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    NBEAL2 neurobeachin like 2 [ Homo sapiens (human) ]

    Gene ID: 23218, updated on 6-Jun-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

      UniProtKB/TrEMBL
      H0Y764

    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

      UniProtKB/TrEMBL
      H0Y764
      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

      UniProtKB/TrEMBL
      H0Y764

    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

      UniProtKB/TrEMBL
      H0Y764

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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