LCE1E

Summary

LCE1E (late cornified envelope 1E, HGNC:29466) is a protein-coding gene on chromosome 1q21.3, encoding Late cornified envelope protein 1E (Q5T753). Precursors of the cornified envelope of the stratum corneum.

Enables identical protein binding activity. Predicted to be involved in keratinization.

Source: NCBI Gene 353135 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_178353

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29466
Approved symbol	LCE1E
Name	late cornified envelope 1E
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	LEP5
Ensembl gene	ENSG00000186226
Ensembl biotype	protein_coding
OMIM	612607
Entrez	353135

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000368770, ENST00000368771, ENST00000619588

RefSeq mRNA: 1 — MANE Select: NM_178353 NM_178353

CCDS: CCDS1024

Canonical transcript exons

ENST00000368770 — 2 exons

Exon	Start	End
ENSE00001447931	152787278	152788426
ENSE00001688415	152786257	152786307

Expression profiles

Bgee: expression breadth broad, 68 present calls, max score 87.92.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2328 / max 101.7781, expressed in 41 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5317	0.2328	41

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	87.92	gold quality
zone of skin	UBERON:0000014	82.51	gold quality
skin of abdomen	UBERON:0001416	79.07	gold quality
upper leg skin	UBERON:0004262	68.26	gold quality
skin of hip	UBERON:0001554	67.28	gold quality
buccal mucosa cell	CL:0002336	60.40	gold quality
lower lobe of lung	UBERON:0008949	59.77	silver quality
oviduct epithelium	UBERON:0004804	58.73	silver quality
epithelium of nasopharynx	UBERON:0001951	55.68	gold quality
penis	UBERON:0000989	54.13	silver quality
oocyte	CL:0000023	53.83	gold quality
dorsal root ganglion	UBERON:0000044	53.05	gold quality
cardia of stomach	UBERON:0001162	52.95	gold quality
ventral tegmental area	UBERON:0002691	52.91	gold quality
inferior vagus X ganglion	UBERON:0005363	52.85	gold quality
nipple	UBERON:0002030	52.83	gold quality
trachea	UBERON:0003126	52.69	gold quality
saphenous vein	UBERON:0007318	52.65	gold quality
superior surface of tongue	UBERON:0007371	51.94	gold quality
thymus	UBERON:0002370	51.76	gold quality
trigeminal ganglion	UBERON:0001675	51.65	gold quality
urethra	UBERON:0000057	51.47	gold quality
pericardium	UBERON:0002407	51.34	gold quality
layer of synovial tissue	UBERON:0007616	51.31	gold quality
medulla oblongata	UBERON:0001896	51.24	gold quality
synovial joint	UBERON:0002217	51.17	gold quality
pharyngeal mucosa	UBERON:0000355	51.00	gold quality
superior vestibular nucleus	UBERON:0007227	50.96	gold quality
tongue	UBERON:0001723	50.93	gold quality
pylorus	UBERON:0001166	50.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting LCE1E, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-190B-3P	99.33	68.29	1382
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-4270	99.02	66.26	1987

Literature-anchored findings (GeneRIF, showing 1)

• paper describing nomenclature changes and expression in range of tissues and in response to UV (PMID:15854049)

Cross-species orthologs

0 orthologs

Paralogs (20): LCE2B (ENSG00000159455), SPRR2G (ENSG00000159516), LCE3D (ENSG00000163202), SPRR3 (ENSG00000163209), SPRR1B (ENSG00000169469), SPRR1A (ENSG00000169474), LCE1D (ENSG00000172155), SPRR4 (ENSG00000184148), LCE3A (ENSG00000185962), LCE3E (ENSG00000185966), LCE5A (ENSG00000186207), LCE2A (ENSG00000187173), LCE2C (ENSG00000187180), LCE2D (ENSG00000187223), LCE3B (ENSG00000187238), KPLCE (ENSG00000198854), PRR9 (ENSG00000203783), LELP1 (ENSG00000203784), LCE1F (ENSG00000240386), LCE3C (ENSG00000244057)

Protein

Protein identifiers

Late cornified envelope protein 1E — Q5T753 (reviewed: Q5T753)

Alternative names: Late envelope protein 5

All UniProt accessions (2): A0A087WWQ4, Q5T753

UniProt curated annotations — full annotation on UniProt →

Function. Precursors of the cornified envelope of the stratum corneum.

Subunit / interactions. Interacts with CYSRT1.

Tissue specificity. Skin-specific. Expression was readily detected in adult trunk skin, adult arm skin, fetal skin, penal skin, vulva, esophagus and tongue. Not expressed in the cervix, rectum, lung, colon, or placenta.

Induction. By UVB.

Miscellaneous. Belongs to the LCE cluster present on 1q21.

Similarity. Belongs to the LCE family.

RefSeq proteins (1): NP_848130* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028205	LCE	Family

Pfam: PF14672

UniProt features (9 total): compositionally biased region 4, region of interest 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T753-F1	53.42	0.00

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6809371	Formation of the cornified envelope
R-HSA-1266738	Developmental Biology
R-HSA-6805567	Keratinization

MSigDB gene sets: 23 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, chr1q21, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, REACTOME_KERATINIZATION, REACTOME_FORMATION_OF_THE_CORNIFIED_ENVELOPE, GOBP_KERATINOCYTE_DIFFERENTIATION, GOBP_EPITHELIAL_CELL_DIFFERENTIATION, MIR6867_5P, MIR493_5P, MIR4692, MIR4428

GO Biological Process (2): keratinization (GO:0031424), epidermis development (GO:0008544)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (0):

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Keratinization	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
keratinocyte differentiation	1
multicellular organismal process	1
tissue development	1
protein binding	1
binding	1

Protein interactions and networks

STRING

248 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCE1E	LCE1D	Q5T752	986
LCE1E	LCE1B	Q5T7P3	850
LCE1E	LCE1C	Q5T751	817
LCE1E	LCE2D	Q5TA82	725
LCE1E	LCE2C	Q5TA81	719
LCE1E	LCE1F	Q5T754	690
LCE1E	LCE1A	Q5T7P2	666
LCE1E	SPRR2D	P22532	645
LCE1E	LCE3D	Q9BYE3	642
LCE1E	LCE3E	Q5T5B0	627
LCE1E	LCE6A	A0A183	604
LCE1E	LCE2A	Q5TA79	582
LCE1E	LCE2B	O14633	571
LCE1E	SPRR1A	P35321	496
LCE1E	SPRR2A	P35326	492

IntAct

192 interactions, top by confidence:

A	B	Type	Score
LCE1E	KRTAP4-12	psi-mi:“MI:0915”(physical association)	0.600
LCE1E	KRTAP5-11	psi-mi:“MI:0915”(physical association)	0.600
KRTAP5-11	LCE1E	psi-mi:“MI:0915”(physical association)	0.600
KRTAP6-3	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP5-2	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	LCE1A	psi-mi:“MI:0915”(physical association)	0.560
TGM1	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP2-4	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLC	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-3	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP4-4	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	RGS17	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP4-11	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	LCE1F	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-11	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	LCE2C	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-1	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP5-6	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	MACO1	psi-mi:“MI:0915”(physical association)	0.560
ALPP	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
KRTAP1-3	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE2B	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	LCE4A	psi-mi:“MI:0915”(physical association)	0.560
EFEMP2	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	LCE1E	psi-mi:“MI:0915”(physical association)	0.560
LCE1E	KRTAP4-2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (68): LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid), LCE1E (Two-hybrid)

ESM2 similar proteins: A0A286YEV6, A0A286YEY9, A0A286YF60, A0A286YF77, A0A286YFG1, A2A591, A2A5X5, A8MUX0, A8MX34, O14633, O70562, P02438, P02439, P02440, P08131, P0C5Y4, P0DSO2, P0DV60, P22532, P35325, P35326, P60329, Q07627, Q3V2C1, Q4KL71, Q5T5A8, Q5T5B0, Q5T750, Q5T751, Q5T752, Q5T753, Q5T754, Q5T7P2, Q5T7P3, Q5TA76, Q5TA77, Q5TA78, Q5TA79, Q5TA81, Q5TA82

Diamond homologs: Q5T751, Q5T752, Q5T753, Q5T754, Q5T7P2, Q5T7P3, Q5T5A8, Q5TA79, O14633, Q5TA81, Q5TA82

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 56 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	37	42.9×	6e-55
Formation of the cornified envelope	10	18.3×	1e-09

GO biological processes:

GO term	Partners	Fold	FDR
hair cycle	5	141.8×	1e-08
keratinization	10	70.9×	1e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

200 predictions. Top by Δscore:

Variant	Effect	Δscore
1:152787067:A:AG	donor_gain	0.9200
1:152786276:TGCCG:T	donor_gain	0.9100
1:152786308:G:GG	donor_gain	0.8000
1:152786304:TTTG:T	donor_loss	0.7900
1:152786305:TTGG:T	donor_loss	0.7900
1:152786306:TGGT:T	donor_loss	0.7900
1:152786307:GGTAT:G	donor_loss	0.7900
1:152786308:G:A	donor_loss	0.7900
1:152786309:T:C	donor_loss	0.7900
1:152786310:ATGT:A	donor_loss	0.7900
1:152786277:GCCGA:G	donor_gain	0.7800
1:152786311:TGTG:T	donor_loss	0.7700
1:152786312:G:C	donor_loss	0.7200
1:152787276:A:AG	acceptor_gain	0.7200
1:152787277:G:GG	acceptor_gain	0.7200
1:152787099:A:T	acceptor_gain	0.7100
1:152787417:G:T	acceptor_gain	0.6700
1:152787414:CCAG:C	acceptor_gain	0.6600
1:152787406:AGTGC:A	acceptor_gain	0.6500
1:152787415:CAG:C	acceptor_gain	0.6500
1:152787416:A:T	acceptor_gain	0.6500
1:152787432:A:AG	acceptor_gain	0.6400
1:152787433:G:GG	acceptor_gain	0.6400
1:152787272:CCTCA:C	acceptor_loss	0.6300
1:152787273:CTCA:C	acceptor_loss	0.6300
1:152787274:TCA:T	acceptor_loss	0.6300
1:152787275:CA:C	acceptor_loss	0.6300
1:152787276:A:G	acceptor_loss	0.6300
1:152787277:G:GC	acceptor_loss	0.6300
1:152787413:TCCAG:T	acceptor_gain	0.6300

AlphaMissense

775 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:152787315:A:C	S6R	0.848
1:152787317:C:A	S6R	0.848
1:152787317:C:G	S6R	0.848
1:152787327:T:C	C10R	0.825
1:152787329:C:G	C10W	0.787
1:152787306:T:C	C3R	0.785
1:152787311:G:C	Q4H	0.780
1:152787311:G:T	Q4H	0.780
1:152787356:G:C	K19N	0.741
1:152787356:G:T	K19N	0.741
1:152787531:A:C	S78R	0.738
1:152787533:C:A	S78R	0.738
1:152787533:C:G	S78R	0.738
1:152787344:G:C	K15N	0.737
1:152787344:G:T	K15N	0.737
1:152787320:G:C	Q7H	0.719
1:152787320:G:T	Q7H	0.719
1:152787522:T:C	C75R	0.717
1:152787651:T:C	C118R	0.707
1:152787314:G:C	Q5H	0.704
1:152787314:G:T	Q5H	0.704
1:152787368:G:C	K23N	0.704
1:152787368:G:T	K23N	0.704
1:152787653:C:G	C118W	0.694
1:152787504:A:C	S69R	0.693
1:152787506:C:A	S69R	0.693
1:152787506:C:G	S69R	0.693
1:152787345:T:C	C16R	0.687
1:152787327:T:A	C10S	0.682
1:152787328:G:C	C10S	0.682

dbSNP variants (sampled 300 via entrez): RS1001643107 (1:152788149 C>T), RS1001699164 (1:152787841 C>T), RS1002497013 (1:152784270 C>T), RS1003621816 (1:152785266 G>A), RS1003768129 (1:152785599 T>C), RS1004012797 (1:152786555 A>G), RS1004278263 (1:152784310 A>T), RS1004404777 (1:152784349 T>C,G), RS1004673480 (1:152784625 A>G,T), RS1004692338 (1:152785750 C>T), RS1007498591 (1:152785894 C>T), RS1008062570 (1:152787433 G>A,C), RS1008473356 (1:152785047 C>T), RS1011076333 (1:152785224 G>A,C), RS1011410283 (1:152786725 C>T)

Disease associations

OMIM: gene MIM:612607 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002740_1	Inflammatory skin disease	2.000000e-17
GCST008916_82	Asthma	5.000000e-27
GCST008916_92	Asthma	6.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Arsenic	affects cotreatment, decreases expression, increases abundance	2
Nickel	decreases expression	2
Cadmium Chloride	increases expression, decreases expression, increases abundance	2
sodium arsenate	decreases expression, increases abundance	1
butyraldehyde	increases expression	1
tobacco tar	decreases reaction, increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
diallyl disulfide	decreases reaction, increases expression	1
nutlin 3	affects cotreatment, increases expression	1
pyrachlostrobin	decreases expression	1
jinfukang	affects cotreatment, increases expression, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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