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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
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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: 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

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)

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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_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

    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

    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

    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

    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