BPI

bactericidal permeability increasing protein, the group of BPI fold containing

Basic information

Region (hg38): 20:38260141-38337505

Links

ENSG00000101425 ∙ NCBI:671 ∙ OMIM:109195 ∙ HGNC:1095 ∙ Uniprot:P17213 ∙ 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 BPI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPI 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				3	2	5
missense			27	6	7	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding						0
Total	0	0	27	9	9

Variants in BPI

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

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

Position	Type	Phenotype	Significance	ClinVar
20-38304218-G-A		not specified	Uncertain significance (Jul 20, 2022)
20-38304228-C-A		not specified	Uncertain significance (Jun 16, 2023)
20-38304245-G-A			Benign (Aug 10, 2018)
20-38304246-C-T			Benign (Jul 13, 2018)
20-38304258-C-T		not specified	Benign (Mar 28, 2016)
20-38304274-G-C		not specified	Benign (Mar 28, 2016)
20-38304275-G-A		not specified	Uncertain significance (Aug 22, 2023)
20-38304284-G-A		not specified	Uncertain significance (May 18, 2023)
20-38304290-G-A		not specified	Likely benign (Aug 04, 2023)
20-38304300-C-T		not specified	Uncertain significance (Oct 27, 2021)
20-38304336-A-G		not specified	Uncertain significance (Oct 06, 2021)
20-38308940-C-T			Benign (Jul 26, 2018)
20-38308983-A-G		not specified	Uncertain significance (Mar 17, 2023)
20-38309011-C-G		not specified	Uncertain significance (Jun 18, 2021)
20-38309029-C-T			Benign (Jul 02, 2018)
20-38310501-G-A		not specified	Uncertain significance (Jun 07, 2023)
20-38310511-A-C		not specified	Uncertain significance (Oct 24, 2023)
20-38310522-G-C			Benign (Jul 15, 2018)
20-38310526-G-C		not specified	Uncertain significance (May 31, 2023)
20-38310566-C-T			Likely benign (Apr 01, 2023)
20-38310569-G-A			Likely benign (Aug 30, 2018)
20-38310650-G-C		not specified	Benign (Mar 28, 2016)
20-38311882-T-C		not specified	Uncertain significance (Nov 09, 2021)
20-38311912-C-T		not specified	Benign (Mar 28, 2016)
20-38318419-G-A		not specified	Likely benign (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPI	protein_coding	protein_coding	ENST00000262865	15	77357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.65e-14	0.0518	125587	0	161	125748	0.000640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.780	322	285	1.13	0.0000156	3204
Missense in Polyphen		79	71.037	1.1121		872
Synonymous	-0.545	128	120	1.06	0.00000800	943
Loss of Function	0.551	23	26.0	0.884	0.00000124	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00383	0.00384
Ashkenazi Jewish	0.00229	0.00228
East Asian	0.000870	0.000870
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.000870	0.000870
South Asian	0.000654	0.000523
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The cytotoxic action of BPI is limited to many species of Gram-negative bacteria; this specificity may be explained by a strong affinity of the very basic N-terminal half for the negatively charged lipopolysaccharides that are unique to the Gram-negative bacterial outer envelope. Has antibacterial activity against the Gram-negative bacterium P.aeruginosa, this activity is inhibited by LPS from P.aeruginosa. {ECO:0000269|PubMed:1937776, ECO:0000269|PubMed:2722846}.
• Pathway: Neutrophil degranulation;Toll-Like Receptors Cascades;Antimicrobial peptides;Innate Immune System;Immune System;Toll Like Receptor 4 (TLR4) Cascade (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 2.6
• rvis_percentile_EVS: 98.77

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0505

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bpi

Gene ontology

• Biological process: antimicrobial humoral response;negative regulation of interleukin-6 production;negative regulation of interleukin-8 production;negative regulation of tumor necrosis factor production;negative regulation of macrophage activation;neutrophil degranulation;defense response to Gram-negative bacterium
• Cellular component: extracellular region;membrane;azurophil granule lumen;specific granule lumen;extracellular exosome
• Molecular function: lipopolysaccharide binding