LBP

Summary

LBP (lipopolysaccharide binding protein, HGNC:6517) is a protein-coding gene on chromosome 20q11.23, encoding Lipopolysaccharide-binding protein (P18428). Plays a role in the innate immune response.

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).

Source: NCBI Gene 3929 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_004139

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6517
Approved symbol	LBP
Name	lipopolysaccharide binding protein
Location	20q11.23
Locus type	gene with protein product
Status	Approved
Aliases	BPIFD2
Ensembl gene	ENSG00000129988
Ensembl biotype	protein_coding
OMIM	151990
Entrez	3929

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000217407, ENST00000901252, ENST00000901253, ENST00000901254, ENST00000901255, ENST00000901256, ENST00000901257, ENST00000901258, ENST00000968709

RefSeq mRNA: 1 — MANE Select: NM_004139 NM_004139

CCDS: CCDS13304

Canonical transcript exons

ENST00000217407 — 15 exons

Exon	Start	End
ENSE00000661940	38349548	38349662
ENSE00000661941	38350811	38350939
ENSE00000661942	38354284	38354439
ENSE00000661943	38355346	38355409
ENSE00000661944	38360704	38360767
ENSE00000661946	38363975	38364066
ENSE00000661949	38364576	38364752
ENSE00000661950	38366769	38366828
ENSE00000661951	38368995	38369162
ENSE00000661952	38370738	38370805
ENSE00000661953	38371280	38371322
ENSE00000661954	38373072	38373135
ENSE00000844631	38346482	38346640
ENSE00000844632	38373937	38374013
ENSE00001037453	38376625	38377013

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 99.00.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 8.0037 / max 3397.9226, expressed in 145 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184565	7.9648	142
184564	0.0389	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	99.00	gold quality
liver	UBERON:0002107	97.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.71	gold quality
pancreatic ductal cell	CL:0002079	80.86	silver quality
tibialis anterior	UBERON:0001385	79.04	silver quality
gastrocnemius	UBERON:0001388	78.67	gold quality
omental fat pad	UBERON:0010414	77.80	gold quality
peritoneum	UBERON:0002358	77.75	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.40	gold quality
adipose tissue of abdominal region	UBERON:0007808	76.23	gold quality
diaphragm	UBERON:0001103	75.89	gold quality
muscle of leg	UBERON:0001383	75.50	gold quality
vermiform appendix	UBERON:0001154	74.69	gold quality
deltoid	UBERON:0001476	74.08	silver quality
subcutaneous adipose tissue	UBERON:0002190	74.05	gold quality
adipose tissue	UBERON:0001013	72.92	gold quality
caecum	UBERON:0001153	72.15	gold quality
muscle organ	UBERON:0001630	71.60	gold quality
skeletal muscle organ	UBERON:0014892	71.60	gold quality
connective tissue	UBERON:0002384	71.43	gold quality
gluteal muscle	UBERON:0002000	71.18	silver quality
right lobe of thyroid gland	UBERON:0001119	71.17	gold quality
pericardium	UBERON:0002407	71.03	gold quality
olfactory bulb	UBERON:0002264	71.02	gold quality
adult mammalian kidney	UBERON:0000082	70.56	gold quality
epithelial cell of pancreas	CL:0000083	70.34	gold quality
type B pancreatic cell	CL:0000169	69.88	gold quality
layer of synovial tissue	UBERON:0007616	69.82	gold quality
superficial temporal artery	UBERON:0001614	69.47	gold quality
ileal mucosa	UBERON:0000331	69.22	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, CEBPA, CEBPB, JUN, NFKB, NR0B1, NR5A1, STAT3, TCF3

miRNA regulators (miRDB)

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

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-4751	98.80	64.95	525
HSA-MIR-6804-3P	98.72	64.82	852
HSA-MIR-4299	98.28	66.96	850
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-4468	98.01	66.85	1187
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-4653-5P	97.22	67.72	1429
HSA-MIR-4689	96.97	65.79	1209
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-6858-5P	96.05	64.59	1020
HSA-MIR-6821-3P	95.21	66.79	578
HSA-MIR-6889-5P	90.26	64.13	291
HSA-MIR-6790-3P	88.15	62.55	113

Literature-anchored findings (GeneRIF, showing 40)

• carboxyl-terminal domain of these closely related endotoxin-binding proteins dictates the route and host responses to complexes they form with endotoxin. (PMID:11773072)
• a new and reliable infection marker after kidney transplantation (PMID:11976738)
• Identification of single amino acid residues essential for the binding of lipopolysaccharide (LPS) to LPS binding protein (LBP) residues 86-99 by using an Ala-scanning library (PMID:11991204)
• plasma factor LBP and cell surface receptor CD14 were necessary for LPS activation of p38, which was tightly associated with LPS priming of the PMN respiratory burst (PMID:12117913)
• Besides a role in the detoxification of bacterial toxin present in the circulation, LBP-chylomicron complexes may be part of a local defense mechanism of the intestine against translocated bacterial toxin. (PMID:12538700)
• innate immune recognition of LTA via LBP, CD14, and TLR-2 represents an important mechanism in the pathogenesis of systemic complications in the course of infectious diseases brought about by Gram-positive pathogens. while TLR-4 and MD-2 are not involved. (PMID:12594207)
• Single nucleotide polymorphism of the LBP gene is not assciated with complicated sepsis after trauma. (PMID:12615620)
• data support the hypothesis that lipopolysaccharide binding protein can inhibit cell responses to lipopolysaccharide(LPS) by inhibiting LPS transfer from membrane CD14 to the Toll-like receptor 4-MD-2 signaling receptor (PMID:12754215)
• plays an essential role in the innate immune response to Gram-positive pneumococci (PMID:12932360)
• In critically ill neonates aged over 48 h and children lipopolysaccharide binding protein is a better marker than procalcitonin, interleukin-6 and C-reactive protein. (PMID:15127192)
• Dual role of LBP and CD14 in initiation of proinflammatory signaling and clearance or neutralization of LPS. (PMID:15618154)
• studies suggest that SP-A could contribute to modulate Re-LPS responses by altering the competence of the LBP-CD14 receptor complex (PMID:15932345)
• LBP mediates the fusion of lipid membranes and LPS aggregates. (PMID:16303759)
• Human pulmonary LBP acts as an important modulator of the LPS response in the respiratory tract in vivo. (PMID:16493079)
• Significantly elevated serum concentrations of LBP and sCD14 are found in severe sepsis patients. (PMID:16512634)
• innate immune recognition of LTA is organ-specific with negative regulation by LBP in serum-containing compartments and sensitive recognition in serum-free compartments like the lung (PMID:16928689)
• Transcriptional regulation of the LBP gene contributes to the risk for developing gram-negative bacteremia and death after hematopoietic stem cell transplantation. (PMID:18056482)
• Chlamydiaceae LPS has low binding affinities for LPS recognition molecules such as CD14 and LBP and exhibit weak biological activities against host immune cells including monocytes. (PMID:18056918)
• Lipopolysaccharide binding protein and sCD14 are not produced as acute phase proteins in cardiac surgery (PMID:18288274)
• The CR3-mediated phagocytosis of Neisseria meningitidis required the presence of lipopolysaccharide-binding protein, LBP. (PMID:18397383)
• Oxidized phospholipid inhibition of toll-like receptor (TLR) signaling is restricted to TLR2 and TLR4: roles for CD14, LPS-binding protein, and MD2 as targets for specificity of inhibition. (PMID:18559343)
• Increase of lipopolysaccharide binding protein and C-reactive protein levels after premature rupture of the membranes (PROM)seem to reflect intramniotic infection, but no cut-off values could be defined for the prediction of intraamniotic infection (PMID:18783308)
• Lipopolysaccharide-binding protein and CD14 are increased in the bronchoalveolar lavage fluid of smokers (PMID:19010986)
• LBP Phe436Leu polymorphisms showed no effect on chlamydial growth. (PMID:19522765)
• The association of the polymorphisms c.291C>T and c.613A>G suggest a role of LBP in the disease manifestation of infective endocarditis. (PMID:19560454)
• This study strongly supports the involvement of LBP gene variants in severe sepsis susceptibility and reinforces the merit of further exploration of the role of lipopolysaccharide-binding protein in sepsis. (PMID:19707138)
• Serial LBP serum measurements may offer a clinically useful biomarker for identification of patients with severe sepsis having the worst outcomes and the highest probability of developing sepsis-induced ARDS (PMID:19718443)
• Elevated circulating LBP was associated with obesity, metabolic syndrome, and type 2 diabetes in apparently healthy Chinese. (PMID:20530747)
• High LBP is associated with Crohn’s disease. (PMID:20865702)
• LBP measurements performed shortly after preterm premature rupture of membranes, are not of value either in the prediction of newborn’s infection, or in the prognosis of latency period duration. (PMID:21353369)
• This study highlights the LBP rs2232596 and CD14 rs4914 polymorphisms as biomarkers for elevated colorectal carcinoma susceptibility in the Chinese Han population (PMID:21633598)
• Cytokine concentrations in amniotic fluid during the mid-trimester did not differ with parity or fetal gender. IL-6, IL-8, and LBP levels appeared stable with gestational week (GW), whereas GW significantly influenced TNF-alpha concentrations. (PMID:21702700)
• Aseptic trauma primes the innate immune system for the posttraumatic release of lipopolysaccharide binding protein and sCD14 (PMID:21722015)
• The availability of commercial methods for the automated measurement of the soluble CD14 subtype presepsin and lipopolysaccharide binding protein represent a challenge for the evaluation in clinical practice of reliable markers of neonatal sepsis. (PMID:21740312)
• During the first 14 days of postoperative sepsis, LBP plasma concentrations showed a time course that was very similar to CRP with a high concordance in the pattern of day-to-day changes (PMID:21901123)
• Association of lipopolysaccharide-binding protein gene polymorphisms with cerebral infarction in a Chinese population (PMID:22476641)
• our study demonstrated that an elevated LBP level of >15000 ng/ml may serve as a biomarker for the prediction and monitoring of aGVHD. (PMID:22552880)
• expression in oral keratinocytes is stimulated by Porphyromonas gingivalis LPS (PMID:22736337)
• LBP is a surrogate marker of microbial translocation in association with physical functioning of older adults. (PMID:22960476)
• Serum LBP concentrations increased with age. Overweight, obesity, and having metabolic syndrome (particularly, low HDL cholesterol levels) were associated with higher LBP concentrations (PMID:23349936)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lbp	ENSMUSG00000016024
rattus_norvegicus	Lbp	ENSRNOG00000014532

Paralogs (12): BPIFB2 (ENSG00000078898), CETP (ENSG00000087237), PLTP (ENSG00000100979), BPI (ENSG00000101425), BPIFB1 (ENSG00000125999), BPIFA2 (ENSG00000131050), BPIFA3 (ENSG00000131059), BPIFB6 (ENSG00000167104), BPIFC (ENSG00000184459), BPIFB3 (ENSG00000186190), BPIFB4 (ENSG00000186191), BPIFA1 (ENSG00000198183)

Protein

Protein identifiers

Lipopolysaccharide-binding protein — P18428 (reviewed: P18428)

All UniProt accessions (1): P18428

UniProt curated annotations — full annotation on UniProt →

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. Acts as an affinity enhancer for CD14, facilitating its association with LPS. Promotes the release of cytokines in response to bacterial lipopolysaccharide.

Subunit / interactions. When bound to LPS, interacts (via C-terminus) with soluble and membrane-bound CD14.

Subcellular location. Secreted. Cytoplasmic granule membrane.

Tissue specificity. Detected in blood serum (at protein level).

Similarity. Belongs to the BPI/LBP/Plunc superfamily. BPI/LBP family.

RefSeq proteins (1): NP_004130* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001124	Lipid-bd_serum_glycop_C	Domain
IPR017942	Lipid-bd_serum_glycop_N	Domain
IPR017943	Bactericidal_perm-incr_a/b_dom	Homologous_superfamily
IPR017954	Lipid-bd_serum_glycop_CS	Conserved_site
IPR030675	BPI/LBP	Family
IPR032942	BPI/LBP/Plunc	Family

Pfam: PF01273, PF02886

UniProt features (30 total): sequence variant 14, sequence conflict 9, glycosylation site 4, signal peptide 1, chain 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P18428-F1	90.83	0.76

Functional residue map

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

Disulfide bonds (1): 159–198

Glycosylation sites (4): 300, 355, 386, 394

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-166016	Toll Like Receptor 4 (TLR4) Cascade
R-HSA-166020	Transfer of LPS from LBP carrier to CD14
R-HSA-5686938	Regulation of TLR by endogenous ligand
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling
R-HSA-1280215	Cytokine Signaling in Immune system
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-168898	Toll-like Receptor Cascades
R-HSA-449147	Signaling by Interleukins

MSigDB gene sets: 300 (showing top): MORF_RAGE, GOBP_REGULATION_OF_RESPIRATORY_BURST, GOBP_REGULATION_OF_CELL_ACTIVATION, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_MACROPHAGE_ACTIVATION, MCLACHLAN_DENTAL_CARIES_UP, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CELL_CHEMOTAXIS, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_INFLAMMATORY_RESPONSE, GOBP_POSITIVE_REGULATION_OF_INTERLEUKIN_8_PRODUCTION, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_MACROPHAGE_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_REGULATION_OF_TOLL_LIKE_RECEPTOR_4_SIGNALING_PATHWAY

GO Biological Process (28): leukocyte chemotaxis involved in inflammatory response (GO:0002232), macrophage activation involved in immune response (GO:0002281), cell surface pattern recognition receptor signaling pathway (GO:0002752), acute-phase response (GO:0006953), cellular defense response (GO:0006968), opsonization (GO:0008228), lipopolysaccharide transport (GO:0015920), neutrophil chemotaxis (GO:0030593), lipopolysaccharide-mediated signaling pathway (GO:0031663), detection of molecule of bacterial origin (GO:0032490), response to lipopolysaccharide (GO:0032496), negative regulation of tumor necrosis factor production (GO:0032720), positive regulation of chemokine production (GO:0032722), positive regulation of interleukin-6 production (GO:0032755), positive regulation of interleukin-8 production (GO:0032757), positive regulation of tumor necrosis factor production (GO:0032760), positive regulation of toll-like receptor 4 signaling pathway (GO:0034145), positive regulation of macrophage activation (GO:0043032), innate immune response (GO:0045087), defense response to Gram-negative bacterium (GO:0050829), defense response to Gram-positive bacterium (GO:0050830), positive regulation of respiratory burst involved in inflammatory response (GO:0060265), cellular response to lipopolysaccharide (GO:0071222), cellular response to lipoteichoic acid (GO:0071223), positive regulation of neutrophil chemotaxis (GO:0090023), immune system process (GO:0002376), lipid transport (GO:0006869), defense response to bacterium (GO:0042742)

GO Molecular Function (7): lipopolysaccharide binding (GO:0001530), signaling receptor binding (GO:0005102), coreceptor activity (GO:0015026), lipoteichoic acid binding (GO:0070891), lipopeptide binding (GO:0071723), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), cell surface (GO:0009986), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Toll-like Receptor Cascades	2
Immune System	2
Toll Like Receptor 4 (TLR4) Cascade	1
Signaling by Interleukins	1
Innate Immune System	1
Cytokine Signaling in Immune system	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of cytokine production	3
cellular anatomical structure	3
immune response	2
macrophage activation	2
response to molecule of bacterial origin	2
tumor necrosis factor production	2
regulation of tumor necrosis factor production	2
lipid binding	2
carbohydrate derivative binding	2
binding	2
leukocyte migration involved in inflammatory response	1
inflammatory response	1
leukocyte chemotaxis	1
myeloid cell activation involved in immune response	1
leukocyte activation involved in immune response	1
innate immune response activating cell surface receptor signaling pathway	1
pattern recognition receptor signaling pathway	1
acute inflammatory response	1
defense response	1
immune effector process	1
phagocytosis, recognition	1
lipid transport	1
carbohydrate derivative transport	1
granulocyte chemotaxis	1
neutrophil migration	1
cell surface receptor signaling pathway	1
cellular response to lipopolysaccharide	1
detection of chemical stimulus	1
detection of external biotic stimulus	1
response to lipid	1
response to oxygen-containing compound	1
negative regulation of tumor necrosis factor superfamily cytokine production	1
chemokine production	1
regulation of chemokine production	1
interleukin-6 production	1
regulation of interleukin-6 production	1
interleukin-8 production	1
regulation of interleukin-8 production	1
positive regulation of tumor necrosis factor superfamily cytokine production	1
toll-like receptor 4 signaling pathway	1

Protein interactions and networks

STRING

914 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LBP	LY96	Q9Y6Y9	960
LBP	TLR4	O00206	958
LBP	CD14	P08571	945
LBP	APOA1	P02647	928
LBP	IL6	P05231	762
LBP	TLR2	O60603	708
LBP	CRP	P02741	696
LBP	TNF	P01375	689
LBP	HP	P00737	679
LBP	TTR	P02766	679
LBP	IL1B	P01584	674
LBP	FABP2	P12104	671
LBP	BPIFA2	Q96DR5	642
LBP	BPIFA1	Q9NP55	571
LBP	GOT2	P00505	555

IntAct

24 interactions, top by confidence:

A	B	Type	Score
LBP	PRDX4	psi-mi:“MI:0915”(physical association)	0.600
PRDX4	LBP	psi-mi:“MI:0915”(physical association)	0.600
LBP	PRDX4	psi-mi:“MI:0403”(colocalization)	0.600
LBP	BDNF	psi-mi:“MI:0915”(physical association)	0.560
	LBP	psi-mi:“MI:0915”(physical association)	0.400
LBP	malP	psi-mi:“MI:0915”(physical association)	0.400
LBP	BST1	psi-mi:“MI:0915”(physical association)	0.370
LBP	C4BPA	psi-mi:“MI:0915”(physical association)	0.370
FTH1	LBP	psi-mi:“MI:0915”(physical association)	0.370
HSPB1	LBP	psi-mi:“MI:0915”(physical association)	0.370
LBP	SMAD3	psi-mi:“MI:0915”(physical association)	0.370
PSMA3	LBP	psi-mi:“MI:0915”(physical association)	0.370
BAG6	LBP	psi-mi:“MI:0915”(physical association)	0.370
CBFA2T2	LBP	psi-mi:“MI:0915”(physical association)	0.370
LBP	SETD1A	psi-mi:“MI:0915”(physical association)	0.370
LBP	TRA2A	psi-mi:“MI:0915”(physical association)	0.370
LBP	PYCR3	psi-mi:“MI:0915”(physical association)	0.370
TSC22D4	LBP	psi-mi:“MI:0915”(physical association)	0.370
		psi-mi:“MI:0914”(association)	0.350

BioGRID (19): LBP (Synthetic Lethality), CFHR1 (Affinity Capture-Western), APOA1 (Affinity Capture-Western), LBP (Reconstituted Complex), LBP (Co-purification), LBP (Affinity Capture-MS), LBP (Two-hybrid), LBP (Two-hybrid), LBP (Two-hybrid), LBP (Two-hybrid), LBP (Two-hybrid), LBP (Two-hybrid), SMAD3 (Two-hybrid), PSMA3 (Two-hybrid), SETD1A (Two-hybrid)

ESM2 similar proteins: A0A481NSZ4, A0JPN3, A2BGH0, A6QP57, D4A5U3, G3HIK4, O02668, O76879, P11597, P17213, P17453, P17454, P18428, P19823, P19827, P22687, P47896, P55058, P55065, P59826, P59827, P97278, Q05701, Q05704, Q08188, Q08189, Q0VCM5, Q10011, Q24764, Q28739, Q29052, Q2TBI0, Q61114, Q61702, Q61703, Q61805, Q63313, Q67E05, Q6AXU0, Q80ZU7

Diamond homologs: A0A481NSZ4, P17213, P17453, P18428, Q28739, Q2TBI0, Q61805, Q63313, Q8NFQ6, P17454, Q67E05, Q6AXU0, P55065

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	14
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

1761 predictions. Top by Δscore:

Variant	Effect	Δscore
20:38346636:GTATG:G	donor_gain	1.0000
20:38349544:ACAGC:A	acceptor_gain	1.0000
20:38349545:C:G	acceptor_gain	1.0000
20:38349546:A:AG	acceptor_gain	1.0000
20:38349546:AGC:A	acceptor_gain	1.0000
20:38349547:G:GT	acceptor_gain	1.0000
20:38349547:GC:G	acceptor_gain	1.0000
20:38349547:GCG:G	acceptor_gain	1.0000
20:38350807:TCA:T	acceptor_loss	1.0000
20:38350808:CAGCC:C	acceptor_loss	1.0000
20:38350810:G:GT	acceptor_loss	1.0000
20:38350810:GCCT:G	acceptor_gain	1.0000
20:38350917:TGGA:T	donor_gain	1.0000
20:38350940:G:GG	donor_gain	1.0000
20:38354282:A:AG	acceptor_gain	1.0000
20:38354283:G:GC	acceptor_gain	1.0000
20:38354283:GC:G	acceptor_gain	1.0000
20:38354283:GCA:G	acceptor_gain	1.0000
20:38354283:GCAA:G	acceptor_gain	1.0000
20:38354283:GCAAA:G	acceptor_gain	1.0000
20:38360693:A:AG	acceptor_gain	1.0000
20:38360694:T:G	acceptor_gain	1.0000
20:38360700:TCAG:T	acceptor_loss	1.0000
20:38360702:A:AG	acceptor_gain	1.0000
20:38360702:AG:A	acceptor_loss	1.0000
20:38360703:G:GA	acceptor_gain	1.0000
20:38360703:GATT:G	acceptor_gain	1.0000
20:38363967:A:AG	acceptor_gain	1.0000
20:38363970:CACA:C	acceptor_loss	1.0000
20:38363972:CAGT:C	acceptor_loss	1.0000

AlphaMissense

3149 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:38369155:T:C	L381P	0.949
20:38350917:T:A	W116R	0.940
20:38350917:T:C	W116R	0.940
20:38369029:T:C	L339P	0.940
20:38376628:T:C	F469L	0.912
20:38376630:C:A	F469L	0.912
20:38376630:C:G	F469L	0.912
20:38364659:G:A	M276I	0.907
20:38364659:G:C	M276I	0.907
20:38364659:G:T	M276I	0.907
20:38364699:A:C	S290R	0.904
20:38364701:C:A	S290R	0.904
20:38364701:C:G	S290R	0.904
20:38346628:G:A	G38R	0.903
20:38346628:G:C	G38R	0.903
20:38369029:T:A	L339H	0.902
20:38364576:G:C	G249R	0.901
20:38369148:T:C	F379L	0.900
20:38369150:C:A	F379L	0.900
20:38369150:C:G	F379L	0.900
20:38350911:G:C	G114R	0.897
20:38369023:T:C	L337P	0.897
20:38369029:T:G	L339R	0.888
20:38346620:C:T	T35I	0.887
20:38369149:T:C	F379S	0.886
20:38346617:T:C	I34T	0.881
20:38354340:T:C	L142P	0.879
20:38354390:T:C	C159R	0.878
20:38376643:G:C	A474P	0.878
20:38354390:T:A	C159S	0.876

dbSNP variants (sampled 300 via entrez): RS1000008739 (20:38374620 AAAAG>A), RS1000124144 (20:38362977 G>A), RS1000255860 (20:38351784 G>A), RS1000286293 (20:38365884 A>T), RS1000366832 (20:38363720 ATGTGTGTGTG>A,ATGTGTG,ATGTGTGTG,ATGTGTGTGTGTG,ATGTGTGTGTGTGTG), RS1000467212 (20:38360448 G>A,T), RS1000475473 (20:38357435 C>T), RS1000591070 (20:38366574 G>A,T), RS1000674069 (20:38358435 C>T), RS1000729434 (20:38361412 T>C), RS1000743629 (20:38357133 G>T), RS1000861610 (20:38356317 C>G), RS1000874575 (20:38374369 C>T), RS1001143395 (20:38344521 A>G), RS1001208552 (20:38350281 T>C)

Disease associations

OMIM: gene MIM:151990 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002129_9	Periodontitis (DPAL)	2.000000e-06
GCST90002380_22	Basophil percentage of white cells	2.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007992	basophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Lipopolysaccharides	decreases reaction, increases response to substance, increases expression, affects cotreatment, affects binding	5
bisphenol A	affects cotreatment, decreases methylation, decreases expression, increases expression	3
Acetaminophen	decreases expression, increases expression, affects cotreatment	3
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
Nickel	affects binding, increases expression	3
Cyclosporine	affects cotreatment, decreases expression	3
6-hydroxy-5-((p- sulfophenyl)azo)-2-naphthalenesulfonic acid disodium salt	affects cotreatment, decreases expression	2
tetrabromobisphenol A	increases expression	2
bisphenol S	increases expression, affects cotreatment	2
Chenodeoxycholic Acid	affects cotreatment, decreases expression	2
Deoxycholic Acid	affects cotreatment, decreases expression	2
Glycochenodeoxycholic Acid	affects cotreatment, decreases expression	2
Glycocholic Acid	affects cotreatment, decreases expression	2
Glycodeoxycholic Acid	affects cotreatment, decreases expression	2
Asian ginseng	decreases reaction, increases expression	1
2,4,6-tribromophenol	increases expression	1
methyleugenol	decreases expression	1
decabromobiphenyl ether	increases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases secretion	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	affects expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
nefazodone	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
monomethyl phthalate	decreases secretion, increases abundance	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
Atazanavir Sulfate	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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