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    LRBA LPS responsive beige-like anchor protein [ Homo sapiens (human) ]

    Gene ID: 987, updated on 10-Dec-2024

    Summary

    Official Symbol
    LRBAprovided by HGNC
    Official Full Name
    LPS responsive beige-like anchor proteinprovided by HGNC
    Primary source
    HGNC:HGNC:1742
    See related
    Ensembl:ENSG00000198589 MIM:606453; AllianceGenome:HGNC:1742
    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
    BGL; LBA; CDC4L; CVID8; LAB300; uc.147
    Summary
    The protein encoded by this gene is a member of the WDL-BEACH-WD (WBW) gene family. Its expression is induced in B cells and macrophages by bacterial lipopolysaccharides (LPS). The encoded protein associates with protein kinase A and may be involved in leading intracellular vesicles to activated receptor complexes, which aids in the secretion and/or membrane deposition of immune effector molecules. Defects in this gene are associated with the disorder common variable immunodeficiency-8 with autoimmunity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in kidney (RPKM 10.0), thyroid (RPKM 9.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LRBA in Genome Data Viewer
    Location:
    4q31.3
    Exon count:
    61
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (150264435..151015727, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (153588433..154339605, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (151185587..151936879, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1230, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14262 Neighboring gene VISTA enhancer hs1614 Neighboring gene doublecortin like kinase 2 Neighboring gene RNA, U7 small nuclear 194 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:151209299-151209799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22014 Neighboring gene Sharpr-MPRA regulatory region 13510 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:151287541-151288222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:151288223-151288903 Neighboring gene nei like DNA glycosylase 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 5429 Neighboring gene uncharacterized LOC729558 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:151550380-151550601 Neighboring gene mab-21 like 2 Neighboring gene Sharpr-MPRA regulatory region 7547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22015 Neighboring gene zinc finger and BTB domain containing 8 opposite strand pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:151795383-151795916 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:151875385-151876005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:151884380-151885210 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:151885211-151886041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:151908831-151909345 Neighboring gene LRBA intron ENCODE-defined enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:151936707-151937304 Neighboring gene RNA, 5S ribosomal pseudogene 168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22019 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:152020037-152021236 Neighboring gene adenylate kinase 4 pseudogene 6 Neighboring gene small nucleolar RNA, C/D box U73B Neighboring gene ribosomal protein S3A

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Combined immunodeficiency due to LRBA deficiency
    MedGen: C3553512 OMIM: 614700 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association of mood-incongruent psychotic bipolar disorder.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ16600, FLJ25686, MGC72098, DKFZp686P2258, DKFZp686A09128, DKFZp686K03100

    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 mitophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein localization to phagophore assembly site IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    lipopolysaccharide-responsive and beige-like anchor protein
    Names
    CDC4-like protein
    LPS-responsive vesicle trafficking, beach and anchor containing
    vesicle trafficking, beach and anchor containing

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_032855.1 RefSeqGene

      Range
      5214..756063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1324

    mRNA and Protein(s)

    1. NM_001199282.2NP_001186211.2  lipopolysaccharide-responsive and beige-like anchor protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR, lacks an alternate in-frame exon, and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 2.
      Source sequence(s)
      AF216648, AF467287
      Consensus CDS
      CCDS58928.1
      UniProtKB/TrEMBL
      E9PEM5
      Related
      ENSP00000421552.1, ENST00000510413.5
      Conserved Domains (4) summary
      smart01026
      Location:22012478
      Beach; Beige/BEACH domain
      cd01201
      Location:20662169
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:25892625
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:25942833
      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_001364905.1NP_001351834.1  lipopolysaccharide-responsive and beige-like anchor protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC092544, AC092612, AC093748, AC097373, AC104796, AC110813
      Consensus CDS
      CCDS93649.1
      UniProtKB/TrEMBL
      A0A494C1L5, E9PEM5
      Related
      ENSP00000498582.2, ENST00000651943.2
      Conserved Domains (7) summary
      sd00039
      Location:25892625
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:22022478
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802047
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20732170
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      cl22861
      Location:229376
      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:25942834
      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. NM_001367550.1NP_001354479.1  lipopolysaccharide-responsive and beige-like anchor protein isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC079794, AC092544, AC092612, AC093748, AC097373, AC104796, AC110813
      Consensus CDS
      CCDS93650.1
      UniProtKB/TrEMBL
      A0A494BZW2, E9PEM5
      Related
      ENSP00000498254.2, ENST00000651695.2
    4. NM_006726.4NP_006717.2  lipopolysaccharide-responsive and beige-like anchor protein isoform 2

      See identical proteins and their annotated locations for NP_006717.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longer isoform (2).
      Source sequence(s)
      AC092612, AF216648, AF467287
      Consensus CDS
      CCDS3773.1
      UniProtKB/Swiss-Prot
      P50851, Q4W5J4, Q4W5L6, Q8NFQ0, Q9H2U3, Q9H2U4
      UniProtKB/TrEMBL
      E9PEM5
      Related
      ENSP00000349629.3, ENST00000357115.9
      Conserved Domains (8) summary
      COG2319
      Location:25902857
      WD40; WD40 repeat [General function prediction only]
      pfam02138
      Location:22132489
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802058
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20842181
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      sd00039
      Location:26002636
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:26052845
      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:229376
      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 ...

    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

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      150264435..151015727 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416462.1XP_047272418.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X4

      UniProtKB/TrEMBL
      A0A494C1L5, E9PEM5
    2. XM_005263373.4XP_005263430.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X1

      See identical proteins and their annotated locations for XP_005263430.1

      UniProtKB/TrEMBL
      E9PEM5
      Conserved Domains (8) summary
      COG2319
      Location:25952862
      WD40; WD40 repeat [General function prediction only]
      pfam02138
      Location:22132489
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802058
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20842181
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      sd00039
      Location:26052641
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:26102850
      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:229376
      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 ...
    3. XM_005263374.4XP_005263431.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X3

      UniProtKB/TrEMBL
      A0A494BZW2, E9PEM5
      Conserved Domains (8) summary
      COG2319
      Location:25842851
      WD40; WD40 repeat [General function prediction only]
      pfam02138
      Location:22022478
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802047
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20732170
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      sd00039
      Location:25942630
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:25992839
      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:229376
      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 ...
    4. XM_011532434.3XP_011530736.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X2

      See identical proteins and their annotated locations for XP_011530736.1

      UniProtKB/Swiss-Prot
      P50851, Q4W5J4, Q4W5L6, Q8NFQ0, Q9H2U3, Q9H2U4
      UniProtKB/TrEMBL
      E9PEM5
      Conserved Domains (8) summary
      COG2319
      Location:25902857
      WD40; WD40 repeat [General function prediction only]
      pfam02138
      Location:22132489
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802058
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20842181
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      sd00039
      Location:26002636
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:26052845
      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:229376
      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 ...
    5. XM_005263372.4XP_005263429.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X1

      See identical proteins and their annotated locations for XP_005263429.1

      UniProtKB/TrEMBL
      E9PEM5
      Conserved Domains (8) summary
      COG2319
      Location:25952862
      WD40; WD40 repeat [General function prediction only]
      pfam02138
      Location:22132489
      Beach; Beige/BEACH domain
      pfam06469
      Location:18802058
      DUF1088; Domain of Unknown Function (DUF1088)
      pfam14844
      Location:20842181
      PH_BEACH; PH domain associated with Beige/BEACH
      pfam15787
      Location:446717
      DUF4704; Domain of unknown function (DUF4704)
      sd00039
      Location:26052641
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:26102850
      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:229376
      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 ...
    6. XM_017008873.3XP_016864362.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X5

      UniProtKB/TrEMBL
      A0A8V8TKR0, Q68D03
      Related
      ENSP00000513123.1, ENST00000503716.5
    7. XM_017008874.2XP_016864363.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X6

      UniProtKB/TrEMBL
      A0A8V8TLZ6
      Related
      ENSP00000513124.1, ENST00000697127.1
      Conserved Domains (4) summary
      sd00039
      Location:493529
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:101377
      Beach; Beige/BEACH domain
      pfam14844
      Location:1069
      PH_BEACH; PH domain associated with Beige/BEACH
      cl25539
      Location:498738
      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 ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      153588433..154339605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351340.1XP_054207315.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X4

      UniProtKB/TrEMBL
      E9PEM5
    2. XM_054351337.1XP_054207312.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X1

      UniProtKB/TrEMBL
      E9PEM5
    3. XM_054351339.1XP_054207314.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X3

      UniProtKB/TrEMBL
      E9PEM5
    4. XM_054351338.1XP_054207313.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X2

      UniProtKB/TrEMBL
      E9PEM5
    5. XM_054351336.1XP_054207311.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X1

      UniProtKB/TrEMBL
      E9PEM5
    6. XM_054351341.1XP_054207316.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X5

      UniProtKB/TrEMBL
      A0A8V8TKR0, Q68D03
    7. XM_054351342.1XP_054207317.1  lipopolysaccharide-responsive and beige-like anchor protein isoform X6

      UniProtKB/TrEMBL
      A0A8V8TLZ6