LCN9

Summary

LCN9 (lipocalin 9, HGNC:17442) is a protein-coding gene on chromosome 9q34.3, encoding Epididymal-specific lipocalin-9 (Q8WX39).

Members of the lipocalin family, such as LCN9, have a common structure consisting of an 8-stranded antiparallel beta-barrel that forms a cup-shaped ligand-binding pocket or calyx. Lipocalins generally bind small hydrophobic ligands and transport them to specific cells (Suzuki et al., 2004 [PubMed 15363845]).

Source: NCBI Gene 392399 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_001393661

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17442
Approved symbol	LCN9
Name	lipocalin 9
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000148386
Ensembl biotype	protein_coding
OMIM	612903
Entrez	392399

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 protein_coding

ENST00000277526, ENST00000430290, ENST00000554343, ENST00000619315

RefSeq mRNA: 1 — MANE Select: NM_001393661 NM_001393661

CCDS: CCDS94528

Canonical transcript exons

ENST00000619315 — 6 exons

Exon	Start	End
ENSE00001094965	135663309	135663417
ENSE00002475759	135665688	135665752
ENSE00003516363	135664162	135664298
ENSE00003545647	135665245	135665355
ENSE00003578507	135664722	135664795
ENSE00003929010	135665861	135666961

Expression profiles

Bgee: expression breadth broad, 68 present calls, max score 54.42.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0104 / max 9.4685, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99464	0.0104	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
substantia nigra	UBERON:0002038	54.42	gold quality
amygdala	UBERON:0001876	53.74	gold quality
temporal lobe	UBERON:0001871	53.38	gold quality
putamen	UBERON:0001874	49.46	gold quality
Ammon’s horn	UBERON:0001954	47.91	gold quality
anterior cingulate cortex	UBERON:0009835	46.56	gold quality
hypothalamus	UBERON:0001898	44.37	gold quality
right frontal lobe	UBERON:0002810	44.01	gold quality
caudate nucleus	UBERON:0001873	42.70	gold quality
nucleus accumbens	UBERON:0001882	42.50	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	41.98	gold quality
right uterine tube	UBERON:0001302	41.63	silver quality
brain	UBERON:0000955	41.48	gold quality
cerebral cortex	UBERON:0000956	41.33	gold quality
granulocyte	CL:0000094	40.74	gold quality
Brodmann (1909) area 9	UBERON:0013540	40.65	gold quality
adenohypophysis	UBERON:0002196	39.14	gold quality
sural nerve	UBERON:0015488	38.91	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
frontal cortex	UBERON:0001870	37.03	gold quality
pituitary gland	UBERON:0000007	36.86	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	36.05	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
ectocervix	UBERON:0012249	35.10	gold quality
leukocyte	CL:0000738	33.82	gold quality
monocyte	CL:0000576	33.66	silver quality
fallopian tube	UBERON:0003889	33.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.58

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lcn9	ENSMUSG00000023210
rattus_norvegicus	Lcn9	ENSRNOG00000027821

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), OBP2A (ENSG00000122136), LCN2 (ENSG00000148346), LCN1 (ENSG00000160349), OBP2B (ENSG00000171102), LCN15 (ENSG00000177984), LCN12 (ENSG00000184925), LCN10 (ENSG00000187922), LCN8 (ENSG00000204001), LCNL1 (ENSG00000214402), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Epididymal-specific lipocalin-9 — Q8WX39 (reviewed: Q8WX39)

Alternative names: MUP-like lipocalin

All UniProt accessions (2): Q8WX39, A0AAA9WZE8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Miscellaneous. Gene prediction based on RNA-Seq exon structure data.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WX39-1	1	yes
Q8WX39-2	2

RefSeq proteins (1): NP_001380590* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000566	Lipocln_cytosolic_FA-bd_dom	Domain
IPR002345	Lipocalin	Family
IPR002971	Maj_urinary	Family
IPR012674	Calycin	Homologous_superfamily
IPR022272	Lipocalin_CS	Conserved_site

Pfam: PF00061

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WX39-F1	85.36	0.61

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): 83–161

Glycosylation sites (2): 68, 129

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: 19 (showing top): GCANCTGNY_MYOD_Q6, MYOD_Q6, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, REACTOME_TRANSPORT_OF_SMALL_MOLECULES, REACTOME_TRANSPORT_OF_FATTY_ACIDS, chr9q34, GLI1_TARGET_GENES, NFKBIA_TARGET_GENES, GSE14769_UNSTIM_VS_20MIN_LPS_BMDM_UP, NCOA4_TARGET_GENES, ZNF224_TARGET_GENES, GSE12505_WT_VS_E2_2_HET_PDC_UP, GSE32423_CTRL_VS_IL4_MEMORY_CD8_TCELL_UP, GSE9037_WT_VS_IRAK4_KO_BMDM_DN, REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT

GO Biological Process (0):

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

GO Cellular Component (2): obsolete extracellular space (GO:0005615), 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

546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCN9	LCN10	Q6JVE6	756
LCN9	LCN8	Q6JVE9	751
LCN9	LCN6	P62502	716
LCN9	TEDDM1	Q5T9Z0	622
LCN9	LCN12	Q6JVE5	619
LCN9	Q5T8A5	Q5T8A5	615
LCN9	SPINT4	Q6UDR6	582
LCN9	LCN1	P31025	558
LCN9	CST11	Q9H112	545
LCN9	TTLL11	Q8NHH1	534
LCN9	ZSCAN20	P17040	519
LCN9	DEFB128	Q7Z7B8	506
LCN9	LCN15	Q6UWW0	485
LCN9	ZNF362	Q5T0B9	480
LCN9	C3orf22	Q8N5N4	479

IntAct

5 interactions, top by confidence:

A	B	Type	Score
LYSMD2	LCN9	psi-mi:“MI:0915”(physical association)	0.560
LCN9	C1QL1	psi-mi:“MI:0914”(association)	0.350
LCN9	LYSMD2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (26): LCN9 (Two-hybrid), CBWD3 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), ITGA8 (Affinity Capture-MS), IMPAD1 (Affinity Capture-MS), C1QL4 (Affinity Capture-MS), ST3GAL4 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), UBE3D (Affinity Capture-MS), SIL1 (Affinity Capture-MS), LAMA1 (Affinity Capture-MS), MICA (Affinity Capture-MS), ITGAV (Affinity Capture-MS), CRELD2 (Affinity Capture-MS), COL14A1 (Affinity Capture-MS)

ESM2 similar proteins: A2AEP0, A2BIM8, B5X0G2, F0UZ12, H2B3G5, O18874, P02761, P02762, P02763, P04119, P04938, P04939, P06911, P07435, P08937, P09465, P09466, P11588, P11589, P11590, P11591, P13613, P19652, P20289, P21760, P25227, P41244, P81245, P81608, P83508, Q01584, Q28133, Q28388, Q29147, Q3SZR3, Q5FW60, Q5VFH6, Q5VSP4, Q62471, Q62472

Diamond homologs: A2BIM8, B5X0G2, C0HJA9, H2B3G5, P02761, P02762, P04938, P04939, P09466, P11588, P11589, P11590, P11591, P81608, Q28388, Q29147, Q5FW60, Q5VFH6, Q8WX39, Q95182, Q9D267, P81648, A2AEP0, F0UZ12, O08976, P08937, P09465, P15399, P81245, P83508, Q28133, Q99MG7, Q9D3H2, Q9QXU1, Q9Z1I7, S5ZYD3, P81647, P02754, P02755, P02756

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1030 predictions. Top by Δscore:

Variant	Effect	Δscore
9:135663399:G:GT	donor_gain	1.0000
9:135663400:A:T	donor_gain	1.0000
9:135663416:GG:G	donor_gain	1.0000
9:135663417:GG:G	donor_gain	1.0000
9:135664190:T:TA	acceptor_gain	1.0000
9:135664329:G:GT	donor_gain	1.0000
9:135665649:A:AG	acceptor_gain	1.0000
9:135665649:AGCAC:A	acceptor_gain	1.0000
9:135665650:G:GG	acceptor_gain	1.0000
9:135665650:GCAC:G	acceptor_gain	1.0000
9:135665650:GCACG:G	acceptor_gain	1.0000
9:135663417:GGTG:G	donor_loss	0.9900
9:135663418:G:T	donor_gain	0.9900
9:135663418:GTGT:G	donor_loss	0.9900
9:135663419:T:G	donor_loss	0.9900
9:135664189:AT:A	acceptor_gain	0.9900
9:135664190:T:G	acceptor_gain	0.9900
9:135664263:G:GT	donor_gain	0.9900
9:135664329:G:T	donor_gain	0.9900
9:135664330:A:T	donor_gain	0.9900
9:135665240:CGCA:C	acceptor_loss	0.9900
9:135665241:GCA:G	acceptor_loss	0.9900
9:135665242:CA:C	acceptor_loss	0.9900
9:135665243:A:AC	acceptor_loss	0.9900
9:135665243:A:AG	acceptor_gain	0.9900
9:135665244:G:GA	acceptor_loss	0.9900
9:135665244:G:GG	acceptor_gain	0.9900
9:135665244:GAT:G	acceptor_gain	0.9900
9:135665244:GATGA:G	acceptor_gain	0.9900
9:135665647:CCA:C	acceptor_loss	0.9900

AlphaMissense

1207 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:135664240:T:C	F59L	0.955
9:135664242:C:A	F59L	0.955
9:135664242:C:G	F59L	0.955
9:135664288:T:C	F75L	0.903
9:135664290:C:A	F75L	0.903
9:135664290:C:G	F75L	0.903
9:135664174:T:A	W37R	0.896
9:135664174:T:C	W37R	0.896
9:135665292:T:C	F119L	0.890
9:135665294:C:A	F119L	0.890
9:135665294:C:G	F119L	0.890
9:135665301:T:C	F122L	0.880
9:135665303:C:A	F122L	0.880
9:135665303:C:G	F122L	0.880
9:135664282:T:C	F73L	0.877
9:135664284:T:A	F73L	0.877
9:135664284:T:G	F73L	0.877
9:135664176:G:C	W37C	0.866
9:135664176:G:T	W37C	0.866
9:135665315:C:A	N126K	0.836
9:135665315:C:G	N126K	0.836
9:135664195:T:C	S44P	0.824
9:135664211:G:C	R49P	0.813
9:135664756:T:C	C90R	0.787
9:135664277:T:C	L71P	0.785
9:135665269:T:A	V111D	0.785
9:135664192:G:C	A43P	0.781
9:135663340:A:C	S7R	0.778
9:135663342:C:A	S7R	0.778
9:135663342:C:G	S7R	0.778

dbSNP variants (sampled 300 via entrez): RS1000281509 (9:135661988 C>A,G,T), RS1000620567 (9:135663170 AGG>A), RS1000642527 (9:135661379 G>A), RS1000875584 (9:135666456 C>T), RS1001632176 (9:135666198 C>T), RS1001671653 (9:135661792 G>A), RS1001965808 (9:135667143 G>T), RS1002148810 (9:135661626 C>T), RS1002167702 (9:135665082 C>T), RS1002587310 (9:135665149 A>T), RS1002799792 (9:135667245 C>G,T), RS1003470887 (9:135661599 G>A), RS1004413833 (9:135664947 C>A,T), RS1004428324 (9:135665104 G>A), RS1004658453 (9:135665515 G>A,C)

Disease associations

OMIM: gene MIM:612903 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	increases expression	1
Valproic Acid	increases methylation	1
Magnetite Nanoparticles	increases expression	1

Clinical trials (associated diseases)

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