LCN10

Summary

LCN10 (lipocalin 10, HGNC:20892) is a protein-coding gene on chromosome 9q34.3, encoding Epididymal-specific lipocalin-10 (Q6JVE6). May play a role in male fertility.

Members of the lipocalin family, such as LCN10, 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 414332 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_001001712

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20892
Approved symbol	LCN10
Name	lipocalin 10
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187922
Ensembl biotype	protein_coding
OMIM	612904
Entrez	414332

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000341040, ENST00000406721, ENST00000474369, ENST00000494294, ENST00000497771, ENST00000527229, ENST00000529013, ENST00000532006, ENST00000928242

RefSeq mRNA: 3 — MANE Select: NM_001001712 NM_001001712, NM_001368089, NM_001368090

CCDS: CCDS35182, CCDS94536, CCDS94537

Canonical transcript exons

ENST00000497771 — 6 exons

Exon	Start	End
ENSE00002168249	136742787	136742940
ENSE00003479554	136739950	136740048
ENSE00003543120	136741252	136741361
ENSE00003577185	136741881	136742020
ENSE00003682541	136740836	136740943
ENSE00003890804	136738170	136739553

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 97.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6001 / max 78.8937, expressed in 133 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103194	0.5345	124
103193	0.0332	15
103195	0.0323	13

Top tissues by expression

134 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	97.98	gold quality
mucosa of stomach	UBERON:0001199	94.37	gold quality
apex of heart	UBERON:0002098	92.57	gold quality
left uterine tube	UBERON:0001303	91.83	gold quality
body of uterus	UBERON:0009853	89.34	gold quality
heart left ventricle	UBERON:0002084	89.31	gold quality
myometrium	UBERON:0001296	88.25	gold quality
endocervix	UBERON:0000458	86.52	gold quality
heart	UBERON:0000948	83.86	gold quality
spleen	UBERON:0002106	83.81	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.40	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	82.76	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.55	gold quality
lower esophagus	UBERON:0013473	82.37	gold quality
right ovary	UBERON:0002118	81.92	gold quality
left coronary artery	UBERON:0001626	81.85	gold quality
fundus of stomach	UBERON:0001160	81.80	gold quality
right atrium auricular region	UBERON:0006631	81.38	gold quality
tibial nerve	UBERON:0001323	80.80	gold quality
right lung	UBERON:0002167	80.58	gold quality
subcutaneous adipose tissue	UBERON:0002190	80.54	gold quality
left lobe of thyroid gland	UBERON:0001120	80.50	gold quality
right lobe of thyroid gland	UBERON:0001119	80.45	gold quality
body of stomach	UBERON:0001161	80.45	gold quality
small intestine	UBERON:0002108	80.31	gold quality
adipose tissue	UBERON:0001013	79.88	gold quality
thyroid gland	UBERON:0002046	79.84	gold quality
ectocervix	UBERON:0012249	79.56	gold quality
omental fat pad	UBERON:0010414	79.45	gold quality
fallopian tube	UBERON:0003889	79.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting LCN10, 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-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-4796-5P	99.34	70.06	810
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-6807-5P	97.51	64.25	1046
HSA-MIR-6802-3P	97.29	65.42	613
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-3192-5P	96.98	65.76	1926
HSA-MIR-1288-3P	96.86	66.95	536
HSA-MIR-1182	96.41	64.89	336
HSA-MIR-6760-3P	96.35	68.31	1001
HSA-MIR-1266-3P	96.23	66.36	778
HSA-MIR-4435	95.90	65.47	1201
HSA-MIR-4268	94.45	64.09	819

Literature-anchored findings (GeneRIF, showing 3)

• Lipocalin 10 as a New Prognostic Biomarker in Sepsis-Induced Myocardial Dysfunction and Mortality: A Pilot Study. (PMID:34121925)
• Loss of Lipocalin 10 Exacerbates Diabetes-Induced Cardiomyopathy via Disruption of Nr4a1-Mediated Anti-Inflammatory Response in Macrophages. (PMID:35757735)
• Lipocalin 10 is essential for protection against inflammation-triggered vascular leakage by activating LDL receptor-related protein 2-slingshot homologue 1 signalling pathway. (PMID:37392461)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lcn10	ENSMUSG00000047356
rattus_norvegicus	Lcn10	ENSRNOG00000028074

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), OBP2A (ENSG00000122136), LCN2 (ENSG00000148346), LCN9 (ENSG00000148386), LCN1 (ENSG00000160349), OBP2B (ENSG00000171102), LCN15 (ENSG00000177984), LCN12 (ENSG00000184925), LCN8 (ENSG00000204001), LCNL1 (ENSG00000214402), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Epididymal-specific lipocalin-10 — Q6JVE6 (reviewed: Q6JVE6)

All UniProt accessions (5): E9PK15, E9PQQ7, E9PRR3, Q6JVE6, H0YCM3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in male fertility. May act as a retinoid carrier protein within the epididymis.

Subcellular location. Secreted.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6JVE6-1	1	yes
Q6JVE6-2	2

RefSeq proteins (3): NP_001001712, NP_001355018, NP_001355019 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002345	Lipocalin	Family
IPR012674	Calycin	Homologous_superfamily
IPR022272	Lipocalin_CS	Conserved_site

UniProt features (6 total): signal peptide 1, chain 1, modified residue 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-Q6JVE6-F1	72.40	0.23

Functional residue map

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

Post-translational modifications (1): 170

Disulfide bonds (1): 90–163

Glycosylation sites (1): 149

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_MYELOID_LEUKOCYTE_ACTIVATION, GOBP_MACROPHAGE_ACTIVATION, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_RESPONSE_TO_RADIATION, GOBP_RESPONSE_TO_LIPID, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_RESPONSE_TO_TYPE_II_INTERFERON, GOBP_RESPONSE_TO_X_RAY, IK3_01, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT

GO Biological Process (7): inflammatory response (GO:0006954), heart development (GO:0007507), response to X-ray (GO:0010165), response to lipopolysaccharide (GO:0032496), response to type II interferon (GO:0034341), macrophage activation (GO:0042116), response to stress (GO:0006950)

GO Molecular Function (1): small molecule binding (GO:0036094)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
defense response	1
animal organ development	1
circulatory system development	1
response to ionizing radiation	1
response to molecule of bacterial origin	1
response to lipid	1
response to oxygen-containing compound	1
response to cytokine	1
innate immune response	1
myeloid leukocyte activation	1
response to stimulus	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

454 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCN10	LCN9	Q8WX39	756
LCN10	LCN6	P62502	726
LCN10	LCN8	Q6JVE9	662
LCN10	LCN12	Q6JVE5	606
LCN10	LCNL1	Q6ZST4	592
LCN10	TMEM141	Q96I45	521
LCN10	Q5T8A5	Q5T8A5	480
LCN10	TEDDM1	Q5T9Z0	445
LCN10	FAM174B	Q3ZCQ3	439
LCN10	STAC2	Q6ZMT1	406
LCN10	CST11	Q9H112	406
LCN10	LCN1	P31025	404
LCN10	XXYLT1	Q8NBI6	398
LCN10	OR2T2	Q6IF00	396
LCN10	PRRC2B	Q5JSZ5	390

IntAct

0 interactions, top by confidence:

BioGRID (1): LCN10 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: B3EY83, B5X0G2, H2B3G5, O02853, O09114, O18873, O97921, P02758, P02761, P04119, P07380, P09466, P11588, P11672, P13613, P19647, P20289, P22057, P30152, P31025, P33685, P33686, P33687, P33688, P41222, P41244, P53715, P62502, P62503, P80188, Q28388, Q29095, Q29487, Q29562, Q5VSP4, Q6JVE6, Q6JVL5, Q6UWW0, Q810Z1, Q8K1H9

Diamond homologs: Q6JVE6, Q810Z1, Q9I9P7, P21760, P80188, Q6UWW0, Q6ZST4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1463 predictions. Top by Δscore:

Variant	Effect	Δscore
9:136739949:CCGT:C	donor_gain	1.0000
9:136740045:CTAT:C	acceptor_gain	1.0000
9:136740046:TAT:T	acceptor_gain	1.0000
9:136740047:AT:A	acceptor_gain	1.0000
9:136740047:ATCT:A	acceptor_loss	1.0000
9:136740049:C:A	acceptor_loss	1.0000
9:136740049:C:CA	acceptor_loss	1.0000
9:136740049:C:CC	acceptor_gain	1.0000
9:136740050:T:A	acceptor_loss	1.0000
9:136740787:C:A	donor_gain	1.0000
9:136740787:C:CA	donor_gain	1.0000
9:136740798:C:CA	donor_gain	1.0000
9:136740808:T:TA	donor_gain	1.0000
9:136740834:A:AC	donor_gain	1.0000
9:136740835:C:CC	donor_gain	1.0000
9:136741266:T:TA	donor_gain	1.0000
9:136741267:C:A	donor_gain	1.0000
9:136739552:CG:C	acceptor_gain	0.9900
9:136739943:AGCTT:A	donor_loss	0.9900
9:136739944:GCTTA:G	donor_loss	0.9900
9:136739945:CTTA:C	donor_loss	0.9900
9:136739946:TTA:T	donor_loss	0.9900
9:136739947:T:TG	donor_loss	0.9900
9:136739948:A:AC	donor_gain	0.9900
9:136739949:C:CC	donor_gain	0.9900
9:136739949:C:CT	donor_loss	0.9900
9:136740055:T:C	acceptor_gain	0.9900
9:136740939:TTTCA:T	acceptor_gain	0.9900
9:136740940:TTCA:T	acceptor_gain	0.9900
9:136740941:TCA:T	acceptor_gain	0.9900

AlphaMissense

1282 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:136740008:G:C	F159L	0.940
9:136740008:G:T	F159L	0.940
9:136740010:A:G	F159L	0.940
9:136742018:A:C	F40L	0.932
9:136742018:A:T	F40L	0.932
9:136742020:A:G	F40L	0.932
9:136740924:G:C	F116L	0.925
9:136740924:G:T	F116L	0.925
9:136740926:A:G	F116L	0.925
9:136741970:G:C	F56L	0.910
9:136741970:G:T	F56L	0.910
9:136741972:A:G	F56L	0.910
9:136740009:A:G	F159S	0.901
9:136742008:A:G	W44R	0.901
9:136742008:A:T	W44R	0.901
9:136740026:G:C	F153L	0.883
9:136740026:G:T	F153L	0.883
9:136740028:A:G	F153L	0.883
9:136742006:C:A	W44C	0.876
9:136742006:C:G	W44C	0.876
9:136742019:A:G	F40S	0.873
9:136740009:A:C	F159C	0.870
9:136741989:G:T	A50D	0.868
9:136742001:A:G	I46T	0.862
9:136740889:A:T	V128D	0.860
9:136742019:A:C	F40C	0.858
9:136742009:G:C	F43L	0.856
9:136742009:G:T	F43L	0.856
9:136742011:A:G	F43L	0.856
9:136742014:C:A	G42W	0.853

dbSNP variants (sampled 300 via entrez): RS1000588224 (9:136742586 C>A,T), RS1000683069 (9:136742798 T>C), RS1000796457 (9:136738479 C>G), RS1000959194 (9:136741653 T>C), RS1002191303 (9:136737804 T>G), RS1002209486 (9:136741162 C>T), RS1002283287 (9:136741001 C>A,T), RS1002548762 (9:136739994 T>A), RS1002591583 (9:136740464 C>A), RS1002678168 (9:136744670 A>G,T), RS1003737263 (9:136739786 C>A,T), RS1003910564 (9:136743570 A>G), RS1003931410 (9:136744126 T>G), RS1003963079 (9:136739073 G>A), RS1003970671 (9:136739157 G>A)

Disease associations

OMIM: gene MIM:612904 | 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

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	increases expression	2
bisphenol A	decreases methylation	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Leflunomide	increases expression	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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