LCE1A (late cornified envelope 1A) - Rat Genome Database

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Gene: LCE1A (late cornified envelope 1A) Homo sapiens
Analyze
Symbol: LCE1A
Name: late cornified envelope 1A
RGD ID: 1345859
HGNC Page HGNC:29459
Description: Predicted to be involved in keratinization. Predicted to be located in cytosol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: late cornified envelope protein 1A; late envelope protein 1; LEP1
RGD Orthologs
Bonobo
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
GRCh381152,827,473 - 152,828,097 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,827,473 - 152,828,097 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,799,949 - 152,800,573 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,066,573 - 151,066,905 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,613,021 - 149,613,354NCBI
Celera1125,870,205 - 125,870,537 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,162,933 - 124,163,557 (+)NCBIHuRef
CHM1_11154,195,309 - 154,195,933 (+)NCBICHM1_1
T2T-CHM13v2.01151,964,030 - 151,964,654 (+)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

Cellular Component
cytosol  (TAS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. 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:21873635   PMID:32296183   PMID:36949045  


Genomics

Comparative Map Data
LCE1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,827,473 - 152,828,097 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,827,473 - 152,828,097 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,799,949 - 152,800,573 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,066,573 - 151,066,905 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,613,021 - 149,613,354NCBI
Celera1125,870,205 - 125,870,537 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,162,933 - 124,163,557 (+)NCBIHuRef
CHM1_11154,195,309 - 154,195,933 (+)NCBICHM1_1
T2T-CHM13v2.01151,964,030 - 151,964,654 (+)NCBIT2T-CHM13v2.0
LOC130541081
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2197,015,995 - 97,016,639 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1196,767,179 - 96,767,823 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl1131,803,002 - 131,803,334 (+)Ensemblpanpan1.1panPan2

Variants

.
Variants in LCE1A
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_178348.2(LCE1A):c.315C>T (p.His105=) single nucleotide variant Malignant melanoma [RCV000059891] Chr1:152827787 [GRCh38]
Chr1:152800263 [GRCh37]
Chr1:151066887 [NCBI36]
Chr1:1q21.3		 not provided
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
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
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 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
GRCh37/hg19 1q21.3(chr1:152648864-153286218)x3 copy number gain not provided [RCV002475654] Chr1:152648864..153286218 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.308G>A (p.Gly103Asp) single nucleotide variant not specified [RCV004220265] Chr1:152827780 [GRCh38]
Chr1:152800256 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.94A>G (p.Lys32Glu) single nucleotide variant not specified [RCV004134938] Chr1:152827566 [GRCh38]
Chr1:152800042 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.11A>G (p.Gln4Arg) single nucleotide variant not specified [RCV004207169] Chr1:152827483 [GRCh38]
Chr1:152799959 [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_178348.2(LCE1A):c.325T>G (p.Cys109Gly) single nucleotide variant not specified [RCV004412412] Chr1:152827797 [GRCh38]
Chr1:152800273 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.307G>A (p.Gly103Ser) single nucleotide variant not specified [RCV004412411] Chr1:152827779 [GRCh38]
Chr1:152800255 [GRCh37]
Chr1:1q21.3		 likely benign
NM_178348.2(LCE1A):c.303C>G (p.Asp101Glu) single nucleotide variant not specified [RCV004412410] Chr1:152827775 [GRCh38]
Chr1:152800251 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.284C>A (p.Ser95Tyr) single nucleotide variant not specified [RCV004412408] Chr1:152827756 [GRCh38]
Chr1:152800232 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_178348.2(LCE1A):c.155G>T (p.Cys52Phe) single nucleotide variant not specified [RCV004412407] Chr1:152827627 [GRCh38]
Chr1:152800103 [GRCh37]
Chr1:1q21.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:239
Count of miRNA genes:224
Interacting mature miRNAs:229
Transcripts:ENST00000335123
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.

Markers in Region
UniSTS:483578  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371152,799,925 - 152,800,373UniSTSGRCh37
Build 361151,066,549 - 151,066,997RGDNCBI36
Celera1125,870,181 - 125,870,629RGD
HuRef1124,162,909 - 124,163,357UniSTS


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 40 39
Medium 1 1188 1 1 2 4 647
Low 111 99 49 11 66 6 209 49 169 3 58 61 5 51 105
Below cutoff 768 1082 389 108 380 65 1144 814 1027 19 428 360 46 484 841

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000335123   ⟹   ENSP00000334869
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1152,827,473 - 152,828,097 (+)Ensembl
RefSeq Acc Id: NM_178348   ⟹   NP_848125
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,827,473 - 152,828,097 (+)NCBI
GRCh371152,799,949 - 152,800,573 (+)ENTREZGENE
Build 361151,066,573 - 151,066,905 (+)NCBI Archive
Celera1125,870,205 - 125,870,537 (+)RGD
HuRef1124,162,933 - 124,163,557 (+)ENTREZGENE
CHM1_11154,195,309 - 154,195,933 (+)NCBI
T2T-CHM13v2.01151,964,030 - 151,964,654 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_848125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EAW53362 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000334869
  ENSP00000334869.2
GenBank Protein Q5T7P2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_848125   ⟸   NM_178348
- UniProtKB: Q5T7P2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000334869   ⟸   ENST00000335123

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5T7P2-F1-model_v2 AlphaFold Q5T7P2 1-110 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:29459 AgrOrtholog
COSMIC LCE1A COSMIC
Ensembl Genes ENSG00000186844 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000335123 ENTREZGENE
  ENST00000335123.4 UniProtKB/Swiss-Prot
GTEx ENSG00000186844 GTEx
HGNC ID HGNC:29459 ENTREZGENE
Human Proteome Map LCE1A Human Proteome Map
InterPro LCE UniProtKB/Swiss-Prot
KEGG Report hsa:353131 UniProtKB/Swiss-Prot
NCBI Gene 353131 ENTREZGENE
OMIM 612603 OMIM
Pfam LCE UniProtKB/Swiss-Prot
PharmGKB PA134885053 PharmGKB
PRINTS PRORICH UniProtKB/Swiss-Prot
UniProt LCE1A_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE