LCE1B

Summary

LCE1B (late cornified envelope 1B, HGNC:16611) is a protein-coding gene on chromosome 1q21.3, encoding Late cornified envelope protein 1B (Q5T7P3). Precursors of the cornified envelope of the stratum corneum.

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

Source: NCBI Gene 353132 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_178349

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16611
Approved symbol	LCE1B
Name	late cornified envelope 1B
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	LEP2
Ensembl gene	ENSG00000196734
Ensembl biotype	protein_coding
OMIM	612604
Entrez	353132

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000360090

RefSeq mRNA: 1 — MANE Select: NM_178349 NM_178349

CCDS: CCDS1027

Canonical transcript exons

ENST00000360090 — 1 exons

Exon	Start	End
ENSE00001421676	152811971	152813108

Expression profiles

Bgee: expression breadth broad, 93 present calls, max score 99.10.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	99.10	gold quality
skin of hip	UBERON:0001554	97.01	gold quality
skin of leg	UBERON:0001511	95.45	gold quality
zone of skin	UBERON:0000014	94.25	gold quality
nipple	UBERON:0002030	93.23	gold quality
skin of abdomen	UBERON:0001416	91.39	gold quality
penis	UBERON:0000989	89.72	gold quality
mammalian vulva	UBERON:0000997	88.65	gold quality
tendon of biceps brachii	UBERON:0008188	56.09	silver quality
oviduct epithelium	UBERON:0004804	53.77	gold quality
trabecular bone tissue	UBERON:0002483	53.42	gold quality
buccal mucosa cell	CL:0002336	52.74	gold quality
urethra	UBERON:0000057	52.46	gold quality
layer of synovial tissue	UBERON:0007616	52.21	gold quality
substantia nigra pars reticulata	UBERON:0001966	52.16	gold quality
saphenous vein	UBERON:0007318	52.12	gold quality
pericardium	UBERON:0002407	52.04	gold quality
dorsal root ganglion	UBERON:0000044	51.87	gold quality
synovial joint	UBERON:0002217	51.84	gold quality
trigeminal ganglion	UBERON:0001675	51.81	gold quality
thymus	UBERON:0002370	51.79	gold quality
inferior vagus X ganglion	UBERON:0005363	51.70	gold quality
pylorus	UBERON:0001166	51.63	gold quality
renal medulla	UBERON:0000362	51.62	gold quality
myocardium	UBERON:0002349	51.51	gold quality
medulla oblongata	UBERON:0001896	51.47	gold quality
gingival epithelium	UBERON:0001949	51.43	silver quality
superior vestibular nucleus	UBERON:0007227	51.39	gold quality
cardia of stomach	UBERON:0001162	51.34	gold quality
pons	UBERON:0000988	51.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting LCE1B, 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-6870-5P	99.99	68.55	2115
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-484	98.16	66.92	1074
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-3187-3P	97.38	65.80	904
HSA-MIR-645	97.28	66.30	486
HSA-MIR-31-3P	95.17	69.82	575

Literature-anchored findings (GeneRIF, showing 2)

• paper describing nomenclature changes and expression in range of tissues and in response to UV (PMID:15854049)
• genetic polymorphism is associated with psoriasis vulgaris among Mongolians from Inner Mongolia (PMID:29397434)

Cross-species orthologs

0 orthologs

Paralogs (1): LCE1C (ENSG00000197084)

Protein

Protein identifiers

Late cornified envelope protein 1B — Q5T7P3 (reviewed: Q5T7P3)

Alternative names: Late envelope protein 2, Small proline-rich-like epidermal differentiation complex protein 2A

All UniProt accessions (1): Q5T7P3

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Interacts with CYSRT1; the interaction is direct.

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_848126* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028205	LCE	Family

Pfam: PF14672

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T7P3-F1	52.32	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: 35 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, MODULE_205, MARTINEZ_RB1_TARGETS_DN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, MARTINEZ_RB1_AND_TP53_TARGETS_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, chr1q21, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP

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

308 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCE1B	LCE1A	Q5T7P2	913
LCE1B	LCE1C	Q5T751	862
LCE1B	LCE1E	Q5T753	850
LCE1B	LCE1D	Q5T752	788
LCE1B	LCE2B	O14633	752
LCE1B	LCE2C	Q5TA81	747
LCE1B	LCE2A	Q5TA79	725
LCE1B	SPRR2D	P22532	658
LCE1B	LCE2D	Q5TA82	620
LCE1B	LCE1F	Q5T754	607
LCE1B	LCE3A	Q5TA76	601
LCE1B	LCE3E	Q5T5B0	578
LCE1B	LCE3D	Q9BYE3	544
LCE1B	SPRR2G	Q9BYE4	528
LCE1B	LCE6A	A0A183	521

IntAct

359 interactions, top by confidence:

A	B	Type	Score
KRTAP5-9	LCE1B	psi-mi:“MI:0915”(physical association)	0.830
HOXA1	LCE1B	psi-mi:“MI:0915”(physical association)	0.830
KRTAP3-2	LCE1B	psi-mi:“MI:0915”(physical association)	0.830
LCE1B	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.830
LCE1B	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.830
LCE1B	HOXA1	psi-mi:“MI:0915”(physical association)	0.830
LCE1B	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.790
KRTAP9-2	LCE1B	psi-mi:“MI:0915”(physical association)	0.790
LCE1B	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.780
KRTAP10-7	LCE1B	psi-mi:“MI:0915”(physical association)	0.780
LCE1B	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.780
KRTAP10-9	LCE1B	psi-mi:“MI:0915”(physical association)	0.780
KRTAP4-12	LCE1B	psi-mi:“MI:0915”(physical association)	0.780
LCE1B	KRTAP4-2	psi-mi:“MI:0915”(physical association)	0.780
KRTAP10-5	LCE1B	psi-mi:“MI:0915”(physical association)	0.780
KRTAP10-8	LCE1B	psi-mi:“MI:0915”(physical association)	0.780
LCE1B	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.780

BioGRID (108): LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (Two-hybrid), LCE1B (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 71 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	47	43.6×	8e-71
Formation of the cornified envelope	15	22.0×	2e-15

GO biological processes:

GO term	Partners	Fold	FDR
hair cycle	5	108.9×	5e-08
keratinization	14	76.2×	2e-21

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

84 predictions. Top by Δscore:

Variant	Effect	Δscore
1:152812424:A:AG	acceptor_gain	0.9500
1:152812425:G:GG	acceptor_gain	0.9500
1:152812422:TCAGC:T	acceptor_loss	0.9100
1:152812425:G:GT	acceptor_loss	0.9100
1:152812425:GCTC:G	acceptor_gain	0.7800
1:152812425:GCT:G	acceptor_gain	0.7600
1:152812425:GC:G	acceptor_gain	0.6800
1:152811995:ACAAG:A	donor_loss	0.6600
1:152811996:CAAG:C	donor_loss	0.6600
1:152811997:AAG:A	donor_loss	0.6600
1:152811998:AG:A	donor_loss	0.6600
1:152811999:GG:G	donor_loss	0.6600
1:152812000:G:GG	donor_loss	0.6600
1:152812001:T:G	donor_loss	0.6600
1:152812002:A:C	donor_loss	0.6200
1:152812401:AACTT:A	acceptor_loss	0.6100
1:152812425:GCTCC:G	acceptor_gain	0.6100
1:152812397:GTCTA:G	acceptor_loss	0.5800
1:152812398:TCTAA:T	acceptor_loss	0.5800
1:152812399:CTAA:C	acceptor_loss	0.5800
1:152812400:TAACT:T	acceptor_loss	0.5800
1:152812415:C:G	acceptor_loss	0.5800
1:152812098:T:A	donor_gain	0.5300
1:152812402:A:G	acceptor_loss	0.5200
1:152812414:ACTCT:A	acceptor_loss	0.5200
1:152812416:TCTCT:T	acceptor_loss	0.5200
1:152812417:CTCTC:C	acceptor_loss	0.5200
1:152812418:TCTCT:T	acceptor_loss	0.5200
1:152812419:CTCTC:C	acceptor_loss	0.5200
1:152812097:GTGT:G	donor_gain	0.5100

AlphaMissense

770 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:152812678:A:C	S78R	0.775
1:152812680:C:A	S78R	0.775
1:152812680:C:G	S78R	0.775
1:152812798:T:C	C118R	0.725
1:152812669:T:C	C75R	0.697
1:152812800:C:G	C118W	0.688
1:152812651:A:C	S69R	0.675
1:152812653:T:A	S69R	0.675
1:152812653:T:G	S69R	0.675
1:152812458:G:C	Q4H	0.641
1:152812458:G:T	Q4H	0.641
1:152812461:G:C	Q5H	0.639
1:152812461:G:T	Q5H	0.639
1:152812474:T:C	C10R	0.630
1:152812467:G:C	Q7H	0.622
1:152812467:G:T	Q7H	0.622
1:152812503:G:C	K19N	0.618
1:152812503:G:T	K19N	0.618
1:152812679:G:T	S78I	0.603
1:152812453:T:C	C3R	0.602
1:152812476:C:G	C10W	0.598
1:152812464:C:A	N6K	0.592
1:152812464:C:G	N6K	0.592
1:152812491:G:C	K15N	0.588
1:152812491:G:T	K15N	0.588
1:152812684:C:G	H80D	0.586
1:152812671:C:G	C75W	0.567

dbSNP variants (sampled 300 via entrez): RS1000113991 (1:152811483 C>T), RS1000168424 (1:152810096 A>G), RS1000526558 (1:152811743 T>G), RS1001681940 (1:152811198 C>T), RS1002297833 (1:152812251 G>T), RS1003218045 (1:152811476 G>A,T), RS1005723637 (1:152812069 C>G,T), RS1005775932 (1:152811741 A>G), RS1005868988 (1:152810993 T>C), RS1005980594 (1:152810672 T>A), RS1006055602 (1:152813425 A>G), RS1006109681 (1:152813113 T>G), RS1006782663 (1:152810458 C>T), RS1006917207 (1:152810301 T>G), RS1006990809 (1:152809997 T>C)

Disease associations

OMIM: gene MIM:612604 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007564_25	Asthma or allergic disease (pleiotropy)	5.000000e-09
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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	increases expression, decreases expression, increases abundance	2
sodium arsenate	decreases expression, increases abundance	1
arsenite	decreases methylation	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Citrulline	increases expression	1
Demecolcine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Mustard Gas	increases expression	1
Nicotine	increases expression	1
Tretinoin	decreases expression	1
Vincristine	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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