BPIFA3

Summary

BPIFA3 (BPI fold containing family A member 3, HGNC:16204) is a protein-coding gene on chromosome 20q11.21, encoding BPI fold-containing family A member 3 (Q9BQP9).

Predicted to enable lipid binding activity. Predicted to be located in extracellular region.

Source: NCBI Gene 128861 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_178466

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16204
Approved symbol	BPIFA3
Name	BPI fold containing family A member 3
Location	20q11.21
Locus type	gene with protein product
Status	Approved
Aliases	bA49G10.4, SPLUNC3
Ensembl gene	ENSG00000131059
Ensembl biotype	protein_coding
OMIM	621167
Entrez	128861

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000375452, ENST00000375454, ENST00000471233, ENST00000490499

RefSeq mRNA: 2 — MANE Select: NM_178466 NM_001042439, NM_178466

CCDS: CCDS13216, CCDS42865

Canonical transcript exons

ENST00000375454 — 7 exons

Exon	Start	End
ENSE00001835768	33217352	33217663
ENSE00003488237	33223811	33223961
ENSE00003489430	33226406	33226490
ENSE00003494920	33226930	33226993
ENSE00003600938	33225098	33225247
ENSE00003648618	33224355	33224462
ENSE00003896106	33227538	33227806

Expression profiles

Bgee: expression breadth broad, 28 present calls, max score 98.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2706 / max 318.4660, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184129	0.2577	4
184128	0.0097	3
209079	0.0031	2

Top tissues by expression

206 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	97.11	gold quality
left testis	UBERON:0004533	95.84	gold quality
right testis	UBERON:0004534	95.77	gold quality
testis	UBERON:0000473	92.78	gold quality
adult organism	UBERON:0007023	85.70	gold quality
kidney epithelium	UBERON:0004819	84.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.11	silver quality
ileal mucosa	UBERON:0000331	80.12	gold quality
pancreatic ductal cell	CL:0002079	78.69	silver quality
epithelial cell of pancreas	CL:0000083	77.33	gold quality
nasal cavity epithelium	UBERON:0005384	71.94	gold quality
epithelium of nasopharynx	UBERON:0001951	71.52	gold quality
cardiac muscle of right atrium	UBERON:0003379	70.13	gold quality
left ventricle myocardium	UBERON:0006566	70.06	gold quality
quadriceps femoris	UBERON:0001377	68.73	gold quality
vastus lateralis	UBERON:0001379	67.41	gold quality
upper arm skin	UBERON:0004263	67.16	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	67.08	gold quality
endothelial cell	CL:0000115	66.40	gold quality
lower lobe of lung	UBERON:0008949	66.00	gold quality
buccal mucosa cell	CL:0002336	65.55	gold quality
parotid gland	UBERON:0001831	65.29	gold quality
biceps brachii	UBERON:0001507	64.30	gold quality
myocardium	UBERON:0002349	64.25	gold quality
epithelium of mammary gland	UBERON:0003244	63.77	gold quality
mammary duct	UBERON:0001765	63.59	gold quality
esophagus squamous epithelium	UBERON:0006920	63.47	gold quality
gingival epithelium	UBERON:0001949	63.27	gold quality
cauda epididymis	UBERON:0004360	63.03	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting BPIFA3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-1237-3P	98.55	67.65	1423
HSA-MIR-4684-3P	98.24	69.91	1075
HSA-MIR-6881-5P	98.16	67.38	665
HSA-MIR-4286	97.20	64.37	1587

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Bpifa3	ENSMUSG00000027482
rattus_norvegicus	Bpifa3	ENSRNOG00000013778
caenorhabditis_elegans		WBGENE00015544

Paralogs (12): BPIFB2 (ENSG00000078898), CETP (ENSG00000087237), PLTP (ENSG00000100979), BPI (ENSG00000101425), BPIFB1 (ENSG00000125999), LBP (ENSG00000129988), BPIFA2 (ENSG00000131050), BPIFB6 (ENSG00000167104), BPIFC (ENSG00000184459), BPIFB3 (ENSG00000186190), BPIFB4 (ENSG00000186191), BPIFA1 (ENSG00000198183)

Protein

Protein identifiers

BPI fold-containing family A member 3 — Q9BQP9 (reviewed: Q9BQP9)

Alternative names: Short palate, lung and nasal epithelium carcinoma-associated protein 3

All UniProt accessions (1): Q9BQP9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the BPI/LBP/Plunc superfamily. Plunc family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BQP9-1	1	yes
Q9BQP9-2	2

RefSeq proteins (2): NP_001035904, NP_848561* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017942	Lipid-bd_serum_glycop_N	Domain
IPR017943	Bactericidal_perm-incr_a/b_dom	Homologous_superfamily
IPR032946	Bpifa3	Family

Pfam: PF01273

UniProt features (9 total): sequence variant 2, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, glycosylation site 1, disulfide bond 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQP9-F1	75.36	0.41

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 165–209

Glycosylation sites (1): 36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): RNGTGGGC_UNKNOWN, WANG_CLIM2_TARGETS_UP, TCF11_01, HFH3_01, chr20q11, YNGTTNNNATT_UNKNOWN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, GOMF_LIPID_BINDING, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_IL2_CULTURE_DN, MIR561_3P, MIR1237_3P, MIR6881_5P, GSE411_WT_VS_SOCS3_KO_MACROPHAGE_IL6_STIM_400MIN_UP, GSE2770_UNTREATED_VS_TGFB_AND_IL12_TREATED_ACT_CD4_TCELL_2H_UP

GO Biological Process (0):

GO Molecular Function (1): lipid binding (GO:0008289)

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

326 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BPIFA3	BPIFB4	P59827	742
BPIFA3	BPIFB3	P59826	679
BPIFA3	BPIFB6	Q8NFQ5	676
BPIFA3	BPIFB2	Q8N4F0	628
BPIFA3	BPIFA2	Q96DR5	608
BPIFA3	BPIFB1	Q8TDL5	600
BPIFA3	WFDC12	Q8WWY7	495
BPIFA3	CAPN14	A8MX76	478
BPIFA3	DEFB127	Q9H1M4	478
BPIFA3	CST9	Q5W186	473
BPIFA3	CLDND2	Q8NHS1	466
BPIFA3	GALNT14	Q96FL9	465
BPIFA3	DEFB128	Q7Z7B8	449
BPIFA3	DEFB131A	P59861	419
BPIFA3	SLFN5	Q08AF3	411

IntAct

3 interactions, top by confidence:

A	B	Type	Score
DNAJC21	TOP2A	psi-mi:“MI:0914”(association)	0.350
PFN1	WASL	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): BPIFA3 (Synthetic Lethality), BPIFA3 (Affinity Capture-MS), BPIFA3 (Affinity Capture-MS), BPIFA3 (Affinity Capture-MS), BPIFA3 (Affinity Capture-MS)

ESM2 similar proteins: A0JPN3, A7E3W2, F6KSY2, G3HIK4, O09051, O13009, O42273, O70418, O70513, P08571, P11597, P11684, P22687, P25914, P28902, P33680, P41234, P47896, P55058, P55065, P59826, P70107, P70664, P70668, P82886, Q05701, Q06318, Q07797, Q08DF2, Q16661, Q28358, Q2VPS3, Q61114, Q63751, Q6TGC4, Q80ZU7, Q86YQ2, Q8BU51, Q8C186, Q8C1E1

Diamond homologs: Q9BQP9, Q9D9J8, P97361

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

48 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	7
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

887 predictions. Top by Δscore:

Variant	Effect	Δscore
20:33217661:GAA:G	donor_gain	1.0000
20:33217664:G:GG	donor_gain	1.0000
20:33217669:C:G	donor_gain	1.0000
20:33225244:C:CG	donor_gain	1.0000
20:33225244:CTGA:C	donor_loss	1.0000
20:33225246:GA:G	donor_gain	1.0000
20:33225247:AG:A	donor_loss	1.0000
20:33225248:G:GG	donor_gain	1.0000
20:33225249:T:A	donor_loss	1.0000
20:33226405:GGGCT:G	acceptor_gain	1.0000
20:33226486:GTCAG:G	donor_gain	1.0000
20:33226489:AGGTA:A	donor_loss	1.0000
20:33226490:GGT:G	donor_loss	1.0000
20:33226491:GT:G	donor_loss	1.0000
20:33226492:TAAG:T	donor_loss	1.0000
20:33217661:G:GT	donor_gain	0.9900
20:33225195:A:AG	donor_gain	0.9900
20:33225200:C:T	donor_gain	0.9900
20:33225243:ACTGA:A	donor_gain	0.9900
20:33225244:C:G	donor_gain	0.9900
20:33225245:TGA:T	donor_gain	0.9900
20:33225246:GAG:G	donor_gain	0.9900
20:33226400:TTCTA:T	acceptor_loss	0.9900
20:33226402:CTA:C	acceptor_loss	0.9900
20:33226404:A:AG	acceptor_gain	0.9900
20:33226404:AG:A	acceptor_gain	0.9900
20:33226404:AGG:A	acceptor_gain	0.9900
20:33226404:AGGG:A	acceptor_loss	0.9900
20:33226405:G:GC	acceptor_loss	0.9900
20:33226405:G:GG	acceptor_gain	0.9900

AlphaMissense

1699 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:33225174:T:C	F155L	0.967
20:33225176:T:A	F155L	0.967
20:33225176:T:G	F155L	0.967
20:33225168:G:C	D153H	0.960
20:33226967:A:T	D220V	0.956
20:33225170:C:A	D153E	0.947
20:33225170:C:G	D153E	0.947
20:33225181:G:C	R157P	0.940
20:33223826:T:C	L48P	0.937
20:33225169:A:T	D153V	0.937
20:33225169:A:C	D153A	0.935
20:33225153:T:C	F148L	0.933
20:33225155:C:A	F148L	0.933
20:33225155:C:G	F148L	0.933
20:33226933:T:C	C209R	0.933
20:33225204:T:A	C165S	0.929
20:33225205:G:C	C165S	0.929
20:33226933:T:A	C209S	0.928
20:33226934:G:C	C209S	0.928
20:33225204:T:C	C165R	0.925
20:33226968:T:A	D220E	0.925
20:33226968:T:G	D220E	0.925
20:33226979:T:C	L224S	0.925
20:33223853:T:C	I57T	0.909
20:33223814:T:A	I44N	0.906
20:33226967:A:C	D220A	0.904
20:33226974:A:C	K222N	0.903
20:33226974:A:T	K222N	0.903
20:33223822:G:C	G47R	0.901
20:33226935:T:G	C209W	0.901

dbSNP variants (sampled 300 via entrez): RS1000055826 (20:33225861 T>C), RS1000069458 (20:33220175 A>G), RS1000408830 (20:33226119 C>A), RS1000846774 (20:33225830 T>A), RS1000920776 (20:33220323 G>A,T), RS1001268150 (20:33220156 T>A), RS1001586633 (20:33222668 A>G,T), RS1001828425 (20:33217010 G>C), RS1001932820 (20:33222566 G>A), RS1002195700 (20:33221591 G>A,C), RS1002379047 (20:33226803 A>G), RS1002413370 (20:33221409 G>A), RS1002711496 (20:33215736 T>G), RS1002831606 (20:33218589 C>T), RS1002926985 (20:33218928 C>G)

Disease associations

OMIM: gene MIM:621167 | disease phenotypes: MIM:189800

GenCC curated gene-disease

Mondo (1): preeclampsia (MONDO:0005081)

Orphanet (1): Preeclampsia (Orphanet:275555)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST000853_7	Ulcerative colitis	4.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D011225	Pre-Eclampsia	C12.050.703.395.249

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	1
Cadmium	decreases expression, increases abundance	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00117546	PHASE4	UNKNOWN	Cardiovascular and Autonomic Reactivity in Women With a History of Pre-eclampsia
NCT00567957	PHASE4	UNKNOWN	Remifentanil for General Anesthesia in Preeclamptics
NCT01030627	PHASE4	COMPLETED	Treatment Approaches to Preeclampsia
NCT01352234	PHASE4	COMPLETED	Comparison of Doses of Acetylsalicylic Acid in Women With Previous History of Preeclampsia
NCT01361425	PHASE4	UNKNOWN	Anti-Hypertensive Treatment In Stable Pregnant Women With Severe Pre-Eclampsia (Metildopape)
NCT01729468	PHASE4	COMPLETED	Prevention of Pre-eclampsia and SGA by Low-Dose Aspirin in Nulliparous Women With Abnormal First-trimester Uterine Artery Dopplers
NCT01761916	PHASE4	COMPLETED	Clonidine Versus Captopril for Treatment of Postpartum Very High Blood Pressure
NCT01912677	PHASE4	COMPLETED	Oral Antihypertensive Regimens for Management of Hypertension in Pregnancy
NCT02025426	PHASE4	TERMINATED	Phenylephrine Versus Ephedrine in Pre-eclampsia
NCT02091401	PHASE4	COMPLETED	A Trial Comparing Treatment With the Springfusor Infusion Pump to the IV Magnesium Sulfate Regimen
NCT02163655	PHASE4	COMPLETED	Diuretics for Postpartum High Blood Pressure in Preeclampsia
NCT02338687	PHASE4	COMPLETED	Low Dose Calcium to Prevent Preeclampsia
NCT02396030	PHASE4	TERMINATED	Different Schemes of Magnesium Sulfate for Preeclampsia
NCT02531490	PHASE4	UNKNOWN	Early Vascular Adjustments During Hypertensive Pregnancy
NCT02699827	PHASE4	COMPLETED	Adding MgSO4 to Epidural Levobupivacaine in CS for Patients With Preeclampsia
NCT02835339	PHASE4	COMPLETED	Magnesium Sulfate in Obese Preeclamptics
NCT02891174	PHASE4	COMPLETED	The Effect of Ibuprofen on Post-partum Blood Pressure in Women With Hypertensive Disorders of Pregnancy
NCT02911701	PHASE4	COMPLETED	Effect of Acetaminophen on Postpartum Blood Pressure Control in Preeclampsia With Severe Features
NCT03171480	PHASE4	COMPLETED	Use of Nitrous Oxide Donor for Labor Induction in Women With PreEclampsia
NCT03233880	PHASE4	UNKNOWN	Impact of Antichlamydial Treatment on the Rate of Preeclampsia
NCT03237000	PHASE4	UNKNOWN	Effect of Administering Intravenous Magnesium Sulfate on Fetal Cardiotocography and Neonatal Outcome in Preeclamptic Patients
NCT03506724	PHASE4	COMPLETED	Response to Anti-hypertensives in Pregnant and Postpartum Patients
NCT03674606	PHASE4	COMPLETED	Trial of Early Screening Test for Pre-eclampsia and Growth Restriction
NCT03735433	PHASE4	TERMINATED	The Effect of Two Aspirin Dosing Strategies for Obese Women at High Risk for Preeclampsia
NCT03824119	PHASE4	UNKNOWN	Postpartum NSAIDS and Maternal Hypertension
NCT04051567	PHASE4	UNKNOWN	Low-dose Aspirin for Prevention of Adverse Pregnancy Outcomes in Twin Pregnancies
NCT04077853	PHASE4	COMPLETED	Progesterone in Expectantly Managed Early-onset Preeclampsia
NCT04158830	PHASE4	WITHDRAWN	Aspirin (ASA) Therapy and Preeclampsia Prevention
NCT04424693	PHASE4	UNKNOWN	Comparing the Incidence of Preeclampsia Between Pregnant Women Receiving Tdap Vaccinations at Week 28 or at Week 36
NCT04631627	PHASE4	UNKNOWN	Early Prediction and Randomised Prevention of Preeclampsia With Low Dose Aspirin in Chinese Cohort
NCT04656665	PHASE4	UNKNOWN	The Effectiveness of Aspirin on Preventing Pre-eclampsia
NCT04797949	PHASE4	WITHDRAWN	Adherence to Universal Aspirin Compared to Screening Indicated Aspirin for Prevention of Preeclampsia
NCT04908982	PHASE4	UNKNOWN	Aspirin for the Prevention of Preeclampsia in Women With Stage 1 Hypertension
NCT05221164	PHASE4	UNKNOWN	162 mg of Aspirin for Prevention of Preeclampsia
NCT05294952	PHASE4	UNKNOWN	co Ihibtory Receptor in Preeclampsia
NCT05514847	PHASE4	ACTIVE_NOT_RECRUITING	Low Dose Aspirin for Preterm Preeclampsia Preventionmg/day Dose in High-risk Patients
NCT05586373	PHASE4	COMPLETED	Ibuprofen vs Dipyrone After C-section in Preeclampsia
NCT06069102	PHASE4	COMPLETED	Optimal Blood Pressure Treatment Thresholds Postpartum
NCT06107335	PHASE4	NOT_YET_RECRUITING	Effect of Albumin Versus Routine Care on Hemodynamic Response and Stability in Patients With Preeclampsia Guided by a Non-invasive Hemodynamic Monitoring System During Cesarean Delivery With Spinal Anesthesia
NCT06281665	PHASE4	RECRUITING	Treatment With Aspirin After Preeclampsia: TAP Trial