BPIFA2

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

Basic information

Region (hg38): 20:33161767-33181412

Previous symbols: [ "C20orf70" ]

Links

ENSG00000131050 ∙ NCBI:140683 ∙ ∙ HGNC:16203 ∙ Uniprot:Q96DR5 ∙ 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 BPIFA2 gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPIFA2 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			5	4		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	5	4	1

Variants in BPIFA2

This is a list of pathogenic ClinVar variants found in the BPIFA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33169299-A-G		not specified	Likely benign (Feb 27, 2023)
20-33172932-G-A		not specified	Uncertain significance (Jul 30, 2023)
20-33172971-A-G		not specified	Uncertain significance (Aug 10, 2021)
20-33172991-C-G		not specified	Uncertain significance (Sep 26, 2022)
20-33173074-T-G		not specified	Likely benign (Jan 05, 2022)
20-33174079-G-T			Benign (Mar 29, 2018)
20-33175409-C-T		not specified	Uncertain significance (May 10, 2022)
20-33175469-T-C		not specified	Uncertain significance (Dec 03, 2021)
20-33178191-C-T		not specified	Uncertain significance (Dec 27, 2023)
20-33179593-TC-T			Benign (Jun 05, 2018)
20-33179604-A-G		not specified	Likely benign (Dec 14, 2021)
20-33179620-G-A		not specified	Likely benign (Aug 12, 2021)
20-33180525-C-T		not specified	Uncertain significance (Jan 22, 2024)
20-33180550-C-A		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPIFA2	protein_coding	protein_coding	ENST00000253362	7	19645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.01e-7	0.306	125731	1	16	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0537	135	137	0.987	0.00000734	1618
Missense in Polyphen		34	33.305	1.0209		479
Synonymous	0.305	58	61.0	0.950	0.00000374	512
Loss of Function	0.353	10	11.3	0.887	4.78e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000261
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has strong antibacterial activity against P. aeruginosa. {ECO:0000269|PubMed:24581853}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.65

Haploinsufficiency Scores

• pHI: 0.0324
• hipred: N
• hipred_score: 0.123

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: Bpifa2

Gene ontology

• Biological process: antimicrobial humoral response;defense response to bacterium
• Cellular component: extracellular region;extracellular exosome
• Molecular function: lipopolysaccharide binding;protein binding