LRBA

gene
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Also known as BGLLAB300LBAuc.147

Summary

LRBA (LPS responsive beige-like anchor protein, HGNC:1742) is a protein-coding gene on chromosome 4q31.3, encoding Lipopolysaccharide-responsive and beige-like anchor protein (P50851). Involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules.

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.

Source: NCBI Gene 987 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): combined immunodeficiency due to LRBA deficiency (Definitive, ClinGen)
  • GWAS associations: 11
  • Clinical variants (ClinVar): 2,607 total — 125 pathogenic, 72 likely-pathogenic
  • Phenotypes (HPO): 45
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_001364905

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1742
Approved symbolLRBA
NameLPS responsive beige-like anchor protein
Location4q31.3
Locus typegene with protein product
StatusApproved
AliasesBGL, LAB300, LBA, uc.147
Ensembl geneENSG00000198589
Ensembl biotypeprotein_coding
OMIM606453
Entrez987

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 18 protein_coding, 4 protein_coding_CDS_not_defined, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000357115, ENST00000502839, ENST00000503716, ENST00000507224, ENST00000508396, ENST00000508606, ENST00000510157, ENST00000510413, ENST00000510841, ENST00000513021, ENST00000514435, ENST00000515096, ENST00000648626, ENST00000648823, ENST00000648878, ENST00000649874, ENST00000651035, ENST00000651695, ENST00000651943, ENST00000697127, ENST00000697128, ENST00000697129, ENST00000697130, ENST00000911749, ENST00000911750, ENST00000911751, ENST00000911752, ENST00000911753

RefSeq mRNA: 4 — MANE Select: NM_001364905 NM_001199282, NM_001364905, NM_001367550, NM_006726

CCDS: CCDS3773, CCDS58928, CCDS93649, CCDS93650

Canonical transcript exons

ENST00000651943 — 57 exons

ExonStartEnd
ENSE00000740094150928516150928616
ENSE00000740095150921198150921293
ENSE00000740096150915608150915727
ENSE00000740097150914195150914341
ENSE00000740098150908660150908857
ENSE00000740099150908334150908467
ENSE00000740100150906297150906405
ENSE00000740101150900049150900217
ENSE00000740104150868182150868305
ENSE00000740106150867671150867863
ENSE00000740109150850724150850902
ENSE00000821053150870525150870606
ENSE00000821054150871345150871453
ENSE00000821057150872663150872755
ENSE00000821058150893052150893149
ENSE00000821060150897739150897818
ENSE00000821061150905838150905990
ENSE00000821062150916401150916527
ENSE00001081815150321191150321368
ENSE00001081818150798081150798142
ENSE00001081820150828180150828621
ENSE00001081822150844658150844779
ENSE00001081823150808320150808398
ENSE00001081824150831817150831976
ENSE00001081825150848818150848998
ENSE00001081826150806271150806404
ENSE00001081827150849422150849575
ENSE00001081828150844100150844207
ENSE00001081829150817124150817257
ENSE00001081830150735258150735366
ENSE00001200926150851885150852943
ENSE00001250081150683551150683717
ENSE00001250470150896394150896456
ENSE00001250476150928834150929065
ENSE00001428255151014427151014861
ENSE00001619686150761783150761847
ENSE00001777660150916617150916738
ENSE00003487176150310229150310384
ENSE00003487821150467673150467785
ENSE00003576042150277853150278004
ENSE00003583036150435589150435708
ENSE00003591436150436724150436864
ENSE00003613524150315561150315623
ENSE00003613781150588048150588184
ENSE00003621548150487732150487834
ENSE00003623119150285933150286034
ENSE00003626043150325809150325898
ENSE00003637749150490918150491035
ENSE00003661993150471624150471739
ENSE00003670996150349992150350159
ENSE00003683208150590713150590859
ENSE00003683395150415438150415590
ENSE00003688095150599007150599131
ENSE00003692138150282450150282646
ENSE00003692871150302625150302792
ENSE00003900801150264435150265812
ENSE00003902903151015202151015284

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 95.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3310 / max 403.3496, expressed in 1806 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
5433511.19641776
543347.38971419
543332.5744923
543360.4726277
543320.2125109
543070.153884
543080.127378
543100.084350
543090.072341
543060.047621

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
upper leg skinUBERON:000426295.01gold quality
bronchial epithelial cellCL:000232894.99gold quality
epithelium of bronchusUBERON:000203193.59gold quality
colonic epitheliumUBERON:000039793.55gold quality
gingival epitheliumUBERON:000194993.19gold quality
bronchusUBERON:000218593.04gold quality
esophagus squamous epitheliumUBERON:000692092.84gold quality
epithelium of nasopharynxUBERON:000195192.80gold quality
corpus epididymisUBERON:000435992.79gold quality
gingivaUBERON:000182892.57gold quality
right uterine tubeUBERON:000130292.54gold quality
choroid plexus epitheliumUBERON:000391192.49gold quality
pigmented layer of retinaUBERON:000178292.33gold quality
skin of hipUBERON:000155492.27gold quality
mucosa of sigmoid colonUBERON:000499392.18gold quality
tonsilUBERON:000237291.97gold quality
pancreatic ductal cellCL:000207991.91gold quality
squamous epitheliumUBERON:000691491.90gold quality
colonic mucosaUBERON:000031791.78gold quality
epithelium of esophagusUBERON:000197691.66gold quality
oviduct epitheliumUBERON:000480491.66gold quality
calcaneal tendonUBERON:000370191.51gold quality
caput epididymisUBERON:000435891.48gold quality
spermCL:000001991.40gold quality
olfactory segment of nasal mucosaUBERON:000538691.06gold quality
lower esophagus mucosaUBERON:003583490.95gold quality
adrenal tissueUBERON:001830390.72gold quality
upper arm skinUBERON:000426390.66gold quality
islet of LangerhansUBERON:000000690.54gold quality
nephron tubuleUBERON:000123190.52gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-119yes49.94
E-ANND-3yes9.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, TP53

miRNA regulators (miRDB)

88 targeting LRBA, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-9-5P100.0072.282361
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-318599.9968.121959
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548N99.9871.944170
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-314899.9775.066478
HSA-MIR-512-3P99.9767.351049
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-218-5P99.9372.222103
HSA-MIR-314399.9371.963104
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-367199.9073.043897
HSA-MIR-806799.8669.592260
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-3121-3P99.8271.963630

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 36)

  • The crystal structure of the aPH-BEACH domains of LRBA were studied. (PMID:15554694)
  • mutations in LRBA cause an immune deficiency characterized by defects in B cell activation and autophagy and by susceptibility to apoptosis, associated with a clinical phenotype of hypogammaglobulinemia and autoimmunity (PMID:22608502)
  • A truncating mutation in LRBA, which abolished protein expression, was identified as the most likely candidate in a consanguineous family with chronic inflammatory bowel disease-like disorder and combined immunodeficiency. (PMID:22721650)
  • LRBA deficiency is a novel cause of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome and Treg cell deficiency associated with metabolic dysfunction and increased apoptosis of Treg cells. (PMID:25468195)
  • A homozygous missense mutation in lipopolysaccharide-responsive and beige-like anchor gene is associated with inflammatory bowel disease. (PMID:25479458)
  • LRBA mutation was associated with an autoimmune lymphoproliferative syndrome-like disease characterized by splenomegaly and lymphadenopathy, cytopenia, elevated double negative T cells and raised serum Fas ligand levels. (PMID:25931386)
  • Variants of LRBA were associated with common variable immunodeficiency. (PMID:26122175)
  • Patients with LRBA deficiency manifested a dramatic and sustained improvement in response to abatacept, a CTLA4 (cytotoxic T lymphocyte antigen-4)-immunoglobulin fusion drug. (PMID:26206937)
  • homozygous frame shift mutation results in refractory Celiac dsease (PMID:26686526)
  • mutations result in various immunodeficiency phenotypes (PMID:26707784)
  • diagnosis of LRBA deficiency was confirmed by a fluorescence-activated cell sorting-based immunoassay (PMID:26745254)
  • Among 2 brothers homozygous for LPS responsive beige-like anchor protein (LRBA) mutation, one developed Evans syndrome and deceased at age 8.5, and his brother carried the same homozygous LRBA mutation with early-onset erosive polyarthritis. (PMID:27057999)
  • Case Report: potential causative role of LRBA gene mutations in juvenile arthritis. (PMID:28134088)
  • Assessing total CTLA-4 expression levels was found to be optimal when restricting analysis to the CD45RA(-)Foxp3(+) fraction. CTLA-4 induction following stimulation, and the use of lysosomal-blocking compounds, distinguished CTLA-4 from LRBA mutations (PMID:28159733)
  • As diabetes was the presenting feature in six of nine individuals, we recommend that testing for LRBA mutations is considered in all patients with newly diagnosed neonatal diabetes and in those with infancy-onset diabetes (<12 months), especially when a recessive inheritance is suspected or additional autoimmune features are present (PMID:28473463)
  • cTFH cell dysregulation in patients with LRBA deficiency reflects impaired control of TFH cell differentiation because of profoundly decreased CTLA4 expression on regulatory T cells and probably contributes to autoimmunity in patients with this disease. Serial monitoring of cTFH cell frequencies is highly useful in gauging the clinical response of LRBA-deficient patients to CTLA4-Ig therapy. (PMID:28601686)
  • LRBA is required for hair bundle maintenance in cochlear hair cells and for hearing. (PMID:28893864)
  • The present results suggest that LRBA SNPs are associated with CWP susceptibility in a Chinese population. (PMID:28953250)
  • Mutations found in 7 out of 18 children with Evans syndrome (ES) involved lipopolysaccharide-responsive beige-like anchor protein (LRBA) and cytotoxic T-lymphocyte protein 4 (CTLA-4). (PMID:29330115)
  • LRBA Deficiency in Siblings. (PMID:29461210)
  • This easy flow cytometry-based assay allows a fast screening of patients with suspicion of LRBA deficiency reducing therefore the number of patients requiring LRBA sequencing and accelerating the treatment implementation. Detection of biallelic mutations in LRBA is however required for a definitive diagnosis. (PMID:29740429)
  • Our findings demonstrated an imbalance in Th subsets, mainly in Th1-like Th17 and Treg cells and their corresponding cytokines in LRBA deficiency, which might be important in the immunopathogenesis of autoimmunity and enteropathy. (PMID:29806698)
  • We are the first to report normal CTLA-4 expression and normal Treg-cell function in the face of overactive TH17 immunity in an LRBA-deficient patient, illustrating that loss of CTLA-4 is not a prerequisite for autoimmunity in LRBA deficiency (PMID:30193839)
  • CTLA-4 Expression in CD4+ T Cells From Patients With LRBA Deficiency. (PMID:30530390)
  • lymphocyte chromosomal radiosensitivity in patients with LPS responsive beige-like anchor protein (LRBA) deficiency (PMID:30714845)
  • Dissecting the localization of lipopolysaccharide-responsive and beige-like anchor protein (LRBA) in the endomembrane system. (PMID:31883622)
  • Clinical Phenotypes and Immunological Characteristics of 18 Egyptian LRBA Deficiency Patients. (PMID:32506362)
  • Evaluation of Expression of LRBA and CTLA-4 Proteins in Common Variable Immunodeficiency Patients. (PMID:33191838)
  • Pulmonary manifestations of immune dysregulation in CTLA-4 haploinsufficiency and LRBA deficiency. (PMID:33710794)
  • Case Report: Refractory Autoimmune Gastritis Responsive to Abatacept in LRBA Deficiency. (PMID:33717114)
  • Comprehensive comparison between 222 CTLA-4 haploinsufficiency and 212 LRBA deficiency patients: a systematic review. (PMID:33788257)
  • Novel compound heterozygous LRBA deletions in a 6-month-old with neonatal diabetes. (PMID:33845048)
  • Comparing the levels of CTLA-4-dependent biological defects in patients with LRBA deficiency and CTLA-4 insufficiency. (PMID:35491430)
  • Clinically Complex LRBA Deficiency Due to a Founder Allele in the Georgian Jewish Population. (PMID:36063261)
  • Various phenotypes of LRBA gene with compound heterozygous variation: A case series report of pediatric cytopenia patients. (PMID:36074705)
  • Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis. (PMID:39325073)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriolrbaENSDARG00000031108
mus_musculusLrbaENSMUSG00000028080
rattus_norvegicusLrbaENSRNOG00000023453
caenorhabditis_elegansWBGENE00004760
caenorhabditis_elegansWBGENE00007752

Paralogs (7): NSMAF (ENSG00000035681), WDFY4 (ENSG00000128815), LYST (ENSG00000143669), NBEAL1 (ENSG00000144426), NBEAL2 (ENSG00000160796), WDFY3 (ENSG00000163625), NBEA (ENSG00000172915)

Protein

Protein identifiers

Lipopolysaccharide-responsive and beige-like anchor proteinP50851 (reviewed: P50851)

Alternative names: Beige-like protein, CDC4-like protein

All UniProt accessions (14): A0A3B3IS13, A0A3B3ISK3, A0A3B3IU76, A0A494BZW2, P50851, A0A494C0R9, A0A494C1L5, A0A8V8TKR0, A0A8V8TL26, A0A8V8TLZ6, A0A8V8TM79, E9PEM5, H0Y9N9, H0YA17

UniProt curated annotations — full annotation on UniProt →

Function. Involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules. Involved in phagophore growth during mitophagy by regulating ATG9A trafficking to mitochondria.

Subunit / interactions. Interacts with TOM1 and TOLLIP.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane. Golgi apparatus. trans-Golgi network membrane. Lysosome membrane.

Tissue specificity. Ubiquitous.

Disease relevance. Immunodeficiency, common variable, 8, with autoimmunity (CVID8) [MIM:614700] An autosomal recessive immunologic disorder associated with defective B-cell differentiation and decreased or absent antibody production. Affected individuals have early-childhood onset of recurrent infections, particularly respiratory infections, and also develop variable autoimmune disorders, including idiopathic thrombocytopenic purpura, autoimmune hemolytic anemia, and inflammatory bowel disease. The disease is caused by variants affecting the gene represented in this entry.

Induction. By bacterial lipopolysaccharides (LPS).

Isoforms (2)

UniProt IDNamesCanonical?
P50851-11yes
P50851-22

RefSeq proteins (4): NP_001186211, NP_001351834, NP_001354479, NP_006717 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000409BEACH_domDomain
IPR001680WD40_rptRepeat
IPR010508NBEA-like_DUF1088Domain
IPR011989ARM-likeHomologous_superfamily
IPR011993PH-like_dom_sfHomologous_superfamily
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR016024ARM-type_foldHomologous_superfamily
IPR023362PH-BEACH_domDomain
IPR031570NBEA/BDCP_DUF4704Domain
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR036372BEACH_dom_sfHomologous_superfamily
IPR046851NBCH_WD40Domain
IPR046852Neurobeachin_a-solDomain
IPR050865BEACH_DomainFamily

Pfam: PF02138, PF06469, PF13385, PF14844, PF15787, PF20425, PF20426

UniProt features (93 total): helix 23, modified residue 17, sequence variant 11, strand 10, compositionally biased region 7, repeat 6, region of interest 6, sequence conflict 3, domain 2, splice variant 2, turn 2, initiator methionine 1, chain 1, coiled-coil region 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1T77X-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

No AlphaFold model available for P50851 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (17): 2, 10, 979, 1003, 1100, 1135, 1139, 1233, 1247, 1261, 1488, 1498, 1605, 1767, 1770, 2064, 2496

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 329 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_VACUOLE_ORGANIZATION, KAAB_FAILED_HEART_ATRIUM_DN, GOCC_VACUOLAR_MEMBRANE, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, CAGCTG_AP4_Q5, GOBP_MACROAUTOPHAGY, KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION, GENTILE_UV_HIGH_DOSE_DN, ATTCTTT_MIR186, GOBP_ORGANELLE_ASSEMBLY, ZHANG_BREAST_CANCER_PROGENITORS_UP, CUI_TCF21_TARGETS_2_DN, CTTTGTA_MIR524

GO Biological Process (3): mitophagy (GO:0000423), intracellular protein localization (GO:0008104), protein localization to phagophore assembly site (GO:0034497)

GO Molecular Function (2): protein kinase binding (GO:0019901), protein binding (GO:0005515)

GO Cellular Component (9): lysosomal membrane (GO:0005765), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), cytoplasm (GO:0005737), lysosome (GO:0005764), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
cellular anatomical structure3
endomembrane system2
intracellular membrane-bounded organelle2
autophagy of mitochondrion1
macroautophagy1
macromolecule localization1
autophagosome assembly1
intracellular protein localization1
kinase binding1
binding1
lysosome1
lytic vacuole membrane1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
intracellular anatomical structure1
lytic vacuole1

Protein interactions and networks

STRING

964 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRBACTLA4P16410800
LRBAPRKACAP17612718
LRBAPRKACGP22612717
LRBAPRKACBP22694717
LRBAFBXW7Q969H0657
LRBAPIK3R4Q99570656
LRBATTC7AQ9ULT0621
LRBATNFRSF13BO14836591
LRBADOCK8Q8NF50582
LRBASTXBP2Q15833558
LRBATNFRSF13CQ96RJ3506
LRBAFOXP3Q9BZS1499
LRBAICOSQ9Y6W8473
LRBAPIK3R1P27986464
LRBAPRKCDQ05655460

IntAct

126 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CTLA4LRBApsi-mi:“MI:0915”(physical association)0.670
RCCD1SPAG9psi-mi:“MI:0914”(association)0.640
RELTOXSR1psi-mi:“MI:0914”(association)0.640
SLC1A1AGPAT2psi-mi:“MI:0914”(association)0.640
NIPAL1ESYT2psi-mi:“MI:0914”(association)0.640
RAB9ACHMpsi-mi:“MI:2364”(proximity)0.610
CT55BLTP3Bpsi-mi:“MI:0914”(association)0.530
GYPBTCAF2psi-mi:“MI:0914”(association)0.530
EPHA1EXOC5psi-mi:“MI:0914”(association)0.530
INSYN2ACHUKpsi-mi:“MI:0914”(association)0.530
RIC3ATP9Apsi-mi:“MI:0914”(association)0.530
CD70METTL15psi-mi:“MI:0914”(association)0.530
CTLA4B4GALT5psi-mi:“MI:0914”(association)0.530
TGOLN2PGRMC1psi-mi:“MI:0914”(association)0.420
LRBACTLA4psi-mi:“MI:0915”(physical association)0.400
LRBAABL1psi-mi:“MI:0915”(physical association)0.400
FYNLRBApsi-mi:“MI:0915”(physical association)0.400
LRBAH3C13psi-mi:“MI:0915”(physical association)0.400
LRBASENP1psi-mi:“MI:0915”(physical association)0.400
RIPK4VWA8psi-mi:“MI:0914”(association)0.350
NOTCH1CNOT1psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (241): LRBA (Affinity Capture-RNA), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Proximity Label-MS), LRBA (Proximity Label-MS), LRBA (Proximity Label-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS), LRBA (Affinity Capture-MS)

ESM2 similar proteins: A0JM23, A0M8T3, A1X154, A6H7D1, A7MBF6, A8Y5U1, B1WC10, E9Q9R9, F1M649, F1MHT9, O00750, O88480, O95876, P0CI65, P50851, Q008S8, Q00PJ3, Q07E17, Q07E30, Q07E43, Q09YN0, Q108U1, Q15052, Q2IBF5, Q2IBG0, Q2QLA4, Q2QLB5, Q32NR4, Q32NR9, Q3UP24, Q3V129, Q4V7F0, Q5XXR3, Q5ZLR6, Q692V3, Q6AZT7, Q6P2S7, Q6P3V7, Q6PIY5, Q6ZS30

Diamond homologs: A8XSV3, D4A929, E7FAW3, E9Q2M9, F4HZB2, F4IG73, F4JD14, F4JHT3, O35242, P0C6P0, P25356, P50851, P97412, Q19317, Q54PP7, Q54RQ8, Q55AV3, Q55DM1, Q562E7, Q5ND34, Q6VNB8, Q6ZNJ1, Q6ZQA0, Q6ZS30, Q6ZS81, Q7LKZ7, Q86JF2, Q8IZQ1, Q8NFP9, Q92636, Q99698, Q9DDD5, Q9EPN1, Q9ESE1, Q9TTK4, Q9W060, Q9W4E2, E7FEV0, F4JY12, Q10122

SIGNOR signaling

2 interactions.

AEffectBMechanism
E2F1“up-regulates quantity by expression”LRBA“transcriptional regulation”
TP53“down-regulates quantity by repression”LRBA“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 167 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
EPHA-mediated growth cone collapse517.6×2e-03
EPH-ephrin mediated repulsion of cells612.2×2e-03
Constitutive Signaling by Aberrant PI3K in Cancer89.4×1e-03
EPH-Ephrin signaling69.2×5e-03
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling87.2×2e-03
PIP3 activates AKT signaling95.6×4e-03

GO biological processes:

GO termPartnersFoldFDR
peptidyl-tyrosine phosphorylation617.0×2e-03
ephrin receptor signaling pathway613.8×2e-03
cell surface receptor protein tyrosine kinase signaling pathway78.2×5e-03
protein autophosphorylation87.8×2e-03
axon guidance106.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

2607 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic125
Likely pathogenic72
Uncertain significance1226
Likely benign910
Benign112

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1069622NM_001364905.1(LRBA):c.5125_5152dup (p.Gln1718delinsArgTer)Pathogenic
1070799NM_001364905.1(LRBA):c.5980C>T (p.Arg1994Ter)Pathogenic
1072644NM_001364905.1(LRBA):c.6909G>A (p.Trp2303Ter)Pathogenic
1072918NM_001364905.1(LRBA):c.3830C>G (p.Ser1277Ter)Pathogenic
1074569NC_000004.11:g.(?151604683)(151604889_?)delPathogenic
1074570NC_000004.11:g.(?151336570)(151520303_?)delPathogenic
1176175NM_001364905.1(LRBA):c.7009C>T (p.Arg2337Ter)Pathogenic
1176176NM_001364905.1(LRBA):c.6829del (p.Tyr2277fs)Pathogenic
1177585NM_001364905.1(LRBA):c.4261A>G (p.Ser1421Gly)Pathogenic
1361756NM_001364905.1(LRBA):c.448+1G>TPathogenic
1376199NM_001364905.1(LRBA):c.6235del (p.Ser2079fs)Pathogenic
1391949NM_001364905.1(LRBA):c.1697del (p.Lys566fs)Pathogenic
1392922NM_001364905.1(LRBA):c.6269_6270delinsAA (p.Ser2090Ter)Pathogenic
1415306NM_001364905.1(LRBA):c.893del (p.Lys298fs)Pathogenic
1419646NC_000004.11:g.(?151814184)(151814321_?)delPathogenic
1419984NM_001364905.1(LRBA):c.5060_5067del (p.Asn1687fs)Pathogenic
1424023NM_001364905.1(LRBA):c.488del (p.Asn163fs)Pathogenic
1424030NM_001364905.1(LRBA):c.2614del (p.Ser872fs)Pathogenic
1452672NM_001364905.1(LRBA):c.6319del (p.Ile2107fs)Pathogenic
1453544NM_001364905.1(LRBA):c.7928del (p.Asn2643fs)Pathogenic
1455821NM_001364905.1(LRBA):c.1736G>A (p.Trp579Ter)Pathogenic
1457482NM_001364905.1(LRBA):c.6551+1delPathogenic
1458653NC_000004.11:g.(?151504182)(151656538_?)delPathogenic
1458881NM_001364905.1(LRBA):c.2836_2839del (p.Glu945_Glu946insTer)Pathogenic
1495928NM_001364905.1(LRBA):c.5646-2A>TPathogenic
162667NM_001364905.1(LRBA):c.2032C>T (p.Gln678Ter)Pathogenic
1687335NM_001364905.1(LRBA):c.534del (p.Asp179fs)Pathogenic
1974806NM_001364905.1(LRBA):c.5903G>A (p.Trp1968Ter)Pathogenic
2011098NM_001364905.1(LRBA):c.6979C>T (p.Arg2327Ter)Pathogenic
2013113NM_001364905.1(LRBA):c.2204_2205dup (p.Arg736fs)Pathogenic

SpliceAI

10976 predictions. Top by Δscore:

VariantEffectΔscore
4:150265813:CTAGG:Cacceptor_loss1.0000
4:150265814:T:Aacceptor_loss1.0000
4:150266459:G:Cacceptor_gain1.0000
4:150266459:G:GCacceptor_gain1.0000
4:150277852:CCT:Cdonor_gain1.0000
4:150277897:T:TAdonor_gain1.0000
4:150282448:A:ACdonor_gain1.0000
4:150282449:C:CCdonor_gain1.0000
4:150282449:CT:Cdonor_gain1.0000
4:150302619:A:ACdonor_gain1.0000
4:150302619:ACTT:Adonor_loss1.0000
4:150302620:C:CCdonor_gain1.0000
4:150302620:CTT:Cdonor_loss1.0000
4:150302621:TTA:Tdonor_loss1.0000
4:150302622:TACTG:Tdonor_loss1.0000
4:150302623:A:ACdonor_gain1.0000
4:150302623:ACTGC:Adonor_gain1.0000
4:150302624:C:CGdonor_gain1.0000
4:150302624:CT:Cdonor_gain1.0000
4:150302624:CTG:Cdonor_gain1.0000
4:150302624:CTGCC:Cdonor_gain1.0000
4:150302789:CTTC:Cacceptor_gain1.0000
4:150302790:TTC:Tacceptor_gain1.0000
4:150302793:C:CCacceptor_gain1.0000
4:150302794:T:Aacceptor_loss1.0000
4:150310381:CTGG:Cacceptor_gain1.0000
4:150310382:TGG:Tacceptor_gain1.0000
4:150310383:GG:Gacceptor_gain1.0000
4:150310383:GGC:Gacceptor_loss1.0000
4:150310384:GC:Gacceptor_loss1.0000

AlphaMissense

18757 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:150302670:A:GW2669R1.000
4:150302670:A:TW2669R1.000
4:150321295:A:TV2520D1.000
4:150471681:A:GW2215R1.000
4:150471681:A:TW2215R1.000
4:150761839:T:AQ1863H1.000
4:150761839:T:GQ1863H1.000
4:150761842:C:AW1862C1.000
4:150761842:C:GW1862C1.000
4:150761843:C:GW1862S1.000
4:150761844:A:GW1862R1.000
4:150761844:A:TW1862R1.000
4:150798087:A:CC1858W1.000
4:150798094:A:GL1856P1.000
4:150806312:A:GL1826P1.000
4:150867841:A:GW866R1.000
4:150867841:A:TW866R1.000
4:150265786:C:AG2843V0.999
4:150265786:C:TG2843E0.999
4:150265798:C:TG2839D0.999
4:150285943:A:CS2714R0.999
4:150285943:A:TS2714R0.999
4:150285945:T:GS2714R0.999
4:150302678:A:GL2666P0.999
4:150302688:C:GD2663H0.999
4:150302694:A:GS2661P0.999
4:150302696:C:TG2660E0.999
4:150302697:C:AG2660W0.999
4:150302753:A:TV2641D0.999
4:150310254:A:CS2619R0.999

dbSNP variants (sampled 300 via entrez): RS1000001906 (4:150877815 A>C), RS1000003629 (4:150518860 TAAC>T), RS1000005145 (4:150560648 C>A,G), RS1000010116 (4:150941862 G>A), RS1000010980 (4:150468756 G>C), RS10000193 (4:150695941 A>G), RS1000022788 (4:150441642 T>C), RS1000026919 (4:150522910 G>A,C), RS1000027368 (4:150529296 A>G), RS1000029531 (4:150965205 A>T), RS1000030116 (4:150695888 A>C), RS1000037461 (4:150551075 T>G), RS1000038587 (4:150385037 C>T), RS1000039179 (4:150943928 T>C), RS1000045363 (4:150381197 ACATT>A)

Disease associations

OMIM: gene MIM:606453 | disease phenotypes: MIM:614700, MIM:156000, MIM:617296, MIM:615877, MIM:181500, MIM:142623, MIM:615401

GenCC curated gene-disease

DiseaseClassificationInheritance
combined immunodeficiency due to LRBA deficiencyStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
combined immunodeficiency due to LRBA deficiencyDefinitiveAR

Mondo (8): combined immunodeficiency due to LRBA deficiency (MONDO:0013863), Meniere disease (MONDO:0007972), spastic paraplegia, intellectual disability, nystagmus, and obesity (MONDO:0015007), colobomatous microphthalmia-rhizomelic dysplasia syndrome (MONDO:0014380), schizophrenia (MONDO:0005090), long QT syndrome (MONDO:0002442), Hirschsprung disease, susceptibility to, 1 (MONDO:0007723), severe combined immunodeficiency due to CORO1A deficiency (MONDO:0014168)

Orphanet (7): Syndromic autoimmune enteropathy due to LRBA deficiency (Orphanet:445018), Spastic paraplegia-intellectual disability-nystagmus-obesity syndrome (Orphanet:521390), Colobomatous microphthalmia-rhizomelic dysplasia syndrome (Orphanet:424099), Hirschsprung disease (Orphanet:388), Severe combined immunodeficiency due to CORO1A deficiency (Orphanet:228003), NON RARE IN EUROPE: Menière disease (Orphanet:45360), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

45 total (30 of 45 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000403Recurrent otitis media
HP:0000509Conjunctivitis
HP:0000554Uveitis
HP:0000821Hypothyroidism
HP:0001045Vitiligo
HP:0001369Arthritis
HP:0001508Failure to thrive
HP:0001510Growth delay
HP:0001744Splenomegaly
HP:0001873Thrombocytopenia
HP:0001876Pancytopenia
HP:0001890Autoimmune hemolytic anemia
HP:0001973Autoimmune thrombocytopenia
HP:0002028Chronic diarrhea
HP:0002037Inflammation of the large intestine
HP:0002090Pneumonia
HP:0002099Asthma
HP:0002110Bronchiectasis
HP:0002205Recurrent respiratory infections
HP:0002582Atrophic gastritis
HP:0002583Colitis
HP:0002665Lymphoma
HP:0002716Lymphadenopathy
HP:0002719Recurrent infections
HP:0002720Decreased circulating IgA concentration
HP:0002721Immunodeficiency
HP:0002850Decreased circulating total IgM
HP:0004315Decreased circulating IgG concentration
HP:0005523Lymphoproliferative disorder

GWAS associations

11 associations (top):

StudyTraitp-value
GCST001715_3Bipolar disorder with mood-incongruent psychosis1.000000e-07
GCST002997_2Helix rolling2.000000e-08
GCST003001_5Ear morphology4.000000e-08
GCST004079_1Drug-induced hepatocellular liver injury5.000000e-09
GCST006628_39Systolic blood pressure4.000000e-10
GCST007209_5Gallstone disease5.000000e-27
GCST010397_65Gut microbiota (bacterial taxa, rank normal transformation method)5.000000e-06
GCST90002398_461Neutrophil count1.000000e-13
GCST90002407_448White blood cell count1.000000e-13
GCST90011900_93Serum alkaline phosphatase levels3.000000e-18
GCST90013406_218Liver enzyme levels (alkaline phosphatase)2.000000e-26

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0007670helix rolling
EFO:0007664outer ear morphology trait
EFO:0006335systolic blood pressure
EFO:0007874gut microbiome measurement
EFO:0004833neutrophil count
EFO:0004533alkaline phosphatase measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D008133Long QT SyndromeC14.280.067.565; C14.280.123.625; C16.131.240.400.715; C23.550.073.547
D008575Meniere DiseaseC09.218.568.217.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066253 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 3 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.78Kd167.1nMCHEMBL5653589
6.78ED50167.1nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148664: Binding affinity to human LRBA incubated for 45 mins by Kinobead based pull down assaykd0.1671uM

CTD chemical–gene interactions

58 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression8
Aflatoxin B1increases methylation, affects expression, decreases expression5
Cisplatinaffects cotreatment, decreases expression, increases expression3
Valproic Acidaffects expression, decreases methylation, increases expression3
Acetaminophendecreases expression2
Air Pollutantsaffects cotreatment, affects expression, affects oxidation, increases abundance, decreases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects oxidation, increases abundance, affects cotreatment, affects expression1
bisphenol Adecreases expression1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression, increases abundance1
cobaltous chloridedecreases expression1
ochratoxin Aincreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2decreases methylation1
coumarindecreases phosphorylation1
methacrylaldehydeaffects oxidation, increases abundance, affects cotreatment, affects expression1
epigallocatechin gallatedecreases expression, affects cotreatment1
bicalutamideincreases expression1
tamibaroteneaffects expression1
ICG 001decreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651706BindingBinding affinity to human LRBA incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0WIUbigene Jurkat, Clone E6-1 LRBA KOCancer cell lineMale
CVCL_SV80HAP1 LRBA (-) 1Cancer cell lineMale
CVCL_SV81HAP1 LRBA (-) 2Cancer cell lineMale
CVCL_SV82HAP1 LRBA (-) 3Cancer cell lineMale
CVCL_SV83HAP1 LRBA (-) 4Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01574313PHASE4COMPLETEDEffect of Stellate Ganglion Block on Meniere’s Disease
NCT02529475PHASE4TERMINATEDEvaluation of Inner Ear and Brain Structures With Contrast-enhanced MRI in Healthy Subjects (HYDROPS)
NCT04815187PHASE4ACTIVE_NOT_RECRUITINGRepurposed Use of Allergic Rhinitis and Allergic Asthma Drug to Reduce Vertigo and Hearing Loss in Meniere’s Disease
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia