LCE1F (late cornified envelope 1F) - Rat Genome Database

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Gene: LCE1F (late cornified envelope 1F) Homo sapiens
Analyze
Symbol: LCE1F
Name: late cornified envelope 1F
RGD ID: 1346167
HGNC Page HGNC:29467
Description: Enables identical protein binding activity. Predicted to be involved in keratinization.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: late cornified envelope protein 1F; late envelope protein 6; LEP6
RGD Orthologs
Mouse
Rat
Pig
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,775,140 - 152,777,024 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,775,140 - 152,777,024 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,747,616 - 152,749,500 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,015,472 - 151,015,828 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,561,920 - 149,562,277NCBI
Celera1125,826,923 - 125,827,279 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,122,294 - 124,122,891 (+)NCBIHuRef
CHM1_11154,144,211 - 154,144,808 (+)NCBICHM1_1
T2T-CHM13v2.01151,911,685 - 151,913,569 (+)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:15854049   PMID:16710414   PMID:18316326   PMID:21873635   PMID:32296183   PMID:36724073  


Genomics

Comparative Map Data
LCE1F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,775,140 - 152,777,024 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,775,140 - 152,777,024 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,747,616 - 152,749,500 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,015,472 - 151,015,828 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,561,920 - 149,562,277NCBI
Celera1125,826,923 - 125,827,279 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,122,294 - 124,122,891 (+)NCBIHuRef
CHM1_11154,144,211 - 154,144,808 (+)NCBICHM1_1
T2T-CHM13v2.01151,911,685 - 151,913,569 (+)NCBIT2T-CHM13v2.0
Lce1f
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,626,003 - 92,627,657 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,625,992 - 92,627,657 (-)EnsemblGRCm39 Ensembl
GRCm38392,718,696 - 92,720,350 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl392,718,685 - 92,720,350 (-)EnsemblGRCm38mm10GRCm38
MGSCv37392,522,618 - 92,524,272 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36392,804,088 - 92,805,753 (-)NCBIMGSCv36mm8
Celera394,362,576 - 94,364,230 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
Lce1f
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82181,001,399 - 181,002,985 (-)NCBIGRCr8
mRatBN7.22178,305,786 - 178,307,372 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,305,786 - 178,307,372 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2185,861,271 - 185,862,874 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02183,842,209 - 183,843,795 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02178,504,372 - 178,505,975 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02192,990,607 - 192,992,193 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2192,990,831 - 192,991,199 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02211,878,085 - 211,879,671 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42185,714,948 - 185,716,534 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2171,952,845 - 171,954,431 (+)NCBICelera
Cytogenetic Map2q34NCBI
LCE1F
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1496,712,422 - 96,713,060 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24105,648,539 - 105,650,279 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in LCE1F
15 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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_178354.3(LCE1F):c.136G>A (p.Val46Ile) single nucleotide variant Inborn genetic diseases [RCV003256137] Chr1:152776507 [GRCh38]
Chr1:152748983 [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(chr1:152554081-152760427)x0 copy number loss not provided [RCV000736695] Chr1:152554081..152760427 [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_178354.3(LCE1F):c.325G>T (p.Gly109Cys) single nucleotide variant Inborn genetic diseases [RCV003286663] Chr1:152776696 [GRCh38]
Chr1:152749172 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.211G>C (p.Gly71Arg) single nucleotide variant Inborn genetic diseases [RCV002754217] Chr1:152776582 [GRCh38]
Chr1:152749058 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.53C>T (p.Pro18Leu) single nucleotide variant Inborn genetic diseases [RCV002683545] Chr1:152776424 [GRCh38]
Chr1:152748900 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q21.3(chr1:152648864-153286218)x3 copy number gain not provided [RCV002475654] Chr1:152648864..153286218 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.302C>T (p.Ala101Val) single nucleotide variant Inborn genetic diseases [RCV002870585] Chr1:152776673 [GRCh38]
Chr1:152749149 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.62C>T (p.Pro21Leu) single nucleotide variant Inborn genetic diseases [RCV002789392] Chr1:152776433 [GRCh38]
Chr1:152748909 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.115C>T (p.Pro39Ser) single nucleotide variant Inborn genetic diseases [RCV002787507] Chr1:152776486 [GRCh38]
Chr1:152748962 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.323G>C (p.Gly108Ala) single nucleotide variant Inborn genetic diseases [RCV002769672] Chr1:152776694 [GRCh38]
Chr1:152749170 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.313T>G (p.Cys105Gly) single nucleotide variant Inborn genetic diseases [RCV003201858] Chr1:152776684 [GRCh38]
Chr1:152749160 [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
NM_178354.3(LCE1F):c.59G>A (p.Cys20Tyr) single nucleotide variant Inborn genetic diseases [RCV003360537] Chr1:152776430 [GRCh38]
Chr1:152748906 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.212G>A (p.Gly71Glu) single nucleotide variant Inborn genetic diseases [RCV003370054] Chr1:152776583 [GRCh38]
Chr1:152749059 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178354.3(LCE1F):c.249T>C (p.Arg83=) single nucleotide variant not provided [RCV003409035] Chr1:152776620 [GRCh38]
Chr1:152749096 [GRCh37]
Chr1:1q21.3		 likely benign
NM_178354.3(LCE1F):c.225T>C (p.Cys75=) single nucleotide variant not provided [RCV003409032] Chr1:152776596 [GRCh38]
Chr1:152749072 [GRCh37]
Chr1:1q21.3		 likely benign
NM_178354.3(LCE1F):c.243A>G (p.Arg81=) single nucleotide variant not provided [RCV003409033] Chr1:152776614 [GRCh38]
Chr1:152749090 [GRCh37]
Chr1:1q21.3		 likely benign
NM_178354.3(LCE1F):c.246G>C (p.Arg82=) single nucleotide variant not provided [RCV003409034] Chr1:152776617 [GRCh38]
Chr1:152749093 [GRCh37]
Chr1:1q21.3		 likely benign
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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:177
Count of miRNA genes:171
Interacting mature miRNAs:176
Transcripts:ENST00000334371
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
High
Medium 1 1 3 1179 1 3 4 3 670
Low 42 24 20 16 283 8 149 23 22 5 26 52 9 19 47
Below cutoff 454 636 217 77 258 42 620 432 572 24 265 212 38 251 445

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000334371   ⟹   ENSP00000334187
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1152,775,140 - 152,777,024 (+)Ensembl
RefSeq Acc Id: NM_178354   ⟹   NP_848131
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,775,140 - 152,777,024 (+)NCBI
GRCh371152,748,848 - 152,749,445 (+)ENTREZGENE
Build 361151,015,472 - 151,015,828 (+)NCBI Archive
Celera1125,826,923 - 125,827,279 (+)RGD
HuRef1124,122,294 - 124,122,891 (+)ENTREZGENE
CHM1_11154,144,211 - 154,144,808 (+)NCBI
T2T-CHM13v2.01151,911,685 - 151,913,569 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_848131 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EAW53368 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000334187
  ENSP00000334187.2
GenBank Protein Q5T754 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_848131   ⟸   NM_178354
- UniProtKB: Q5T754 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000334187   ⟸   ENST00000334371

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5T754-F1-model_v2 AlphaFold Q5T754 1-118 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:29467 AgrOrtholog
COSMIC LCE1F COSMIC
Ensembl Genes ENSG00000240386 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000334371 ENTREZGENE
  ENST00000334371.4 UniProtKB/Swiss-Prot
GTEx ENSG00000240386 GTEx
HGNC ID HGNC:29467 ENTREZGENE
Human Proteome Map LCE1F Human Proteome Map
InterPro LCE UniProtKB/Swiss-Prot
KEGG Report hsa:353137 UniProtKB/Swiss-Prot
NCBI Gene 353137 ENTREZGENE
OMIM 612608 OMIM
Pfam LCE UniProtKB/Swiss-Prot
PharmGKB PA134962947 PharmGKB
PRINTS PRORICH UniProtKB/Swiss-Prot
UniProt LCE1F_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE