GeneBe

LBP

lipopolysaccharide binding protein, the group of BPI fold containing

Basic information

Region (hg38): 20:38346482-38377013

Links

ENSG00000129988 ∙ NCBI:3929 ∙ OMIM:151990 ∙ HGNC:6517 ∙ Uniprot:P18428 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LBP gene.

  • not_specified (68 variants)
  • not_provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LBP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004139.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
1
clinvar
 4
missense
61
clinvar
10
clinvar
4
clinvar
 75
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 61 13 5
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LBPprotein_codingprotein_codingENST00000217407 1530907
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.19e-150.023312535813891257480.00155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1542872801.030.00001573126
Missense in Polyphen7881.490.957171000
Synonymous-0.004891201201.000.00000747965
Loss of Function0.2802324.50.9390.00000122290

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002900.00275
Ashkenazi Jewish0.00009940.0000992
East Asian0.005490.00545
Finnish0.000.00
European (Non-Finnish)0.0005370.000536
Middle Eastern0.005490.00545
South Asian0.004800.00478
Other0.0004900.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in the innate immune response. Binds to the lipid A moiety of bacterial lipopolysaccharides (LPS), a glycolipid present in the outer membrane of all Gram-negative bacteria (PubMed:7517398, PubMed:24120359). Acts as an affinity enhancer for CD14, facilitating its association with LPS. Promotes the release of cytokines in response to bacterial lipopolysaccharide (PubMed:7517398, PubMed:24120359). {ECO:0000269|PubMed:1698311, ECO:0000269|PubMed:20133493, ECO:0000269|PubMed:24120359, ECO:0000269|PubMed:7517398, ECO:0000305|PubMed:17481951}.;
Pathway
Salmonella infection - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Interleukin-4 and 13 signaling;Fibrin Complement Receptor 3 Signaling Pathway;Toll-like Receptor Signaling Pathway;TLR NFkB;Toll-Like Receptors Cascades;Innate Immune System;Immune System;TLR p38;Regulation of TLR by endogenous ligand;TLR ECSIT MEKK1 JNK;TLR ECSIT MEKK1 p38;Transfer of LPS from LBP carrier to CD14;TLR JNK;Toll Like Receptor 4 (TLR4) Cascade;IL6-mediated signaling events (Consensus)

Recessive Scores

pRec
0.187

Intolerance Scores

loftool
0.971
rvis_EVS
3.18
rvis_percentile_EVS
99.32

Haploinsufficiency Scores

pHI
0.336
hipred
N
hipred_score
0.112
ghis
0.468

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.641

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lbp
Phenotype
hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
toll-like receptor signaling pathway;leukocyte chemotaxis involved in inflammatory response;macrophage activation involved in immune response;acute-phase response;cellular defense response;opsonization;lipopolysaccharide transport;cytokine-mediated signaling pathway;lipopolysaccharide-mediated signaling pathway;detection of molecule of bacterial origin;response to lipopolysaccharide;negative regulation of tumor necrosis factor production;positive regulation of chemokine production;positive regulation of interleukin-6 production;positive regulation of interleukin-8 production;positive regulation of tumor necrosis factor production;macromolecule localization;toll-like receptor 4 signaling pathway;positive regulation of toll-like receptor 4 signaling pathway;positive regulation of tumor necrosis factor biosynthetic process;positive regulation of macrophage activation;negative regulation of growth of symbiont in host;innate immune response;positive regulation of cytolysis;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive regulation of respiratory burst involved in inflammatory response;cellular response to lipopolysaccharide;cellular response to lipoteichoic acid;positive regulation of neutrophil chemotaxis
Cellular component
extracellular region;extracellular space;cell surface;membrane;extracellular exosome
Molecular function
lipopolysaccharide binding;signaling receptor binding;protein binding;lipoteichoic acid binding;lipopeptide binding