BPIFA1
Basic information
Region (hg38): 20:33235995-33243311
Previous symbols: [ "PLUNC" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (38 variants)
- not_provided (2 variants)
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. These statistics are base on transcript: NM_000130852.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 35 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 35 | 4 | 1 |
GnomAD
Source:
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:
- 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
- loftool
- 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