
Location:2651 → 2950

WD40; WD40 repeat [General function prediction only]

pfam02138
Location:2287 → 2584

Beach; Beige/BEACH domain

pfam06469
Location:1966 → 2132

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2158 → 2255

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

sd00039
Location:2740 → 2794

7WD40; WD40 repeat [structural motif]

cl02567
Location:2693 → 2950

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_005266346.5 → XP_005266403.1 neurobeachin isoform X5

Conserved Domains (8) summary

COG2319
Location:2630 → 2929

WD40; WD40 repeat [General function prediction only]

pfam02138
Location:2287 → 2563

Beach; Beige/BEACH domain

pfam06469
Location:1966 → 2132

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2158 → 2255

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

sd00039
Location:2719 → 2773

7WD40; WD40 repeat [structural motif]

cl02567
Location:2672 → 2929

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_017020544.2 → XP_016876033.1 neurobeachin isoform X2
XM_017020545.2 → XP_016876034.1 neurobeachin isoform X6
XM_006719806.4 → XP_006719869.1 neurobeachin isoform X4

See identical proteins and their annotated locations for XP_006719869.1

UniProtKB/TrEMBL

Q5T321

Conserved Domains (7) summary

sd00039
Location:2721 → 2775

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2284 → 2560

Beach; Beige/BEACH domain

pfam06469
Location:1963 → 2129

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2155 → 2252

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

cl25539
Location:2674 → 2931

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_006719805.4 → XP_006719868.1 neurobeachin isoform X7

Conserved Domains (8) summary

COG2319
Location:2627 → 2926

WD40; WD40 repeat [General function prediction only]

pfam02138
Location:2284 → 2560

Beach; Beige/BEACH domain

pfam06469
Location:1963 → 2129

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2155 → 2252

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

sd00039
Location:2716 → 2770

7WD40; WD40 repeat [structural motif]

cl02567
Location:2669 → 2926

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_047430269.1 → XP_047286225.1 neurobeachin isoform X3
XM_011535047.3 → XP_011533349.1 neurobeachin isoform X10

Conserved Domains (5) summary

pfam02138
Location:2287 → 2392

Beach; Beige/BEACH domain

pfam06469
Location:1966 → 2132

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:2158 → 2255

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:472 → 743

DUF4704; Domain of unknown function (DUF4704)

cl22861
Location:255 → 402

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_011535046.2 → XP_011533348.1 neurobeachin isoform X9

UniProtKB/TrEMBL

A0A8I5QKR1

Related

ENSP00000509239.1, ENST00000688626.1

Conserved Domains (7) summary

COG2319
Location:2177 → 2476

WD40; WD40 repeat [General function prediction only]

pfam02138
Location:1808 → 2105

Beach; Beige/BEACH domain

pfam06469
Location:1487 → 1653

DUF1088; Domain of Unknown Function (DUF1088)

pfam14844
Location:1679 → 1776

PH_BEACH; PH domain associated with Beige/BEACH

pfam15787
Location:42 → 264

DUF4704; Domain of unknown function (DUF4704)

sd00039
Location:2266 → 2320

7WD40; WD40 repeat [structural motif]

cl02567
Location:2219 → 2476

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047430272.1 → XP_047286228.1 neurobeachin isoform X11

Related

ENSP00000509879.1, ENST00000685686.1