LCE6A

Summary

LCE6A (late cornified envelope 6A, HGNC:31824) is a protein-coding gene on chromosome 1q21.3, encoding Late cornified envelope protein 6A (A0A183). Precursors of the cornified envelope of the stratum corneum.

Predicted to be involved in keratinization.

Source: NCBI Gene 448835 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_001128600

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31824
Approved symbol	LCE6A
Name	late cornified envelope 6A
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000235942
Ensembl biotype	protein_coding
Entrez	448835

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000431011

RefSeq mRNA: 1 — MANE Select: NM_001128600 NM_001128600

CCDS: CCDS44227

Canonical transcript exons

ENST00000431011 — 2 exons

Exon	Start	End
ENSE00001632567	152843500	152843983
ENSE00001788899	152842856	152843011

Expression profiles

Bgee: expression breadth broad, 71 present calls, max score 95.09.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2166 / max 237.4823, expressed in 14 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5321	0.2166	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	95.09	gold quality
cerebellar vermis	UBERON:0004720	94.28	gold quality
quadriceps femoris	UBERON:0001377	93.62	gold quality
zone of skin	UBERON:0000014	93.52	gold quality
skin of abdomen	UBERON:0001416	91.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.03	gold quality
thymus	UBERON:0002370	64.30	silver quality
apex of heart	UBERON:0002098	42.10	silver quality
mucosa of stomach	UBERON:0001199	41.49	silver quality
lower esophagus mucosa	UBERON:0035834	40.88	silver quality
bone marrow cell	CL:0002092	38.48	gold quality
skeletal muscle tissue	UBERON:0001134	37.59	gold quality
gastrocnemius	UBERON:0001388	37.59	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
muscle of leg	UBERON:0001383	36.42	gold quality
bone marrow	UBERON:0002371	36.23	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
heart left ventricle	UBERON:0002084	34.54	gold quality
muscle tissue	UBERON:0002385	34.18	gold quality
tibial artery	UBERON:0007610	33.44	gold quality
popliteal artery	UBERON:0002250	33.31	gold quality
multicellular organism	UBERON:0000468	32.75	gold quality
blood	UBERON:0000178	32.63	gold quality
right lung	UBERON:0002167	32.45	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
heart	UBERON:0000948	31.43	gold quality
subcutaneous adipose tissue	UBERON:0002190	31.28	gold quality
right atrium auricular region	UBERON:0006631	30.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting LCE6A, 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-6077	99.99	68.04	2299
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-455-3P	98.94	67.68	878
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-1226-5P	96.50	65.28	643
HSA-MIR-6782-5P	96.45	64.42	612
HSA-MIR-4264	96.35	64.76	1480
HSA-MIR-624-5P	96.00	68.88	728

Literature-anchored findings (GeneRIF, showing 1)

• Describes neighboring LCE family members that are present in the same cluster on chromosome 1q21. (PMID:15854049)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Late cornified envelope protein 6A — A0A183 (reviewed: A0A183)

All UniProt accessions (1): A0A183

UniProt curated annotations — full annotation on UniProt →

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

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

Similarity. Belongs to the LCE family.

RefSeq proteins (1): NP_001122072* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031716	LCE6A	Family

Pfam: PF15858

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A183-F1	63.86	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: 13 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, chr1q21, REACTOME_KERATINIZATION, REACTOME_FORMATION_OF_THE_CORNIFIED_ENVELOPE, GOBP_KERATINOCYTE_DIFFERENTIATION, GOBP_EPITHELIAL_CELL_DIFFERENTIATION, MIR455_3P, MIR6782_5P, GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGM_BCELL_DN

GO Biological Process (1): keratinization (GO:0031424)

GO Molecular Function (0):

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

Protein interactions and networks

STRING

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LCE6A	LCE2D	Q5TA82	727
LCE6A	LCE2C	Q5TA81	710
LCE6A	LCE1A	Q5T7P2	691
LCE6A	LCE2A	Q5TA79	675
LCE6A	LCE1F	Q5T754	653
LCE6A	LCE1D	Q5T752	620
LCE6A	LCE1E	Q5T753	604
LCE6A	LCE5A	Q5TCM9	601
LCE6A	LCE2B	O14633	598
LCE6A	LCE1C	Q5T751	597
LCE6A	LCE3C	Q5T5A8	584
LCE6A	LCE3E	Q5T5B0	571
LCE6A	LCE1B	Q5T7P3	521
LCE6A	SPRR4	Q96PI1	505
LCE6A	C3orf22	Q8N5N4	474

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A183, O12161, O41801, O70889, O89943, O91083, P04605, P04609, P04611, P04613, P04614, P05905, P05907, P05908, P05910, P05911, P0C1J9, P0C1K0, P0C1K1, P0C1K2, P0C1K3, P0C1K4, P11263, P12506, P12513, P17759, P18044, P18098, P18804, P19507, P19552, P19553, P20879, P20880, P20893, P24738, P35965, Q02838, Q1A246, Q1A264

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

114 predictions. Top by Δscore:

Variant	Effect	Δscore
1:152842907:GG:G	donor_gain	0.9100
1:152842908:GG:G	donor_gain	0.9100
1:152842996:G:GT	donor_gain	0.8700
1:152843007:GCCAG:G	donor_gain	0.8400
1:152843494:TTCCA:T	acceptor_loss	0.8200
1:152843495:TCCAG:T	acceptor_loss	0.8200
1:152843496:CCA:C	acceptor_loss	0.8200
1:152843497:CAGA:C	acceptor_loss	0.8200
1:152843498:A:AG	acceptor_gain	0.8200
1:152843498:A:T	acceptor_loss	0.8200
1:152843499:G:A	acceptor_loss	0.8200
1:152843499:G:GG	acceptor_gain	0.8200
1:152843008:CCAG:C	donor_loss	0.8000
1:152843009:CAG:C	donor_loss	0.8000
1:152843011:GGTA:G	donor_loss	0.8000
1:152843012:G:C	donor_loss	0.8000
1:152843013:T:G	donor_loss	0.8000
1:152842905:TAGG:T	donor_loss	0.7800
1:152842906:AGGGT:A	donor_loss	0.7800
1:152842907:GGGTA:G	donor_loss	0.7800
1:152842908:GGTA:G	donor_loss	0.7800
1:152842909:GTAA:G	donor_loss	0.7800
1:152842910:T:A	donor_loss	0.7800
1:152843499:GATTC:G	acceptor_gain	0.7800
1:152842911:AAG:A	donor_loss	0.7400
1:152842909:G:GG	donor_gain	0.7300
1:152843040:G:T	donor_gain	0.7000
1:152843487:ATTTT:A	acceptor_loss	0.6800
1:152843488:TTTTT:T	acceptor_loss	0.6800
1:152842912:AGGCT:A	donor_loss	0.6600

AlphaMissense

512 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:152843739:A:C	K73N	0.615
1:152843739:A:T	K73N	0.615
1:152843707:T:A	C63S	0.580
1:152843708:G:C	C63S	0.580

dbSNP variants (sampled 300 via entrez): RS1000002818 (1:152844240 A>T), RS1000815254 (1:152841660 C>T), RS1001167274 (1:152840911 G>A), RS1002229306 (1:152842229 A>G), RS1002433596 (1:152842503 A>T), RS1002992572 (1:152842133 G>A,T), RS1003235851 (1:152840865 G>A), RS1003896154 (1:152844038 C>T), RS1004504772 (1:152842394 A>G), RS1006862807 (1:152844185 G>A,T), RS1006916931 (1:152844478 T>A,C), RS1007239448 (1:152841580 C>A), RS1008024109 (1:152841375 G>A), RS1008596163 (1:152840977 G>A,T), RS1009831808 (1:152842196 T>C,G)

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

3 associations (top):

Study	Trait	p-value
GCST007564_25	Asthma or allergic disease (pleiotropy)	5.000000e-09
GCST008916_87	Asthma	2.000000e-13
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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenate	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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