BPIFA1

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

Basic information

Region (hg38): 20:33235995-33243311

Previous symbols: [ "PLUNC" ]

Links

ENSG00000198183 ∙ NCBI:51297 ∙ OMIM:607412 ∙ HGNC:15749 ∙ Uniprot:Q9NP55 ∙ 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 BPIFA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPIFA1 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						0
missense			18	2	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	1

Variants in BPIFA1

This is a list of pathogenic ClinVar variants found in the BPIFA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33237734-T-C		not specified	Uncertain significance (Mar 31, 2023)
20-33237773-T-A		not specified	Uncertain significance (Dec 06, 2022)
20-33237782-T-A		not specified	Uncertain significance (Mar 08, 2025)
20-33237787-G-A		not specified	Uncertain significance (Oct 22, 2021)
20-33237787-G-T		not specified	Likely benign (Nov 08, 2022)
20-33237799-C-G		not specified	Uncertain significance (Aug 21, 2024)
20-33237832-C-T		not specified	Uncertain significance (Dec 21, 2023)
20-33237833-C-T		not specified	Uncertain significance (Jan 16, 2025)
20-33237845-C-T		not specified	Uncertain significance (Feb 27, 2025)
20-33238062-C-A		not specified	Uncertain significance (Jan 23, 2025)
20-33238133-G-A		not specified	Uncertain significance (Feb 20, 2025)
20-33238186-G-A		not specified	Uncertain significance (Sep 02, 2024)
20-33238203-C-G			Likely benign (May 19, 2018)
20-33239806-A-G		not specified	Uncertain significance (Jan 04, 2022)
20-33239825-C-G		not specified	Uncertain significance (Nov 26, 2024)
20-33239874-T-C		not specified	Uncertain significance (Oct 26, 2021)
20-33240234-C-T		not specified	Uncertain significance (Nov 25, 2024)
20-33240241-T-A		not specified	Uncertain significance (Feb 25, 2025)
20-33240259-G-A		not specified	Likely benign (Dec 23, 2024)
20-33240279-A-T		not specified	Uncertain significance (Apr 08, 2024)
20-33240282-A-G		not specified	Uncertain significance (Feb 13, 2023)
20-33240300-G-A		not specified	Uncertain significance (May 16, 2024)
20-33240348-C-T		not specified	Uncertain significance (Dec 19, 2023)
20-33240366-C-A			Benign (Jul 26, 2018)
20-33241389-G-A		not specified	Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPIFA1	protein_coding	protein_coding	ENST00000354297	7	7315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-8	0.106	125630	0	114	125744	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.439	147	133	1.11	0.00000648	1617
Missense in Polyphen		27	31.748	0.85046		431
Synonymous	-0.575	64	58.4	1.10	0.00000291	583
Loss of Function	-0.0818	12	11.7	1.03	6.92e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000432	0.000431
Middle Eastern	0.000218	0.000217
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the innate immune responses of the upper airways. Reduces the surface tension in secretions from airway epithelia and inhibits the formation of biofilm by pathogenic Gram-negative bacteria, such as P.aeruginosa and K.pneumoniae. Binds bacterial lipopolysaccharide (LPS). Negatively regulates proteolytic cleavage of SCNN1G, an event that is required for activation of the epithelial sodium channel (ENaC), and thereby contributes to airway surface liquid homeostasis and proper clearance of mucus. Plays a role in the airway inflammatory response after exposure to irritants. May attract macrophages and neutrophils. May be associated with tumor progression. {ECO:0000269|PubMed:11425234, ECO:0000269|PubMed:23132494, ECO:0000269|PubMed:23499554, ECO:0000269|PubMed:24043776, ECO:0000269|PubMed:24124190}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.341

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.0917
• hipred: N
• hipred_score: 0.112
• ghis: 0.422

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	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bpifa1
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hearing/vestibular/ear phenotype; immune system phenotype

Gene ontology

• Biological process: immune response in nasopharyngeal-associated lymphoid tissue;antimicrobial humoral response;antibacterial humoral response;innate immune response;regulation of liquid surface tension;multicellular organismal water homeostasis;defense response to virus;antimicrobial humoral immune response mediated by antimicrobial peptide;negative regulation of single-species biofilm formation in or on host organism;regulation of sodium ion transmembrane transport
• Cellular component: extracellular region;extracellular space
• Molecular function: molecular_function;protein binding;lipid binding