BPIFB1

protein-coding

BPI fold containing family B member 1, the group of BPI fold containing

Gene summary

The protein encoded by this gene may be involved in the innate immune response to bacterial exposure in the mouth, nasal cavities, and lungs. The encoded protein is secreted and is a member of the BPI/LBP/PLUNC protein superfamily. This gene is found with other members of the superfamily in a cluster on chromosome 20. [provided by RefSeq, Jul 2008]

Previous symbols:

C20orf114

MANE transcript

NM_033197.3

Inheritance

—

ClinVar variants

U:59B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr20:33,273,480-33,309,871

External References & Databases

Ensembl (ENSG00000125999)

Transcript & Mutation Effects

hg38 • Region Span ~36.4 kb

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GenCC 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 BPIFB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033197.3. 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					1 clinvar	1
missense			59 clinvar	5 clinvar	3 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	5	4	68

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033197.3	RefSeq	NP_149974.2	15	MANE Select
ENST00000253354.2	Ensembl	ENSP00000253354.1	15	MANE Select
ENST00000423645.5	Ensembl	ENSP00000390471.1	4	Standard
ENST00000865831.1	Ensembl	ENSP00000535890.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antimicrobial peptides
Innate Immune System
Immune System

Biological Process

innate immune response in mucosa
antimicrobial humoral response
negative regulation of toll-like receptor 4 signaling pathway

Molecular Function

molecular_function
lipid binding

Cellular Component

extracellular region
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253354
Coding exons: 15
Length: 36399
Individuals with no LoFs: 125675
Homozygous LoFs: 0
Heterozygous LoFs: 73
Defined: 125748
p: 0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.630	245	274	0.893	0.0000148	3124
Missense (PolyPhen)		56	64.432	0.86913		787
Synonymous	0.541	112	120	0.937	0.00000693	1017
Loss of Function	1.73	16	25.4	0.630	0.00000125	278

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00016	0.00016	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in innate immunity in mouth, nose and lungs. Binds bacterial lipopolysaccharide (LPS) and modulates the cellular responses to LPS. {ECO:0000269|PubMed:21900486}.;

Recessive Scores

pRec: 0.0906

Intolerance Scores

RVIS EVS: 1.49
RVIS percentile EVS: 95.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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