LENEP

Summary

LENEP (lens epithelial protein, HGNC:14429) is a protein-coding gene on chromosome 1q21.3, encoding Lens epithelial cell protein LEP503 (Q9Y5L5). May play a role in lens epithelial cell differentiation.

The ocular lens is a tissue of epithelial origin and devoid of blood vessels and nerves. Cells of the lens epithelium are responsible for the growth and maintenance of the lens through mitosis, protein synthesis, and active transport of ions and metabolites across the lens capsule. Lens epithelial protein is expressed exclusively in lens epithelial cells and may play a role in cell differentiation.

Source: NCBI Gene 55891 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001394530

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14429
Approved symbol	LENEP
Name	lens epithelial protein
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	LEP503
Ensembl gene	ENSG00000163352
Ensembl biotype	protein_coding
OMIM	607377
Entrez	55891

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000368427, ENST00000392487

RefSeq mRNA: 2 — MANE Select: NM_001394530 NM_001394530, NM_018655

CCDS: CCDS1080

Canonical transcript exons

ENST00000392487 — 1 exons

Exon	Start	End
ENSE00001512090	154993586	154994315

Expression profiles

Bgee: expression breadth broad, 99 present calls, max score 56.99.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0575 / max 44.4910, expressed in 16 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5549	0.0575	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	56.99	gold quality
mucosa of transverse colon	UBERON:0004991	51.59	gold quality
right lobe of thyroid gland	UBERON:0001119	50.68	gold quality
adrenal tissue	UBERON:0018303	48.98	gold quality
thyroid gland	UBERON:0002046	47.72	gold quality
left lobe of thyroid gland	UBERON:0001120	47.34	gold quality
stromal cell of endometrium	CL:0002255	47.04	gold quality
right uterine tube	UBERON:0001302	46.23	silver quality
uterine cervix	UBERON:0000002	44.53	gold quality
ectocervix	UBERON:0012249	43.92	gold quality
blood	UBERON:0000178	43.78	gold quality
left ovary	UBERON:0002119	43.58	gold quality
myometrium	UBERON:0001296	42.82	gold quality
skeletal muscle tissue	UBERON:0001134	42.78	gold quality
ovary	UBERON:0000992	42.70	gold quality
colonic epithelium	UBERON:0000397	42.66	gold quality
tonsil	UBERON:0002372	42.51	silver quality
gastrocnemius	UBERON:0001388	42.19	gold quality
saliva-secreting gland	UBERON:0001044	42.00	gold quality
right ovary	UBERON:0002118	41.83	gold quality
lower esophagus mucosa	UBERON:0035834	41.59	silver quality
urinary bladder	UBERON:0001255	41.49	silver quality
bone marrow cell	CL:0002092	41.46	gold quality
minor salivary gland	UBERON:0001830	41.25	gold quality
muscle of leg	UBERON:0001383	41.02	gold quality
prostate gland	UBERON:0002367	40.94	gold quality
endometrium	UBERON:0001295	40.35	gold quality
body of uterus	UBERON:0009853	40.31	gold quality
left adrenal gland	UBERON:0001234	40.05	gold quality
muscle tissue	UBERON:0002385	39.92	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.49

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

28 targeting LENEP, 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-3064-3P	100.00	70.09	1254
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-455-3P	98.94	67.68	878
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-1246	98.54	66.21	959
HSA-MIR-92A-1-5P	98.28	64.51	631
HSA-MIR-6769A-5P	97.99	64.16	851
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-924	97.78	66.21	681
HSA-MIR-4433A-3P	97.75	62.82	1435
HSA-MIR-2467-5P	97.36	67.71	991
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-6805-5P	95.79	64.86	670

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lenep	ENSDARG00000095553
mus_musculus	Lenep	ENSMUSG00000078173
rattus_norvegicus	Lenep	ENSRNOG00000049513

Protein

Protein identifiers

Lens epithelial cell protein LEP503 — Q9Y5L5 (reviewed: Q9Y5L5)

All UniProt accessions (1): Q9Y5L5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in lens epithelial cell differentiation.

Tissue specificity. Restricted to lens epithelial cells.

RefSeq proteins (2): NP_001381459, NP_061125 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029194	LEP503	Family

Pfam: PF15221

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5L5-F1	69.71	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): AP1_01, GGGTGGRR_PAX4_03, TGANTCA_AP1_C, CAAGGAT_MIR362, GOBP_SENSORY_ORGAN_DEVELOPMENT, GOBP_LENS_DEVELOPMENT_IN_CAMERA_TYPE_EYE, chr1q21, SENGUPTA_EBNA1_ANTICORRELATED, MZF1_01, HSF1_01, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GOBP_SENSORY_SYSTEM_DEVELOPMENT, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, KRAS.AMP.LUNG_UP.V1_UP, EBNA1BP2_TARGET_GENES

GO Biological Process (2): lens development in camera-type eye (GO:0002088), multicellular organism development (GO:0007275)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anatomical structure development	2
camera-type eye development	1
multicellular organismal process	1
nucleic acid binding	1
binding	1

Protein interactions and networks

STRING

278 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LENEP	FLAD1	Q8NFF5	524
LENEP	OR6K3	Q8NGY3	474
LENEP	SPATA45	Q537H7	474
LENEP	CRYBA4	P53673	421
LENEP	BFSP2	Q13515	410
LENEP	VSTM2B	A6NLU5	410
LENEP	FRMPD1	Q5SYB0	409
LENEP	BFSP1	Q12934	390
LENEP	GCNA	Q96QF7	389
LENEP	CRYGA	P11844	383
LENEP	DCST2	Q5T1A1	377
LENEP	PCP4L1	A6NKN8	373
LENEP	BLOC1S4	Q9NUP1	372
LENEP	GRIFIN	A4D1Z8	366
LENEP	ENTREP3	P81408	357

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TMEM72	LENEP	psi-mi:“MI:0915”(physical association)	0.560
LENEP	MACROH2A1	psi-mi:“MI:0914”(association)	0.350
TMEM72	LENEP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): TMEM72 (Two-hybrid), NMNAT1 (Affinity Capture-MS), HIST1H1C (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1A (Affinity Capture-MS), RBM28 (Affinity Capture-MS), SRSF12 (Affinity Capture-MS), H2AFY (Affinity Capture-MS), CENPV (Affinity Capture-MS), ZNF800 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RRN3, A0T0A3, A0T0U2, A4IHD1, A5GIB0, B2JA13, B7K6Q5, C9JBD0, E9Q9R3, O64242, O70337, O70903, P04601, P0C420, P0C421, P0C422, P10302, P19052, P30637, P35091, P49473, P86994, Q05268, Q06FN9, Q06J11, Q0IDJ7, Q0VDE8, Q16517, Q3AN56, Q3J8F4, Q3KPU7, Q3M4N8, Q4G3C2, Q61979, Q6B8K4, Q6ENE5, Q6JL78, Q7U9P9, Q86Y28, Q8C5Y2

Diamond homologs: Q9WVB6, Q9WVB7, Q9Y5L5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

165 predictions. Top by Δscore:

Variant	Effect	Δscore
1:154993804:G:T	donor_gain	0.9900
1:154993779:G:GT	donor_gain	0.9800
1:154993740:G:GT	donor_gain	0.9700
1:154993788:GAT:G	donor_gain	0.9200
1:154993803:G:GT	donor_gain	0.9200
1:154993928:A:AG	acceptor_gain	0.9200
1:154993929:G:GG	acceptor_gain	0.9200
1:154993780:A:T	donor_gain	0.9000
1:154993845:TCAGG:T	donor_loss	0.9000
1:154993847:AGG:A	donor_loss	0.9000
1:154993848:GG:G	donor_loss	0.9000
1:154993849:G:A	donor_loss	0.9000
1:154993850:T:G	donor_loss	0.9000
1:154993860:AG:A	donor_gain	0.8800
1:154993740:G:T	donor_gain	0.8700
1:154993927:TAGCC:T	acceptor_loss	0.8700
1:154993928:A:G	acceptor_loss	0.8700
1:154993701:A:G	donor_gain	0.8600
1:154993859:TA:T	donor_gain	0.8600
1:154993927:TAGC:T	acceptor_gain	0.8600
1:154993929:GC:G	acceptor_gain	0.8600
1:154993926:TTAGC:T	acceptor_gain	0.8500
1:154993928:A:T	acceptor_gain	0.8500
1:154993929:G:T	acceptor_gain	0.8500
1:154993929:GCCCC:G	acceptor_gain	0.8500
1:154993861:GA:G	donor_gain	0.8300
1:154993925:TTTAG:T	acceptor_gain	0.8300
1:154993929:GCCC:G	acceptor_gain	0.8200
1:154993929:GCC:G	acceptor_gain	0.8100
1:154993799:GCAG:G	donor_loss	0.8000

AlphaMissense

379 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:154993778:G:C	K57N	0.919
1:154993778:G:T	K57N	0.919
1:154993739:G:C	K44N	0.849
1:154993739:G:T	K44N	0.849
1:154993764:T:C	C53R	0.846
1:154993761:T:C	C52R	0.819
1:154993783:T:C	L59P	0.795
1:154993759:T:A	L51H	0.781
1:154993770:T:C	C55R	0.771
1:154993756:T:A	L50H	0.749
1:154993777:A:T	K57M	0.749
1:154993747:C:A	A47D	0.745
1:154993767:T:A	W54R	0.742
1:154993767:T:C	W54R	0.742
1:154993769:G:C	W54C	0.738
1:154993769:G:T	W54C	0.738
1:154993763:C:G	C52W	0.723
1:154993772:T:G	C55W	0.709
1:154993766:C:G	C53W	0.708
1:154993789:A:T	D61V	0.706
1:154993756:T:G	L50R	0.702
1:154993777:A:C	K57T	0.692
1:154993715:G:C	W36C	0.684
1:154993715:G:T	W36C	0.684
1:154993759:T:G	L51R	0.666
1:154993744:T:A	V46D	0.664
1:154993762:G:A	C52Y	0.655
1:154993774:T:A	I56N	0.655
1:154993765:G:A	C53Y	0.654
1:154993786:T:C	L60P	0.639

dbSNP variants (sampled 300 via entrez): RS1000265522 (1:154992210 C>T), RS1000516980 (1:154994055 T>G), RS1001586161 (1:154993096 C>A,G,T), RS1001918307 (1:154991788 G>C,T), RS1002582467 (1:154994783 A>G), RS1004695867 (1:154994500 G>A,C), RS1005153553 (1:154994142 G>A,T), RS1008447066 (1:154993917 T>C), RS1008780711 (1:154992378 G>A,T), RS1009166322 (1:154993436 T>A,C,G), RS1010279721 (1:154992449 A>G), RS1011249367 (1:154992167 G>A), RS1011705334 (1:154994029 G>A,C), RS1012863772 (1:154994822 T>C), RS1013296360 (1:154994454 G>A)

Disease associations

OMIM: gene MIM:607377 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001942_19	Prostate cancer	2.000000e-08
GCST007294_124	Body fat distribution (trunk fat ratio)	8.000000e-35
GCST007294_3	Body fat distribution (trunk fat ratio)	6.000000e-21
GCST007294_50	Body fat distribution (trunk fat ratio)	1.000000e-15
GCST007295_17	Body fat distribution (leg fat ratio)	3.000000e-13
GCST007295_37	Body fat distribution (leg fat ratio)	7.000000e-17
GCST007295_72	Body fat distribution (leg fat ratio)	1.000000e-28
GCST008103_81	Bipolar disorder	1.000000e-06
GCST90002403_20	Red blood cell count	6.000000e-21

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004341	body fat distribution
EFO:0004305	erythrocyte count

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
2-methyl-4-isothiazolin-3-one	increases expression	1
arsenite	increases methylation	1
CGP 52608	affects binding, increases reaction	1
Leflunomide	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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