LCE3E (late cornified envelope 3E) - Rat Genome Database

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Gene: LCE3E (late cornified envelope 3E) Homo sapiens
Analyze
Symbol: LCE3E
Name: late cornified envelope 3E
RGD ID: 1346899
HGNC Page HGNC:29463
Description: Predicted to be involved in keratinization.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: late cornified envelope protein 3E; late envelope protein 17; LEP17
RGD Orthologs
Mouse
Pig
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,565,654 - 152,566,780 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,565,654 - 152,566,780 (-)EnsemblGRCh38hg38GRCh38
GRCh371152,538,130 - 152,539,256 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361150,804,754 - 150,805,872 (-)NCBINCBI36Build 36hg18NCBI36
Build 341149,351,202 - 149,352,321NCBI
Celera1125,648,938 - 125,650,056 (-)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1123,911,661 - 123,912,715 (-)NCBIHuRef
CHM1_11153,933,522 - 153,934,576 (-)NCBICHM1_1
T2T-CHM13v2.01151,702,207 - 151,703,333 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11698679   PMID:12477932   PMID:15854049   PMID:16710414   PMID:19721433   PMID:20585627   PMID:21873635   PMID:25416956   PMID:31515488   PMID:32296183   PMID:36949045  


Genomics

Comparative Map Data
LCE3E
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,565,654 - 152,566,780 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,565,654 - 152,566,780 (-)EnsemblGRCh38hg38GRCh38
GRCh371152,538,130 - 152,539,256 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361150,804,754 - 150,805,872 (-)NCBINCBI36Build 36hg18NCBI36
Build 341149,351,202 - 149,352,321NCBI
Celera1125,648,938 - 125,650,056 (-)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1123,911,661 - 123,912,715 (-)NCBIHuRef
CHM1_11153,933,522 - 153,934,576 (-)NCBICHM1_1
T2T-CHM13v2.01151,702,207 - 151,703,333 (-)NCBIT2T-CHM13v2.0
Lce3e
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,874,368 - 92,875,588 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,874,368 - 92,875,588 (+)EnsemblGRCm39 Ensembl
GRCm38392,967,061 - 92,968,281 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl392,967,061 - 92,968,281 (+)EnsemblGRCm38mm10GRCm38
MGSCv37392,770,983 - 92,772,199 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36392,770,705 - 92,772,203 (+)NCBIMGSCv36mm8
Celera394,109,601 - 94,110,829 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
LOC106510159
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1496,828,768 - 96,829,266 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24105,824,529 - 105,837,360 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in LCE3E
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q21.3(chr1:152566461-152613805)x1 copy number loss See cases [RCV000136484] Chr1:152566461..152613805 [GRCh38]
Chr1:152538937..152586281 [GRCh37]
Chr1:150805561..150852905 [NCBI36]
Chr1:1q21.3		 benign
GRCh38/hg38 1q21.3(chr1:152365299-152618044)x3 copy number gain See cases [RCV000138737] Chr1:152365299..152618044 [GRCh38]
Chr1:152337775..152590520 [GRCh37]
Chr1:150604399..150857144 [NCBI36]
Chr1:1q21.3		 likely benign
GRCh38/hg38 1q21.3(chr1:152526704-152729716)x1 copy number loss See cases [RCV000141197] Chr1:152526704..152729716 [GRCh38]
Chr1:152499180..152702192 [GRCh37]
Chr1:150765804..150968816 [NCBI36]
Chr1:1q21.3		 benign
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q21.1-21.3(chr1:144927578-153223600)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV000223957] Chr1:144927578..153223600 [GRCh37]
Chr1:1q21.1-21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NM_178435.4(LCE3E):c.209C>T (p.Ser70Phe) single nucleotide variant not specified [RCV004296862] Chr1:152566000 [GRCh38]
Chr1:152538476 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q21.3(chr1:150853044-154647786)x3 copy number gain not provided [RCV000684655] Chr1:150853044..154647786 [GRCh37]
Chr1:1q21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q21.3(chr1:152507156-152586936)x0 copy number loss not provided [RCV000736693] Chr1:152507156..152586936 [GRCh37]
Chr1:1q21.3		 benign
GRCh37/hg19 1q21.3(chr1:152519570-152656640)x0 copy number loss not provided [RCV000736694] Chr1:152519570..152656640 [GRCh37]
Chr1:1q21.3		 benign
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
GRCh37/hg19 1q21.3(chr1:152520371-152749733)x1 copy number loss not provided [RCV001827979] Chr1:152520371..152749733 [GRCh37]
Chr1:1q21.3		 uncertain significance
NC_000001.10:g.(?_149895434)_(156851434_?)dup duplication Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency [RCV001958273]|Congenital neutropenia-myelofibrosis-nephromegaly syndrome [RCV001958271]|Kostmann syndrome [RCV003120769]|MHC class II deficiency [RCV001992607] Chr1:149895434..156851434 [GRCh37]
Chr1:1q21.2-23.1		 uncertain significance
NM_178435.4(LCE3E):c.128G>T (p.Gly43Val) single nucleotide variant not specified [RCV004289666] Chr1:152566081 [GRCh38]
Chr1:152538557 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178435.4(LCE3E):c.269G>A (p.Gly90Asp) single nucleotide variant not specified [RCV004219437] Chr1:152565940 [GRCh38]
Chr1:152538416 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178435.4(LCE3E):c.85T>C (p.Cys29Arg) single nucleotide variant not specified [RCV004111135] Chr1:152566124 [GRCh38]
Chr1:152538600 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178435.4(LCE3E):c.193C>T (p.Arg65Cys) single nucleotide variant not specified [RCV004159270] Chr1:152566016 [GRCh38]
Chr1:152538492 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178435.4(LCE3E):c.33A>T (p.Gln11His) single nucleotide variant not specified [RCV004245459] Chr1:152566176 [GRCh38]
Chr1:152538652 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178435.4(LCE3E):c.184C>G (p.Arg62Gly) single nucleotide variant not specified [RCV004281257] Chr1:152566025 [GRCh38]
Chr1:152538501 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q12-23.1(chr1:142535935-157648813)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV003329522] Chr1:142535935..157648813 [GRCh37]
Chr1:1q12-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 copy number gain not specified [RCV003986717] Chr1:144368497..158992086 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:146577511-157155587)x3 copy number gain not specified [RCV003987261] Chr1:146577511..157155587 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
NM_178435.4(LCE3E):c.15G>C (p.Gln5His) single nucleotide variant not specified [RCV004412449] Chr1:152566194 [GRCh38]
Chr1:152538670 [GRCh37]
Chr1:1q21.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:209
Count of miRNA genes:197
Interacting mature miRNAs:203
Transcripts:ENST00000368789
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High 1
Medium 4 14 1 603 2 2 61 6 16 428
Low 24 3 6 30 6 6 684 20 3 5 58 24 29 5 267
Below cutoff 249 246 107 60 140 30 248 234 219 19 162 113 32 85 174 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000368789   ⟹   ENSP00000357778
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1152,565,654 - 152,566,780 (-)Ensembl
RefSeq Acc Id: NM_178435   ⟹   NP_848522
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,565,654 - 152,566,780 (-)NCBI
GRCh371152,538,175 - 152,539,229 (-)NCBI
Build 361150,804,754 - 150,805,872 (-)NCBI Archive
Celera1125,648,938 - 125,650,056 (-)RGD
HuRef1123,911,661 - 123,912,715 (-)NCBI
CHM1_11153,933,522 - 153,934,576 (-)NCBI
T2T-CHM13v2.01151,702,207 - 151,703,333 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_848522 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI31717 (Get FASTA)   NCBI Sequence Viewer  
  EAW53378 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000357778
  ENSP00000357778.1
GenBank Protein Q5T5B0 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_848522   ⟸   NM_178435
- UniProtKB: A2RRM6 (UniProtKB/Swiss-Prot),   Q5T5B0 (UniProtKB/Swiss-Prot),   Q0VAS7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000357778   ⟸   ENST00000368789

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5T5B0-F1-model_v2 AlphaFold Q5T5B0 1-92 view protein structure

Promoters
RGD ID:6857130
Promoter ID:EPDNEW_H1730
Type:multiple initiation site
Name:LCE3E_1
Description:late cornified envelope 3E
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,566,780 - 152,566,840EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:29463 AgrOrtholog
COSMIC LCE3E COSMIC
Ensembl Genes ENSG00000185966 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000368789 ENTREZGENE
  ENST00000368789.2 UniProtKB/Swiss-Prot
GTEx ENSG00000185966 GTEx
HGNC ID HGNC:29463 ENTREZGENE
Human Proteome Map LCE3E Human Proteome Map
InterPro LCE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:353145 UniProtKB/Swiss-Prot
NCBI Gene 353145 ENTREZGENE
OMIM 612617 OMIM
Pfam LCE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134941153 PharmGKB
UniProt A2RRM6 ENTREZGENE
  LCE3E_HUMAN UniProtKB/Swiss-Prot
  Q0VAS7 ENTREZGENE, UniProtKB/TrEMBL
  Q5T5B0 ENTREZGENE
UniProt Secondary A2RRM6 UniProtKB/Swiss-Prot