LCN15

Summary

LCN15 (lipocalin 15, HGNC:33777) is a protein-coding gene on chromosome 9q34.3, encoding Lipocalin-15 (Q6UWW0).

Predicted to enable small molecule binding activity. Predicted to be located in extracellular region.

Source: NCBI Gene 389812 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_203347

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33777
Approved symbol	LCN15
Name	lipocalin 15
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	UNQ2541, PRO6093
Ensembl gene	ENSG00000177984
Ensembl biotype	protein_coding
Entrez	389812

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000316144, ENST00000482511, ENST00000495223

RefSeq mRNA: 1 — MANE Select: NM_203347 NM_203347

CCDS: CCDS7006

Canonical transcript exons

ENST00000316144 — 7 exons

Exon	Start	End
ENSE00001309232	136759634	136759783
ENSE00001317405	136763870	136764009
ENSE00001381688	136764393	136764518
ENSE00003506765	136761787	136761853
ENSE00003641356	136763357	136763467
ENSE00003654300	136762188	136762289
ENSE00003679923	136763713	136763783

Expression profiles

Bgee: expression breadth ubiquitous, 103 present calls, max score 73.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3786 / max 137.8115, expressed in 75 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103214	0.2971	67
103213	0.0815	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.13	silver quality
prefrontal cortex	UBERON:0000451	70.91	gold quality
right frontal lobe	UBERON:0002810	69.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	69.02	gold quality
anterior cingulate cortex	UBERON:0009835	66.34	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	66.02	gold quality
apex of heart	UBERON:0002098	65.87	gold quality
frontal cortex	UBERON:0001870	64.93	gold quality
rectum	UBERON:0001052	64.32	gold quality
neocortex	UBERON:0001950	64.07	gold quality
duodenum	UBERON:0002114	62.74	gold quality
cerebral cortex	UBERON:0000956	60.17	gold quality
mucosa of transverse colon	UBERON:0004991	58.93	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	57.99	gold quality
gastrocnemius	UBERON:0001388	56.91	gold quality
primary visual cortex	UBERON:0002436	56.86	gold quality
transverse colon	UBERON:0001157	56.55	gold quality
heart left ventricle	UBERON:0002084	56.23	gold quality
cardiac ventricle	UBERON:0002082	55.69	gold quality
muscle of leg	UBERON:0001383	54.71	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	53.66	gold quality
amygdala	UBERON:0001876	53.33	gold quality
jejunal mucosa	UBERON:0000399	53.16	silver quality
occipital lobe	UBERON:0002021	52.59	gold quality
spinal cord	UBERON:0002240	52.42	gold quality
cartilage tissue	UBERON:0002418	52.30	gold quality
small intestine	UBERON:0002108	51.96	gold quality
forebrain	UBERON:0001890	51.50	gold quality
small intestine Peyer’s patch	UBERON:0003454	50.77	gold quality
brain	UBERON:0000955	50.52	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting LCN15, 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-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-5585-3P	98.25	67.41	941
HSA-MIR-6787-5P	97.54	63.85	457
HSA-MIR-7847-3P	96.63	64.58	952
HSA-MIR-10396B-5P	94.99	63.57	358
HSA-MIR-1908-5P	94.99	63.41	352
HSA-MIR-663A	94.99	63.54	378

Cross-species orthologs

0 orthologs

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), OBP2A (ENSG00000122136), LCN2 (ENSG00000148346), LCN9 (ENSG00000148386), LCN1 (ENSG00000160349), OBP2B (ENSG00000171102), LCN12 (ENSG00000184925), LCN10 (ENSG00000187922), LCN8 (ENSG00000204001), LCNL1 (ENSG00000214402), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Lipocalin-15 — Q6UWW0 (reviewed: Q6UWW0)

All UniProt accessions (1): Q6UWW0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

RefSeq proteins (1): NP_976222* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000566	Lipocln_cytosolic_FA-bd_dom	Domain
IPR002345	Lipocalin	Family
IPR012674	Calycin	Homologous_superfamily
IPR022272	Lipocalin_CS	Conserved_site

Pfam: PF00061

UniProt features (22 total): strand 9, helix 7, sequence variant 2, signal peptide 1, chain 1, disulfide bond 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2XST	X-RAY DIFFRACTION	1.63

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWW0-F1	91.34	0.82

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): 83–176

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-804914	Transport of fatty acids
R-HSA-382551	Transport of small molecules
R-HSA-425397	Transport of vitamins, nucleosides, and related molecules
R-HSA-425407	SLC-mediated transmembrane transport

MSigDB gene sets: 22 (showing top): GATA1_02, CAMPS_COLON_CANCER_COPY_NUMBER_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, REACTOME_TRANSPORT_OF_SMALL_MOLECULES, REACTOME_TRANSPORT_OF_FATTY_ACIDS, chr9q34, SNAI1_TARGET_GENES, ZNF597_TARGET_GENES, MIR5585_3P, GSE13485_DAY3_VS_DAY21_YF17D_VACCINE_PBMC_DN, GAO_LARGE_INTESTINE_ADULT_CA_ENTEROENDOCRINE_CELLS, DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_BOWMANS_GLAND, BUSSLINGER_DUODENAL_EC_CELLS, DESCARTES_MAIN_FETAL_INTESTINAL_EPITHELIAL_CELLS, DESCARTES_FETAL_INTESTINE_CHROMAFFIN_CELLS

GO Biological Process (0):

GO Molecular Function (2): small molecule binding (GO:0036094), protein binding (GO:0005515)

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

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Transport of vitamins, nucleosides, and related molecules	1
SLC-mediated transmembrane transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	1

Protein interactions and networks

STRING

490 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCN15	Q5T8A5	Q5T8A5	582
LCN15	OBP2B	Q9NPH6	561
LCN15	LCN8	Q6JVE9	555
LCN15	LCN9	Q8WX39	485
LCN15	IGSF23	A1L1A6	474
LCN15	LCN12	Q6JVE5	470
LCN15	LCN1	P31025	426
LCN15	BPIFB4	P59827	426
LCN15	TM4SF20	Q53R12	396
LCN15	PAEP	P09466	383
LCN15	EDA2R	Q9HAV5	380
LCN15	EPS8L3	Q8TE67	366
LCN15	APOD	P05090	365
LCN15	LCN10	Q6JVE6	345
LCN15	ITM2A	O43736	314

IntAct

9 interactions, top by confidence:

A	B	Type	Score
MEOX2	LCN15	psi-mi:“MI:0915”(physical association)	0.560
rep	LCN15	psi-mi:“MI:0915”(physical association)	0.560
LCN15	POTEF	psi-mi:“MI:0914”(association)	0.530
LCN15	MEOX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): MYO9B (Affinity Capture-MS), ALKBH2 (Affinity Capture-MS), DIS3L (Affinity Capture-MS), NUDT15 (Affinity Capture-MS), SETX (Affinity Capture-MS), ATG4A (Affinity Capture-MS), ALKBH2 (Affinity Capture-MS), ATG4A (Affinity Capture-MS), DIS3L (Affinity Capture-MS), ARID3A (Affinity Capture-MS), NUDT15 (Affinity Capture-MS), POTEF (Affinity Capture-MS), WDR54 (Affinity Capture-MS), LCN15 (Two-hybrid), ALKBH2 (Affinity Capture-MS)

ESM2 similar proteins: A2AEP0, A2AJB7, M5AXY1, O18874, O95445, P00978, P02753, P02763, P02764, P04916, P04939, P06910, P06911, P06912, P07361, P09465, P11944, P14630, P19652, P21350, P21352, P21760, P27485, P35578, P36992, P41263, P61641, P81608, Q00724, Q07456, Q28369, Q28388, Q29147, Q29614, Q2LE37, Q3SZR3, Q5R894, Q5VFH6, Q60559, Q60590

Diamond homologs: O02853, O09114, O97921, P11672, P22057, P30152, P41222, P80188, Q01584, Q29095, Q29487, Q29562, Q6UWW0, Q8WNM0, Q8WNM1, Q9TUI1, Q9XS65, Q9XSM0, Q6JVE5, P07360, Q28679, Q8VCG4, P00978, Q07456, Q60559, B3EY83, Q6ZST4, Q9I9P7, P36992, P21760, Q6JVE6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1130 predictions. Top by Δscore:

Variant	Effect	Δscore
9:136761849:TGCAT:T	acceptor_gain	1.0000
9:136761850:GCAT:G	acceptor_gain	1.0000
9:136761851:CAT:C	acceptor_gain	1.0000
9:136761851:CATC:C	acceptor_gain	1.0000
9:136761852:AT:A	acceptor_gain	1.0000
9:136761852:ATCT:A	acceptor_loss	1.0000
9:136761853:TCT:T	acceptor_loss	1.0000
9:136761854:C:CA	acceptor_loss	1.0000
9:136761854:C:CC	acceptor_gain	1.0000
9:136761855:T:A	acceptor_loss	1.0000
9:136761856:G:C	acceptor_gain	1.0000
9:136763352:CTCA:C	donor_gain	1.0000
9:136763353:TCA:T	donor_loss	1.0000
9:136763354:CAC:C	donor_loss	1.0000
9:136763355:A:AC	donor_gain	1.0000
9:136763355:ACT:A	donor_loss	1.0000
9:136763356:C:CA	donor_gain	1.0000
9:136763356:CT:C	donor_gain	1.0000
9:136763356:CTG:C	donor_gain	1.0000
9:136763356:CTGT:C	donor_gain	1.0000
9:136763356:CTGTA:C	donor_gain	1.0000
9:136763463:CAAGG:C	acceptor_gain	1.0000
9:136763464:AAGG:A	acceptor_gain	1.0000
9:136763465:AGG:A	acceptor_gain	1.0000
9:136763465:AGGCT:A	acceptor_loss	1.0000
9:136763466:GG:G	acceptor_gain	1.0000
9:136763468:C:CC	acceptor_gain	1.0000
9:136763468:CT:C	acceptor_loss	1.0000
9:136763469:T:A	acceptor_loss	1.0000
9:136763471:C:CT	acceptor_gain	1.0000

AlphaMissense

1206 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:136763960:A:C	F49C	0.983
9:136763723:G:C	F99L	0.981
9:136763723:G:T	F99L	0.981
9:136763725:A:G	F99L	0.981
9:136763995:C:A	W37C	0.981
9:136763995:C:G	W37C	0.981
9:136763959:G:C	F49L	0.977
9:136763959:G:T	F49L	0.977
9:136763961:A:G	F49L	0.977
9:136763997:A:G	W37R	0.977
9:136763997:A:T	W37R	0.977
9:136763418:G:C	F119L	0.975
9:136763418:G:T	F119L	0.975
9:136763420:A:G	F119L	0.975
9:136763446:C:G	R110P	0.970
9:136763397:C:A	K126N	0.969
9:136763397:C:G	K126N	0.969
9:136763724:A:G	F99S	0.969
9:136764405:G:C	F28L	0.967
9:136764405:G:T	F28L	0.967
9:136764407:A:G	F28L	0.967
9:136763960:A:G	F49S	0.963
9:136763724:A:C	F99C	0.962
9:136763416:G:T	A120D	0.957
9:136763417:C:G	A120P	0.957
9:136763772:C:G	C83S	0.957
9:136763773:A:T	C83S	0.957
9:136762249:G:C	F153L	0.954
9:136762249:G:T	F153L	0.954
9:136762251:A:G	F153L	0.954

dbSNP variants (sampled 300 via entrez): RS1000047995 (9:136761923 C>G,T), RS1000070715 (9:136762149 G>A,C), RS1000142633 (9:136762363 A>G), RS1000409757 (9:136766370 T>A,C), RS1001080477 (9:136760895 T>C,G), RS1001288704 (9:136762407 A>G), RS1001361012 (9:136762645 G>T), RS1001463981 (9:136760663 C>A), RS1001575134 (9:136766132 G>A), RS1001945014 (9:136764747 C>G,T), RS1003037577 (9:136764142 G>A,T), RS1003066786 (9:136759788 G>A), RS1003205988 (9:136759139 G>A), RS1003549945 (9:136759453 GC>G), RS1004484065 (9:136764544 C>G,T)

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

1 associations (top):

Study	Trait	p-value
GCST005171_4	QT interval	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004682	QT interval

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	5
Aflatoxin B1	affects expression, increases expression	4
Cyclosporine	decreases expression	3
OTX015	decreases expression	1
dicrotophos	decreases expression	1
bisphenol A	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
pentanal	increases expression	1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	increases expression	1
Ampicillin	increases expression	1
Copper	affects cotreatment, decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Diethylnitrosamine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Rotenone	increases expression	1
Triclosan	decreases expression	1
Valproic Acid	increases methylation	1
Oxyquinoline	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases methylation	1

Clinical trials (associated diseases)

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