PNLIPRP3

Summary

PNLIPRP3 (pancreatic lipase related protein 3, HGNC:23492) is a protein-coding gene on chromosome 10q25.3, encoding Pancreatic lipase-related protein 3 (Q17RR3).

Predicted to enable lipoprotein lipase activity and phospholipase A1 activity. Predicted to be involved in several processes, including cholesterol homeostasis; high-density lipoprotein particle remodeling; and triglyceride catabolic process. Predicted to be located in extracellular region.

Source: NCBI Gene 119548 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_001011709

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23492
Approved symbol	PNLIPRP3
Name	pancreatic lipase related protein 3
Location	10q25.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203837
Ensembl biotype	protein_coding
Entrez	119548

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000369230

RefSeq mRNA: 1 — MANE Select: NM_001011709 NM_001011709

CCDS: CCDS31292

Canonical transcript exons

ENST00000369230 — 12 exons

Exon	Start	End
ENSE00001449246	116477090	116477957
ENSE00001449247	116476652	116476819
ENSE00001449248	116471768	116471879
ENSE00001449249	116469185	116469317
ENSE00001449250	116466050	116466168
ENSE00001449252	116461168	116461290
ENSE00001449254	116460966	116461085
ENSE00001449257	116455722	116455830
ENSE00001449258	116444382	116444513
ENSE00001449259	116443055	116443174
ENSE00001449260	116436711	116436865
ENSE00001449261	116427847	116428061

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 94.41.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6982 / max 161.1235, expressed in 64 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107196	0.4077	55
107194	0.1713	34
107195	0.0743	30
107197	0.0352	14
107193	0.0096	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	94.41	gold quality
mammalian vulva	UBERON:0000997	93.60	gold quality
penis	UBERON:0000989	90.77	gold quality
nipple	UBERON:0002030	84.04	gold quality
zone of skin	UBERON:0000014	83.48	gold quality
skin of abdomen	UBERON:0001416	83.46	gold quality
skin of leg	UBERON:0001511	83.39	gold quality
lower esophagus mucosa	UBERON:0035834	77.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.24	gold quality
mucosa of stomach	UBERON:0001199	75.33	gold quality
skin of hip	UBERON:0001554	74.48	gold quality
buccal mucosa cell	CL:0002336	72.96	gold quality
gingival epithelium	UBERON:0001949	68.20	silver quality
gingiva	UBERON:0001828	66.44	silver quality
esophagus squamous epithelium	UBERON:0006920	65.23	gold quality
esophagus mucosa	UBERON:0002469	61.61	gold quality
pharyngeal mucosa	UBERON:0000355	58.22	silver quality
subcutaneous adipose tissue	UBERON:0002190	58.18	gold quality
vagina	UBERON:0000996	55.90	gold quality
cartilage tissue	UBERON:0002418	54.65	gold quality
popliteal artery	UBERON:0002250	49.11	gold quality
tibial artery	UBERON:0007610	49.09	gold quality
body of tongue	UBERON:0011876	48.83	gold quality
esophagus	UBERON:0001043	48.43	gold quality
lower lobe of lung	UBERON:0008949	47.45	silver quality
oral cavity	UBERON:0000167	46.36	silver quality
adipose tissue	UBERON:0001013	45.84	gold quality
body of pancreas	UBERON:0001150	45.31	gold quality
body of stomach	UBERON:0001161	45.02	gold quality
aorta	UBERON:0000947	44.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting PNLIPRP3, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-7151-5P	99.37	67.82	613
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844

Literature-anchored findings (GeneRIF, showing 1)

• Over expression of pancreatic lipase-related protein 3 is associated with hepatocellular carcinoma. (PMID:19640199)

Cross-species orthologs

28 orthologs

Organism	Symbol	Gene ID
danio_rerio	lipib	ENSDARG00000005332
danio_rerio		ENSDARG00000034667
drosophila_melanogaster	Yp1	FBGN0004045
drosophila_melanogaster	Yp3	FBGN0004047
drosophila_melanogaster	Yp2	FBGN0005391
drosophila_melanogaster	CG5162	FBGN0030828
drosophila_melanogaster	CG6847	FBGN0030884
drosophila_melanogaster	CG7367	FBGN0031976
drosophila_melanogaster	CG13282	FBGN0032612
drosophila_melanogaster	CG6675	FBGN0032973
drosophila_melanogaster	CG6472	FBGN0034166
drosophila_melanogaster	CG10163	FBGN0035697
drosophila_melanogaster	CG10116	FBGN0036367
drosophila_melanogaster	CG5665	FBGN0036977
drosophila_melanogaster	sxe2	FBGN0038398
drosophila_melanogaster	CG4582	FBGN0039344
drosophila_melanogaster	CG6296	FBGN0039470
drosophila_melanogaster	CG6295	FBGN0039471
drosophila_melanogaster	CG17192	FBGN0039472
drosophila_melanogaster	CG17191	FBGN0039473
drosophila_melanogaster	CG6283	FBGN0039474
drosophila_melanogaster	CG6277	FBGN0039475
drosophila_melanogaster	CG6271	FBGN0039476
drosophila_melanogaster	CG34447	FBGN0085476
drosophila_melanogaster	CG34448	FBGN0085477
drosophila_melanogaster	CG14034	FBGN0250847
drosophila_melanogaster	CG4267	FBGN0264979
drosophila_melanogaster	CG18258	FBGN0265267

Paralogs (9): LIPG (ENSG00000101670), PLA1A (ENSG00000144837), LIPH (ENSG00000163898), LIPC (ENSG00000166035), LPL (ENSG00000175445), PNLIP (ENSG00000175535), PNLIPRP1 (ENSG00000187021), LIPI (ENSG00000188992), PNLIPRP2 (ENSG00000266200)

Protein

Protein identifiers

Pancreatic lipase-related protein 3 — Q17RR3 (reviewed: Q17RR3)

All UniProt accessions (1): Q17RR3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Tissue specificity. Overexpressed in hepatocellular carcinoma.

Similarity. Belongs to the AB hydrolase superfamily. Lipase family.

RefSeq proteins (1): NP_001011709* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000734	TAG_lipase	Family
IPR001024	PLAT/LH2_dom	Domain
IPR002331	Lipase_panc	Family
IPR013818	Lipase	Domain
IPR016272	Lipase_LIPH	Family
IPR029058	AB_hydrolase_fold	Homologous_superfamily
IPR033906	Lipase_N	Domain
IPR036392	PLAT/LH2_dom_sf	Homologous_superfamily

Pfam: PF00151, PF01477

Catalyzed reactions (Rhea), 1 shown:

• a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) (RHEA:12044)

UniProt features (19 total): disulfide bond 6, sequence variant 5, active site 3, glycosylation site 2, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RR3-F1	89.10	0.72

Functional residue map

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

Catalytic / active sites (3): 168 (nucleophile); 191 (charge relay system); 279 (charge relay system)

Disulfide bonds (6): 252–277, 301–312, 315–320, 451–467, 21–27, 107–118

Glycosylation sites (2): 74, 125

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-192456	Digestion of dietary lipid
R-HSA-8935690	Digestion
R-HSA-8963743	Digestion and absorption

MSigDB gene sets: 62 (showing top): GOBP_STEROL_HOMEOSTASIS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_LIPID_HOMEOSTASIS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_NEUTRAL_LIPID_CATABOLIC_PROCESS, GOBP_PROTEIN_LIPID_COMPLEX_ORGANIZATION, GOBP_FATTY_ACID_BIOSYNTHETIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_TRIGLYCERIDE_CATABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_NEUTRAL_LIPID_METABOLIC_PROCESS

GO Biological Process (6): fatty acid biosynthetic process (GO:0006633), triglyceride catabolic process (GO:0019433), high-density lipoprotein particle remodeling (GO:0034375), cholesterol homeostasis (GO:0042632), lipid metabolic process (GO:0006629), lipid catabolic process (GO:0016042)

GO Molecular Function (7): lipoprotein lipase activity (GO:0004465), glycerophospholipid phospholipase A1 activity (GO:0008970), triacylglycerol lipase activity (GO:0004806), protein binding (GO:0005515), lipase activity (GO:0016298), hydrolase activity (GO:0016787), carboxylic ester hydrolase activity (GO:0052689)

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

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Digestion	1
Digestion and absorption	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
hydrolase activity, acting on ester bonds	2
fatty acid metabolic process	1
lipid biosynthetic process	1
monocarboxylic acid biosynthetic process	1
triglyceride metabolic process	1
acylglycerol catabolic process	1
plasma lipoprotein particle remodeling	1
sterol homeostasis	1
primary metabolic process	1
lipid metabolic process	1
catabolic process	1
triacylglycerol lipase activity	1
A1-type glycerophospholipase activity	1
lipase activity	1
carboxylic ester hydrolase activity	1
binding	1
catalytic activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

640 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNLIPRP3	SERPINB12	Q96P63	465
PNLIPRP3	LIPF	P07098	434
PNLIPRP3	CCDC102B	Q68D86	419
PNLIPRP3	GAGE12J	A6NER3	419
PNLIPRP3	HEPACAM	Q14CZ8	397
PNLIPRP3	GAGE12B	A1L429	393
PNLIPRP3	CWH43	Q9H720	380
PNLIPRP3	GCNT3	O95395	375
PNLIPRP3	HEPACAM2	A8MVW5	358
PNLIPRP3	EMC10	Q5UCC4	357
PNLIPRP3	UCP2	P55851	353
PNLIPRP3	ZNF691	Q5VV52	353
PNLIPRP3	VIL1	P09327	352
PNLIPRP3	CLPS	P04118	352
PNLIPRP3	FASN	P49327	352

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0M3KKW3, A2VBC4, A5PK46, A8PUY1, B2D0J5, C0HLL3, D7EZN2, O88354, P00591, P06857, P0CH47, P0CH86, P0CH87, P0DMB4, P0DMB5, P0DPT0, P0DSI2, P16233, P17892, P27657, P29183, P35501, P35502, P49369, P50903, P51528, P53357, P54315, P54316, P54317, P54318, P81139, P86100, P9WEM6, Q02157, Q04456, Q06478, Q17RR3, Q3ZU95, Q5BKQ4

Diamond homologs: A0A0M3KKW3, A2VBC4, A5PK46, C0HLL3, J3RZ81, O46559, O88354, P02843, P06607, P06857, P07867, P0CH47, P0CH86, P0CH87, P0DMB4, P0DMB5, P0DPT0, P0DSI2, P11150, P16233, P27656, P49369, P51528, P53357, P54316, P81139, P83542, P97535, Q06478, Q17RR3, Q32PY2, Q3SZ79, Q3ZU95, Q5BKQ4, Q641F6, Q64425, Q68KK0, Q6NYZ4, Q6P8U6, Q6PA23

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1522 predictions. Top by Δscore:

Variant	Effect	Δscore
10:116443043:T:A	acceptor_gain	1.0000
10:116443169:TGCA:T	donor_gain	1.0000
10:116443171:CAAT:C	donor_gain	1.0000
10:116443175:G:GG	donor_gain	1.0000
10:116443186:A:AG	donor_gain	1.0000
10:116444509:TCATG:T	donor_loss	1.0000
10:116444511:ATGGT:A	donor_loss	1.0000
10:116444512:TGGT:T	donor_loss	1.0000
10:116444515:T:TC	donor_loss	1.0000
10:116460962:CTAGG:C	acceptor_loss	1.0000
10:116460964:A:AG	acceptor_gain	1.0000
10:116460964:AG:A	acceptor_gain	1.0000
10:116460965:G:GG	acceptor_gain	1.0000
10:116460965:GG:G	acceptor_gain	1.0000
10:116461081:GCTTG:G	donor_gain	1.0000
10:116461082:CTTGG:C	donor_loss	1.0000
10:116461083:TTGGT:T	donor_loss	1.0000
10:116461085:GGTA:G	donor_loss	1.0000
10:116461086:G:GC	donor_loss	1.0000
10:116461086:G:GG	donor_gain	1.0000
10:116461087:T:A	donor_loss	1.0000
10:116461158:T:G	acceptor_gain	1.0000
10:116461161:A:AG	acceptor_gain	1.0000
10:116461162:TTTCA:T	acceptor_loss	1.0000
10:116461163:TTCA:T	acceptor_loss	1.0000
10:116461164:TCA:T	acceptor_loss	1.0000
10:116461165:CAG:C	acceptor_loss	1.0000
10:116461166:A:AG	acceptor_gain	1.0000
10:116461166:AG:A	acceptor_gain	1.0000
10:116461166:AGGT:A	acceptor_gain	1.0000

AlphaMissense

3103 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:116466085:A:C	S282R	0.978
10:116466087:T:A	S282R	0.978
10:116466087:T:G	S282R	0.978
10:116466106:A:C	S289R	0.973
10:116466108:C:A	S289R	0.973
10:116466108:C:G	S289R	0.973
10:116461203:T:C	F241L	0.972
10:116461205:T:A	F241L	0.972
10:116461205:T:G	F241L	0.972
10:116455767:A:C	S168R	0.967
10:116455769:C:A	S168R	0.967
10:116455769:C:G	S168R	0.967
10:116461041:T:A	V214D	0.966
10:116461031:G:C	A211P	0.964
10:116455830:G:T	G189W	0.963
10:116455823:A:C	R186S	0.959
10:116455823:A:T	R186S	0.959
10:116466127:T:C	F296L	0.959
10:116466129:T:A	F296L	0.959
10:116466129:T:G	F296L	0.959
10:116466134:C:A	A298D	0.956
10:116444408:T:A	N117K	0.952
10:116444408:T:G	N117K	0.952
10:116436834:T:C	L58P	0.951
10:116460972:A:G	D191G	0.951
10:116460972:A:T	D191V	0.950
10:116469311:T:C	F352L	0.949
10:116469313:T:A	F352L	0.949
10:116469313:T:G	F352L	0.949
10:116461214:T:A	N244K	0.946

dbSNP variants (sampled 300 via entrez): RS1000022242 (10:116438304 T>C), RS1000025801 (10:116467383 C>A), RS1000036491 (10:116472902 C>T), RS1000236931 (10:116470615 T>C), RS1000272463 (10:116456483 A>G), RS1000312677 (10:116454131 A>G,T), RS1000366522 (10:116453850 T>C), RS1000479287 (10:116434976 T>C), RS1000521018 (10:116427211 A>G), RS1000521633 (10:116432332 A>C,G), RS1000550806 (10:116427572 A>G), RS1000564468 (10:116468009 T>C), RS1000580577 (10:116456273 T>C), RS1000674423 (10:116461866 A>G), RS1000702385 (10:116465899 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003124_34	Mild influenza (H1N1) infection	1.000000e-12
GCST003125_6	Influenza A (H1N1) infection	3.000000e-08
GCST005951_66	Body mass index	4.000000e-08
GCST010572_13	Sweet taste preference	9.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:1001488	influenza A (H1N1)
EFO:0004340	body mass index
EFO:0010156	sweet liking measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
Particulate Matter	increases abundance, increases expression, decreases expression	3
Nickel	decreases expression	2
Cyclosporine	increases expression	2
6-hydroxy-5-((p- sulfophenyl)azo)-2-naphthalenesulfonic acid disodium salt	affects cotreatment, increases expression	1
3,4-dichloroaniline	increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cannabidiol	increases expression	1
Chenodeoxycholic Acid	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Deoxycholic Acid	affects cotreatment, increases expression	1
Diuron	increases expression	1
Glycochenodeoxycholic Acid	affects cotreatment, increases expression	1
Glycocholic Acid	affects cotreatment, increases expression	1
Glycodeoxycholic Acid	affects cotreatment, increases expression	1
Gold	increases expression	1
Dihydrotestosterone	increases expression	1
Tartrazine	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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