LBP
protein-codinglipopolysaccharide binding protein, the group of BPI fold containing
Gene summary
The protein encoded by this gene is involved in the acute-phase immunologic response to gram-negative bacterial infections. Gram-negative bacteria contain a glycolipid, lipopolysaccharide (LPS), on their outer cell wall. Together with bactericidal permeability-increasing protein (BPI), the encoded protein binds LPS and interacts with the CD14 receptor, probably playing a role in regulating LPS-dependent monocyte responses. Studies in mice suggest that the encoded protein is necessary for the rapid acute-phase response to LPS but not for the clearance of LPS from circulation. This protein is part of a family of structurally and functionally related proteins, including BPI, plasma cholesteryl ester transfer protein (CETP), and phospholipid transfer protein (PLTP). [provided by RefSeq, Apr 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LBP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004139.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 70 | 10 | 4 | 84 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 72 | 13 | 5 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004130.2 | 15 | MANE Select | |
| Ensembl | ENSP00000217407.2 | 15 | MANE Select | |
| Ensembl | ENSP00000571311.1 | 14 | Standard | |
| Ensembl | ENSP00000571311.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
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
Molecular Function
- lipopolysaccharide binding
- signaling receptor binding
- protein binding
- lipoteichoic acid binding
- lipopeptide binding
Cellular Component
- extracellular region
- extracellular space
- cell surface
- membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000217407
- Coding exons
- 15
- Length
- 30907
- Individuals with no LoFs
- 125358
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 389
- Defined
- 125748
- p
- 0.00155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.154 | 287 | 280 | 1.03 | 0.0000157 | 3126 |
| Missense (PolyPhen) | 78 | 81.49 | 0.95717 | 1000 | ||
| Synonymous | -0.00489 | 120 | 120 | 1.00 | 0.00000747 | 965 |
| Loss of Function | 0.280 | 23 | 24.5 | 0.939 | 0.00000122 | 290 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0010 | 0.00086 | notable |
| Latino/Admixed American | 0.0019 | 0.0019 | notable |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0055 | 0.0055 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00054 | 0.00054 | rare |
| South Asian | 0.0048 | 0.0048 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.187
Intolerance Scores
- LoFtool
- 0.971
- RVIS EVS
- 3.18
- RVIS percentile EVS
- 99.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.641
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |