BPIFA3

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

Basic information

Region (hg38): 20:33217310-33227806

Previous symbols: [ "C20orf71" ]

Links

ENSG00000131059 ∙ NCBI:128861 ∙ ∙ HGNC:16204 ∙ Uniprot:Q9BQP9 ∙ 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 BPIFA3 gene.

• not_specified (35 variants)
• BPIFA3-related_disorder (4 variants)
• Preeclampsia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPIFA3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178466.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			30	6	1	37
nonsense					2	2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPIFA3	protein_coding	protein_coding	ENST00000375454	7	10449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.94e-13	0.00851	125302	5	435	125742	0.00175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.455	157	142	1.11	0.00000707	1689
Missense in Polyphen		40	37.479	1.0673		539
Synonymous	-0.521	60	55.1	1.09	0.00000306	470
Loss of Function	-0.748	17	14.0	1.22	7.81e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0366	0.0223
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000564	0.000457
Middle Eastern	0.000163	0.000163
South Asian	0.000457	0.000327
Other	0.000816	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1
• rvis_percentile_EVS: 90.62

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

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: Bpifa3

Gene ontology

• Cellular component: extracellular region
• Molecular function: lipid binding