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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	3	5
missense			40	8	4	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	40	10	7

Variants in LBP

This is a list of pathogenic ClinVar variants found in the LBP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-38346536-C-T		not specified	Uncertain significance (Feb 21, 2024)
20-38346565-C-A		not specified	Uncertain significance (May 15, 2024)
20-38346575-C-T		not specified	Uncertain significance (Mar 30, 2024)
20-38346598-C-G		not specified	Uncertain significance (May 28, 2024)
20-38346610-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-38349567-A-G			Benign (Dec 31, 2019)
20-38349637-G-A		not specified	Uncertain significance (Jun 17, 2024)
20-38349637-G-T		not specified	Uncertain significance (Apr 12, 2024)
20-38349647-G-T		not specified	Uncertain significance (Aug 04, 2023)
20-38349654-G-C		not specified	Uncertain significance (Apr 05, 2023)
20-38350811-C-T		not specified	Likely benign (Jan 23, 2024)
20-38350812-C-G		not specified	Uncertain significance (Sep 27, 2021)
20-38350842-T-A			Likely benign (Jan 01, 2024)
20-38350847-G-A			Likely benign (Jul 31, 2018)
20-38350902-C-T		not specified	Uncertain significance (Dec 10, 2024)
20-38350909-A-G		not specified	Uncertain significance (May 03, 2023)
20-38350938-T-C		not specified	Likely benign (Dec 21, 2023)
20-38354288-C-A			Benign (Jun 29, 2018)
20-38354363-G-A		not specified	Uncertain significance (Jul 18, 2024)
20-38354367-G-A		not specified	Uncertain significance (Aug 28, 2024)
20-38354416-G-T		not specified	Likely benign (Aug 21, 2024)
20-38354417-G-A		not specified	Uncertain significance (Feb 12, 2024)
20-38354438-G-C		not specified	Uncertain significance (Feb 26, 2024)
20-38355373-G-T		not specified	Uncertain significance (Aug 21, 2024)
20-38360727-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LBP	protein_coding	protein_coding	ENST00000217407	15	30907

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.19e-15	0.0233	125358	1	389	125748	0.00155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.154	287	280	1.03	0.0000157	3126
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00290	0.00275
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00549	0.00545
Finnish	0.00	0.00
European (Non-Finnish)	0.000537	0.000536
Middle Eastern	0.00549	0.00545
South Asian	0.00480	0.00478
Other	0.000490	0.000489

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

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