LCNL1

Summary

LCNL1 (lipocalin like 1, HGNC:34436) is a protein-coding gene on chromosome 9q34.3, encoding Lipocalin-like 1 protein (Q6ZST4).

Predicted to enable small molecule binding activity.

Source: NCBI Gene 401562 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 31 total
• MANE Select transcript: NM_207510

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34436
Approved symbol	LCNL1
Name	lipocalin like 1
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ45224
Ensembl gene	ENSG00000214402
Ensembl biotype	protein_coding
Entrez	401562

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 retained_intron, 2 protein_coding

ENST00000408973, ENST00000432827, ENST00000460177, ENST00000482657, ENST00000870827

RefSeq mRNA: 1 — MANE Select: NM_207510 NM_207510

CCDS: CCDS43908

Canonical transcript exons

ENST00000408973 — 3 exons

Exon	Start	End
ENSE00001761607	136982993	136983708
ENSE00001797370	136984713	136985758
ENSE00003546367	136984490	136984563

Expression profiles

Bgee: expression breadth ubiquitous, 146 present calls, max score 96.39.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5546 / max 868.3864, expressed in 252 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99625	0.4490	109
99626	0.4162	99
99623	0.3219	113
99624	0.2900	97
99627	0.0775	31

Top tissues by expression

241 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	96.39	silver quality
left testis	UBERON:0004533	91.35	gold quality
apex of heart	UBERON:0002098	90.62	gold quality
right testis	UBERON:0004534	90.30	gold quality
right frontal lobe	UBERON:0002810	89.45	gold quality
tibial nerve	UBERON:0001323	87.46	gold quality
testis	UBERON:0000473	86.48	gold quality
anterior cingulate cortex	UBERON:0009835	85.85	gold quality
amygdala	UBERON:0001876	85.50	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.40	gold quality
putamen	UBERON:0001874	83.85	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.54	gold quality
caudate nucleus	UBERON:0001873	83.41	gold quality
nucleus accumbens	UBERON:0001882	81.80	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.87	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.13	gold quality
spinal cord	UBERON:0002240	79.77	gold quality
hypothalamus	UBERON:0001898	79.34	gold quality
sural nerve	UBERON:0015488	78.94	gold quality
stromal cell of endometrium	CL:0002255	78.88	gold quality
cerebellar hemisphere	UBERON:0002245	77.95	gold quality
cerebellar cortex	UBERON:0002129	77.82	gold quality
right atrium auricular region	UBERON:0006631	77.81	gold quality
cardiac atrium	UBERON:0002081	76.86	gold quality
left uterine tube	UBERON:0001303	76.77	gold quality
substantia nigra	UBERON:0002038	76.33	gold quality
cerebellum	UBERON:0002037	75.92	gold quality
heart left ventricle	UBERON:0002084	74.96	gold quality
endocervix	UBERON:0000458	74.14	gold quality
cardiac ventricle	UBERON:0002082	73.84	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-25	yes	4.86
E-ANND-3	no	1.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting LCNL1, 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-4283	100.00	66.42	2097
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-6784-3P	98.39	64.88	662
HSA-MIR-6862-3P	97.92	64.86	531
HSA-MIR-3200-5P	97.34	65.97	826
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-4486	96.96	60.61	931
HSA-MIR-9899	91.24	59.59	90
HSA-MIR-6499-5P	87.01	61.21	38

Cross-species orthologs

0 orthologs

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), OBP2A (ENSG00000122136), LCN2 (ENSG00000148346), LCN9 (ENSG00000148386), LCN1 (ENSG00000160349), OBP2B (ENSG00000171102), LCN15 (ENSG00000177984), LCN12 (ENSG00000184925), LCN10 (ENSG00000187922), LCN8 (ENSG00000204001), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Lipocalin-like 1 protein — Q6ZST4 (reviewed: Q6ZST4)

All UniProt accessions (1): Q6ZST4

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the calycin superfamily. Lipocalin family.

RefSeq proteins (1): NP_997393* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00061

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZST4-F1	71.29	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): RNGTGGGC_UNKNOWN, chr9q34, LCORL_TARGET_GENES, NFKBIA_TARGET_GENES, ZFP91_TARGET_GENES, ZNF184_TARGET_GENES, ZNF274_TARGET_GENES, ZNF410_TARGET_GENES, MIR1227_5P, MIR4527, DESCARTES_MAIN_FETAL_RETINAL_PIGMENT_CELLS, ZBTB5_TARGET_GENES, MCM3_TARGET_GENES, HDGF_TARGET_GENES, NFXL1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCNL1	LCN10	Q6JVE6	592
LCNL1	LCN8	Q6JVE9	511
LCNL1	LCN6	P62502	506
LCNL1	GRAPL	Q8TC17	488
LCNL1	LCN9	Q8WX39	453
LCNL1	OBP2B	Q9NPH6	430
LCNL1	Q5T8A5	Q5T8A5	388
LCNL1	PTGDS	P41222	381
LCNL1	LCN12	Q6JVE5	370
LCNL1	CLIC3	O95833	361
LCNL1	KIAA1586	Q9HCI6	358
LCNL1	CPO	Q8IVL8	355
LCNL1	PTPDC1	A2A3K4	348
LCNL1	ACRBP	Q8NEB7	304
LCNL1	GPR153	Q6NV75	302

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LCNL1	AGTR1	psi-mi:“MI:0915”(physical association)	0.370
LCNL1	OXTR	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (2): LCNL1 (Two-hybrid), LCNL1 (Two-hybrid)

ESM2 similar proteins: B3EY83, H3BQJ8, O02853, O09114, O18873, O97921, P02758, P04119, P07380, P09466, P11672, P13613, P19647, P20289, P21760, P22057, P30152, P31025, P33688, P41222, P41244, P53715, P62502, P62503, Q29095, Q29487, Q29562, Q5VSP4, Q62471, Q6JVE6, Q6JVE9, Q6JVL5, Q6UWW0, Q6ZST4, Q7L513, Q810Z1, Q8BH06, Q8VCG4, Q8WNM0, Q8WNM1

Diamond homologs: O02853, O09114, O97921, P07360, P22057, P41222, Q01584, Q28679, Q29095, Q29487, Q29562, Q6UWW0, Q6ZST4, Q8VCG4, Q8WNM0, Q8WNM1, Q9I9P7, Q9TUI1, Q9XS65, Q9XSM0, P21760, P80188, Q6JVE6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

898 predictions. Top by Δscore:

Variant	Effect	Δscore
9:136983709:G:GG	donor_gain	0.9900
9:136984484:CCCCA:C	acceptor_loss	0.9900
9:136984485:CCCA:C	acceptor_loss	0.9900
9:136984486:CCAG:C	acceptor_loss	0.9900
9:136984487:CAGG:C	acceptor_loss	0.9900
9:136984488:A:AG	acceptor_gain	0.9900
9:136984488:A:T	acceptor_loss	0.9900
9:136984489:G:GA	acceptor_gain	0.9900
9:136984561:CAGGT:C	donor_loss	0.9900
9:136984562:AG:A	donor_loss	0.9900
9:136984564:GTGAG:G	donor_loss	0.9900
9:136984565:T:G	donor_loss	0.9900
9:136984913:G:GT	donor_gain	0.9900
9:136985133:GTCGG:G	donor_gain	0.9900
9:136984488:AG:A	acceptor_gain	0.9800
9:136984489:GG:G	acceptor_gain	0.9800
9:136984489:GGC:G	acceptor_gain	0.9800
9:136984489:GGCCC:G	acceptor_gain	0.9800
9:136984711:A:AG	acceptor_gain	0.9800
9:136984712:G:GG	acceptor_gain	0.9800
9:136984712:GCC:G	acceptor_gain	0.9800
9:136984914:A:T	donor_gain	0.9800
9:136985034:A:AG	acceptor_gain	0.9800
9:136985035:G:GG	acceptor_gain	0.9800
9:136983705:CCACG:C	donor_loss	0.9700
9:136983707:ACG:A	donor_loss	0.9700
9:136983708:CG:C	donor_loss	0.9700
9:136983709:G:GC	donor_loss	0.9700
9:136983710:T:A	donor_loss	0.9700
9:136983711:AAGT:A	donor_loss	0.9700

AlphaMissense

1051 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:136984760:T:C	F82L	0.952
9:136984762:T:A	F82L	0.952
9:136984762:T:G	F82L	0.952
9:136984551:T:C	F62L	0.945
9:136984553:C:A	F62L	0.945
9:136984553:C:G	F62L	0.945
9:136983617:T:C	F11L	0.939
9:136983619:C:A	F11L	0.939
9:136983619:C:G	F11L	0.939
9:136984742:T:C	F76L	0.920
9:136984744:C:A	F76L	0.920
9:136984744:C:G	F76L	0.920
9:136983631:G:C	K15N	0.905
9:136983631:G:T	K15N	0.905
9:136983695:T:C	F37L	0.905
9:136983697:T:A	F37L	0.905
9:136983697:T:G	F37L	0.905
9:136983618:T:G	F11C	0.861
9:136984552:T:G	F62C	0.843
9:136984750:C:A	D78E	0.842
9:136984750:C:G	D78E	0.842
9:136983646:G:A	M20I	0.841
9:136983646:G:C	M20I	0.841
9:136983646:G:T	M20I	0.841
9:136984552:T:C	F62S	0.818
9:136983618:T:C	F11S	0.812
9:136984524:T:C	F53L	0.809
9:136984526:C:A	F53L	0.809
9:136984526:C:G	F53L	0.809
9:136984731:T:C	I72T	0.777

dbSNP variants (sampled 300 via entrez): RS1000092726 (9:136980997 C>T), RS1000199699 (9:136986234 T>C), RS1000654865 (9:136984935 G>C), RS1000779596 (9:136984464 A>C,G), RS1001330783 (9:136982330 C>T), RS1001446297 (9:136982051 C>T), RS1001883721 (9:136985801 G>T), RS1003431530 (9:136983380 C>G,T), RS1003603992 (9:136986111 T>A,C), RS1004394856 (9:136983964 G>A,T), RS1004566140 (9:136982910 G>A), RS1005599143 (9:136985189 C>A,T), RS1006507361 (9:136981405 C>T), RS1007224153 (9:136984409 C>A,T), RS1007276603 (9:136984229 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
clothianidin	decreases expression	1
prothioconazole	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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