BPIFB3

BPI fold containing family B member 3, the group of BPI fold containing

Basic information

Region (hg38): 20:33053902-33073847

Previous symbols: [ "C20orf185" ]

Links

ENSG00000186190 ∙ NCBI:359710 ∙ OMIM:615717 ∙ HGNC:16178 ∙ Uniprot:P59826 ∙ 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 BPIFB3 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPIFB3 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				1		1
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in BPIFB3

This is a list of pathogenic ClinVar variants found in the BPIFB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33055516-C-T			Likely benign (Jul 01, 2022)
20-33055517-G-T		not specified	Uncertain significance (Oct 12, 2021)
20-33056566-A-G		not specified	Likely benign (Dec 01, 2022)
20-33056604-G-A		not specified	Uncertain significance (Sep 14, 2021)
20-33056632-G-A		not specified	Uncertain significance (Jan 20, 2023)
20-33056664-G-C		not specified	Uncertain significance (Aug 13, 2021)
20-33059398-C-T		not specified	Uncertain significance (Jul 25, 2023)
20-33059917-C-T		not specified	Uncertain significance (Nov 15, 2021)
20-33059941-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-33059967-G-A		not specified	Uncertain significance (Jun 11, 2021)
20-33060001-C-G		not specified	Uncertain significance (Oct 06, 2021)
20-33060010-G-A		not specified	Uncertain significance (Apr 12, 2022)
20-33061808-C-G		not specified	Uncertain significance (Aug 17, 2021)
20-33064532-T-C		not specified	Uncertain significance (Jul 14, 2022)
20-33064701-C-A		not specified	Uncertain significance (Mar 07, 2023)
20-33064732-C-T		not specified	Uncertain significance (Feb 26, 2024)
20-33064825-A-C		not specified	Uncertain significance (Dec 16, 2023)
20-33064837-C-A		not specified	Uncertain significance (Feb 21, 2024)
20-33068882-A-G		not specified	Uncertain significance (Nov 17, 2022)
20-33068884-A-G		not specified	Uncertain significance (Jul 14, 2021)
20-33068891-C-A		not specified	Uncertain significance (Dec 06, 2021)
20-33068938-A-G		not specified	Uncertain significance (May 31, 2022)
20-33068961-T-G		not specified	Uncertain significance (Oct 26, 2022)
20-33069946-C-A		not specified	Uncertain significance (Oct 26, 2022)
20-33072719-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPIFB3	protein_coding	protein_coding	ENST00000375494	15	18205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.68e-13	0.0855	123473	19	2256	125748	0.00909

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.302	290	276	1.05	0.0000158	2965
Missense in Polyphen		130	109.8	1.184		1265
Synonymous	0.0272	132	132	0.997	0.00000823	1084
Loss of Function	0.597	21	24.2	0.869	0.00000122	266

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00754	0.00747
Ashkenazi Jewish	0.00519	0.00517
East Asian	0.000545	0.000544
Finnish	0.0160	0.0157
European (Non-Finnish)	0.0130	0.0128
Middle Eastern	0.000545	0.000544
South Asian	0.00587	0.00586
Other	0.00754	0.00752

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have the capacity to recognize and bind specific classes of odorants. May act as a carrier molecule, transporting odorants across the mucus layer to access receptor sites. May serve as a primary defense mechanism by recognizing and removing potentially harmful odorants or pathogenic microorganisms from the mucosa or clearing excess odorant from mucus to enable new odorant stimuli to be received (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0879

Intolerance Scores

• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.33

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.198

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bpifb3
• Phenotype: normal phenotype

Gene ontology

• Biological process: innate immune response
• Cellular component: extracellular region;cytoplasm
• Molecular function: lipid binding