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NBEAL2 neurobeachin like 2 [ Homo sapiens (human) ]

Gene ID: 23218, updated on 16-Apr-2024

Summary

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Official Symbol
NBEAL2provided by HGNC
Official Full Name
neurobeachin like 2provided by HGNC
Primary source
HGNC:HGNC:31928
See related
Ensembl:ENSG00000160796 MIM:614169; AllianceGenome:HGNC:31928
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
GPS; BDPLT4
Summary
The protein encoded by this gene contains a beige and Chediak-Higashi (BEACH) domain and multiple WD40 domains, and may play a role in megakaryocyte alpha-granule biogenesis. Mutations in this gene are a cause of gray platelet syndrome. [provided by RefSeq, Dec 2011]
Expression
Broad expression in bone marrow (RPKM 26.4), esophagus (RPKM 17.9) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See NBEAL2 in Genome Data Viewer
Location:
3p21.31
Exon count:
57
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46979666..47009701)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46996032..47026064)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47021156..47051191)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46966125-46966626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46972095-46972610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:46972611-46973126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46975255-46976022 Neighboring gene Sharpr-MPRA regulatory region 2536 Neighboring gene BLVRB pseudogene 1 Neighboring gene uncharacterized LOC124909375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981287-46981788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981789-46982288 Neighboring gene coiled-coil domain containing 12 Neighboring gene Sharpr-MPRA regulatory region 10220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47002103-47002604 Neighboring gene NANOG hESC enhancer GRCh37_chr3:47006121-47006678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47007588-47008518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47008519-47009448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47016719-47017421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47017422-47018123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47018827-47019527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47021430-47022210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47022211-47022991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47026300-47027052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47039103-47039996 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47050749-47051546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47051547-47052343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47054299-47054798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14303 Neighboring gene neurotrophin receptor associated death domain, pseudogene Neighboring gene SET domain containing 2, histone lysine methyltransferase Neighboring gene mitochondrial ribosomal protein L57 pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Gray platelet syndrome: NBEAL2 mutations are associated with pathology beyond megakaryocyte and platelet function defects. Pluthero FG, et al. J Thromb Haemost, 2021 Feb. PMID 33300270
  2. NBEAL2 mutations and bleeding in patients with gray platelet syndrome. Pluthero FG, et al. Platelets, 2018 Sep. PMID 29869935
  3. Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome. Kahr WH, et al. Nat Genet, 2011 Jul 17. PMID 21765413, Free PMC Article
  4. NBEAL2 deficiency in humans leads to low CTLA-4 expression in activated conventional T cells. Delage L, et al. Nat Commun, 2023 Jun 22. PMID 37349339, Free PMC Article
  5. The endoplasmic reticulum protein SEC22B interacts with NBEAL2 and is required for megakaryocyte α-granule biogenesis. Lo RW, et al. Blood, 2020 Aug 6. PMID 32384141

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Neurobeachin-like 2 protein (NBEAL2) controls the homeostatic level of the ribosomal protein RPS6 in mast cells.
    Title: The Neurobeachin-like 2 protein (NBEAL2) controls the homeostatic level of the ribosomal protein RPS6 in mast cells.
  2. NBEAL2 deficiency in humans leads to low CTLA-4 expression in activated conventional T cells.
    Title: NBEAL2 deficiency in humans leads to low CTLA-4 expression in activated conventional T cells.
  3. Gray platelet syndrome: NBEAL2 mutations are associated with pathology beyond megakaryocyte and platelet function defects.
    Title: Gray platelet syndrome: NBEAL2 mutations are associated with pathology beyond megakaryocyte and platelet function defects.
  4. The endoplasmic reticulum protein SEC22B interacts with NBEAL2 and is required for megakaryocyte alpha-granule biogenesis.
    Title: The endoplasmic reticulum protein SEC22B interacts with NBEAL2 and is required for megakaryocyte α-granule biogenesis.
  5. Defective Zn(2+) homeostasis in mouse and human platelets with alpha- and delta-storage pool diseases.
    Title: Defective Zn(2+) homeostasis in mouse and human platelets with α- and δ-storage pool diseases.
  6. NBEAL2 is required for the retention of both endocytosed and megakaryocyte-synthesized proteins by maturing alpha-granules, and possibly by platelet-borne granules. This function may involve interaction of NBEAL2 with P-selectin.
    Title: NBEAL2 (Neurobeachin-Like 2) Is Required for Retention of Cargo Proteins by α-Granules During Their Production by Megakaryocytes.
  7. Nbeal2 interacts with Dock7, Sec16a, and Vac14.
    Title: Nbeal2 interacts with Dock7, Sec16a, and Vac14.
  8. Author observed absence of NBEAL2 in platelets from GPS patients with 3 different genotypes, and reduced/truncated platelet NBEAL2 has been reported for others.
    Title: NBEAL2 mutations and bleeding in patients with gray platelet syndrome.
  9. NBEAL2 has an essential role in neutrophil and NK cell function and pathogen defense
    Title: NBEAL2 is required for neutrophil and NK cell function and pathogen defense.
  10. we herein show a long-distance regulatory region with GATA1 binding sites as being a strong enhancer for NBEAL2 expression.
    Title: The transcription factor GATA1 regulates NBEAL2 expression through a long-distance enhancer.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Gray platelet syndrome
MedGen: C0272302 OMIM: 139090 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of neurobeachin-like 2 (NBEAL2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0540

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in platelet formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in tertiary granule membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
neurobeachin-like protein 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

  1. NG_031914.1 RefSeqGene

    Range
    5001..35022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_568

mRNA and Protein(s)

  1. NM_001365116.2 → NP_001352045.1  neurobeachin-like protein 2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC094020
    Consensus CDS
    CCDS93260.1
    UniProtKB/TrEMBL
    A0A494C1V1
    Related
    ENSP00000499216.1, ENST00000651747.1
    Conserved Domains (6) summary
    smart01026
    Location:2031 → 2311
    Beach; Beige/BEACH domain
    cd01201
    Location:1884 → 2009
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2429 → 2466
    7WD40; WD40 repeat [structural motif]
    pfam15787
    Location:843 → 1092
    DUF4704; Domain of unknown function (DUF4704)
    pfam16057
    Location:1553 → 1827
    DUF4800; Domain of unknown function (DUF4800)
    cl25539
    Location:2430 → 2688
    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 ...

  2. NM_015175.3 → NP_055990.1  neurobeachin-like protein 2 isoform 1

    See identical proteins and their annotated locations for NP_055990.1

    Status: REVIEWED

    Source sequence(s)
    AB011112, AC094020, AK131104, BC029944, BQ017286, CR988681
    Consensus CDS
    CCDS46817.1
    UniProtKB/Swiss-Prot
    O60288, Q6P994, Q6UX91, Q6ZNJ1, Q8NAC9
    Related
    ENSP00000415034.2, ENST00000450053.8
    Conserved Domains (7) summary
    smart01026
    Location:2065 → 2345
    Beach; Beige/BEACH domain
    COG2319
    Location:2380 → 2713
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:1918 → 2043
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    pfam15787
    Location:877 → 1126
    DUF4704; Domain of unknown function (DUF4704)
    pfam16057
    Location:1587 → 1861
    DUF4800; Domain of unknown function (DUF4800)
    sd00039
    Location:2463 → 2500
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:2464 → 2722
    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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46979666..47009701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533533.3 → XP_011531835.1  neurobeachin-like protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q6ZNJ1
    Conserved Domains (7) summary
    smart01026
    Location:2065 → 2345
    Beach; Beige/BEACH domain
    COG2319
    Location:2391 → 2683
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:1918 → 2043
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    pfam15787
    Location:877 → 1126
    DUF4704; Domain of unknown function (DUF4704)
    pfam16057
    Location:1587 → 1861
    DUF4800; Domain of unknown function (DUF4800)
    sd00039
    Location:2433 → 2470
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:2434 → 2692
    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 ...

  2. XM_006713072.4 → XP_006713135.1  neurobeachin-like protein 2 isoform X2

    Conserved Domains (7) summary
    smart01026
    Location:2038 → 2318
    Beach; Beige/BEACH domain
    COG2319
    Location:2353 → 2686
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:1891 → 2016
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    pfam15787
    Location:850 → 1099
    DUF4704; Domain of unknown function (DUF4704)
    pfam16057
    Location:1560 → 1834
    DUF4800; Domain of unknown function (DUF4800)
    sd00039
    Location:2436 → 2473
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:2437 → 2695
    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 ...

  3. XM_047447786.1 → XP_047303742.1  neurobeachin-like protein 2 isoform X4

  4. XM_047447787.1 → XP_047303743.1  neurobeachin-like protein 2 isoform X5

  5. XM_047447790.1 → XP_047303746.1  neurobeachin-like protein 2 isoform X8

  6. XM_047447792.1 → XP_047303748.1  neurobeachin-like protein 2 isoform X10

  7. XM_047447793.1 → XP_047303749.1  neurobeachin-like protein 2 isoform X11

  8. XM_047447785.1 → XP_047303741.1  neurobeachin-like protein 2 isoform X1

  9. XM_047447789.1 → XP_047303745.1  neurobeachin-like protein 2 isoform X7

  10. XM_047447788.1 → XP_047303744.1  neurobeachin-like protein 2 isoform X6

  11. XM_047447791.1 → XP_047303747.1  neurobeachin-like protein 2 isoform X9

    Related
    ENSP00000410405.1, ENST00000416683.5

  12. XM_047447794.1 → XP_047303750.1  neurobeachin-like protein 2 isoform X12

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46996032..47026064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345838.1 → XP_054201813.1  neurobeachin-like protein 2 isoform X3

  2. XM_054345837.1 → XP_054201812.1  neurobeachin-like protein 2 isoform X2

  3. XM_054345839.1 → XP_054201814.1  neurobeachin-like protein 2 isoform X4

  4. XM_054345840.1 → XP_054201815.1  neurobeachin-like protein 2 isoform X5

  5. XM_054345843.1 → XP_054201818.1  neurobeachin-like protein 2 isoform X8

  6. XM_054345845.1 → XP_054201820.1  neurobeachin-like protein 2 isoform X10

  7. XM_054345846.1 → XP_054201821.1  neurobeachin-like protein 2 isoform X11

  8. XM_054345836.1 → XP_054201811.1  neurobeachin-like protein 2 isoform X1

  9. XM_054345842.1 → XP_054201817.1  neurobeachin-like protein 2 isoform X7

  10. XM_054345841.1 → XP_054201816.1  neurobeachin-like protein 2 isoform X6

  11. XM_054345844.1 → XP_054201819.1  neurobeachin-like protein 2 isoform X9

  12. XM_054345847.1 → XP_054201822.1  neurobeachin-like protein 2 isoform X12

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZNJ1.2 GenPept UniProtKB/Swiss-Prot:Q6ZNJ1

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