BPIFB2

protein-coding

BPI fold containing family B member 2, the group of BPI fold containing

Gene summary

This gene encodes a member of the lipid transfer/lipopolysaccharide binding protein (LT/LBP) gene family. It is highly expressed in hypertrophic tonsils. This gene and three other members of the LT/LBP gene family form a cluster on the long arm of chromosome 20. [provided by RefSeq, Jul 2008]

Previous symbols:

C20orf184
BPIL1

MANE transcript

NM_025227.3

Inheritance

—

ClinVar variants

U:66B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr20:33,007,704-33,023,703

External References & Databases

Ensembl (ENSG00000078898)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 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 BPIFB2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025227.3. 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			66 clinvar	8 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	9	0	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025227.3	RefSeq	NP_079503.1	15	MANE Select
ENST00000170150.4	Ensembl	ENSP00000170150.3	15	MANE Select
ENST00000864169.1	Ensembl	ENSP00000534228.1	15	Standard
ENST00000864169.2	Ensembl	ENSP00000534228.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins
Antimicrobial peptides
Innate Immune System

Biological Process

antimicrobial humoral response
post-translational protein modification
cellular protein metabolic process

Molecular Function

lipid binding

Cellular Component

extracellular region
endoplasmic reticulum lumen
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000170150
Coding exons: 15
Length: 16110
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125747
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.325	257	272	0.945	0.0000161	2903
Missense (PolyPhen)		76	80.715	0.94159		972
Synonymous	-0.0951	123	122	1.01	0.00000751	1022
Loss of Function	0.534	19	21.7	0.876	9.98e-7	240

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000098	0.000098	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0953

Intolerance Scores

RVIS EVS: -0.06
RVIS percentile EVS: 48.84

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