LCE6A (late cornified envelope 6A) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LCE6A (late cornified envelope 6A) Homo sapiens
Analyze
Symbol: LCE6A
Name: late cornified envelope 6A
RGD ID: 1343793
HGNC Page HGNC:31824
Description: Predicted to be involved in keratinization.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C1orf44; chromosome 1 open reading frame 44; late cornified envelope protein 6A
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
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
GRCh381152,842,856 - 152,843,983 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,842,856 - 152,843,983 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,815,332 - 152,816,459 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,082,621 - 151,083,082 (+)NCBINCBI36Build 36hg18NCBI36
Celera1125,885,590 - 125,886,719 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,178,318 - 124,179,447 (+)NCBIHuRef
CHM1_11154,210,693 - 154,211,822 (+)NCBICHM1_1
T2T-CHM13v2.01151,979,388 - 151,980,541 (+)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

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
Additional References at PubMed
PMID:11329013   PMID:15854049  


Genomics

Comparative Map Data
LCE6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,842,856 - 152,843,983 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,842,856 - 152,843,983 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,815,332 - 152,816,459 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,082,621 - 151,083,082 (+)NCBINCBI36Build 36hg18NCBI36
Celera1125,885,590 - 125,886,719 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,178,318 - 124,179,447 (+)NCBIHuRef
CHM1_11154,210,693 - 154,211,822 (+)NCBICHM1_1
T2T-CHM13v2.01151,979,388 - 151,980,541 (+)NCBIT2T-CHM13v2.0
Lce6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,512,128 - 92,528,975 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,527,388 - 92,528,967 (-)EnsemblGRCm39 Ensembl
GRCm38392,604,821 - 92,621,660 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl392,620,081 - 92,621,660 (-)EnsemblGRCm38mm10GRCm38
MGSCv37392,424,007 - 92,425,582 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera394,461,933 - 94,463,508 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
Lce6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82180,889,761 - 180,890,847 (-)NCBIGRCr8
mRatBN7.22178,194,148 - 178,195,234 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,194,318 - 178,194,563 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2185,749,716 - 185,750,802 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02183,730,391 - 183,731,477 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02178,392,813 - 178,393,899 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02192,811,593 - 192,813,142 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2192,811,766 - 192,812,008 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02212,058,270 - 212,058,685 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42185,603,359 - 185,603,774 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2172,062,797 - 172,064,346 (+)NCBICelera
Cytogenetic Map2q34NCBI
LCE6A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2197,000,349 - 97,001,612 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1196,751,596 - 96,752,769 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01128,187,490 - 128,188,665 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11131,818,031 - 131,819,157 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1131,818,696 - 131,818,938 (+)Ensemblpanpan1.1panPan2
LCE6A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11761,653,363 - 61,654,514 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1761,121,196 - 61,122,349 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01762,801,489 - 62,802,641 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11761,530,222 - 61,531,374 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01761,599,902 - 61,601,054 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01762,356,395 - 62,357,547 (+)NCBIUU_Cfam_GSD_1.0
Lce6a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505823,809,039 - 23,810,785 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365802,840,642 - 2,841,167 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCE6A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12010,878,229 - 10,879,885 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2010,878,566 - 10,878,805 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603810,355,219 - 10,356,348 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lce6a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624885333,046 - 333,357 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LCE6A
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001128600.1(LCE6A):c.132C>T (p.Ser44=) single nucleotide variant Malignant melanoma [RCV000064167] Chr1:152843652 [GRCh38]
Chr1:152816128 [GRCh37]
Chr1:151082752 [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_001128600.2(LCE6A):c.200G>A (p.Gly67Asp) single nucleotide variant not specified [RCV004127878] Chr1:152843720 [GRCh38]
Chr1:152816196 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_001128600.2(LCE6A):c.168G>C (p.Arg56Ser) single nucleotide variant not specified [RCV004108745] Chr1:152843688 [GRCh38]
Chr1:152816164 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_001128600.2(LCE6A):c.8A>C (p.Gln3Pro) single nucleotide variant not specified [RCV004214872] Chr1:152843528 [GRCh38]
Chr1:152816004 [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_001128600.2(LCE6A):c.172C>T (p.Arg58Cys) single nucleotide variant not specified [RCV004412454] Chr1:152843692 [GRCh38]
Chr1:152816168 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_001128600.2(LCE6A):c.184C>T (p.Arg62Cys) single nucleotide variant not specified [RCV004412455] Chr1:152843704 [GRCh38]
Chr1:152816180 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_001128600.2(LCE6A):c.7C>G (p.Gln3Glu) single nucleotide variant not specified [RCV004412456] Chr1:152843527 [GRCh38]
Chr1:152816003 [GRCh37]
Chr1:1q21.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:271
Count of miRNA genes:251
Interacting mature miRNAs:259
Transcripts:ENST00000431011
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 1 1
Medium 1 1 1 1 1221 1 1 3 677
Low 17 27 13 3 12 2 103 14 22 3 31 22 1 14 38
Below cutoff 581 858 269 103 365 55 898 600 747 25 376 294 50 370 669

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000431011   ⟹   ENSP00000411070
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1152,842,856 - 152,843,983 (+)Ensembl
RefSeq Acc Id: NM_001128600   ⟹   NP_001122072
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,842,856 - 152,843,983 (+)NCBI
GRCh371152,815,330 - 152,816,459 (+)RGD
Celera1125,885,590 - 125,886,719 (+)RGD
HuRef1124,178,318 - 124,179,447 (+)RGD
CHM1_11154,210,693 - 154,211,822 (+)NCBI
T2T-CHM13v2.01151,979,414 - 151,980,541 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017001327   ⟹   XP_016856816
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,842,856 - 152,843,983 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054336696   ⟹   XP_054192671
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01151,979,388 - 151,980,541 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001122072 (Get FASTA)   NCBI Sequence Viewer  
  XP_016856816 (Get FASTA)   NCBI Sequence Viewer  
  XP_054192671 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A183 (Get FASTA)   NCBI Sequence Viewer  
  ABJ55982 (Get FASTA)   NCBI Sequence Viewer  
  CAK32457 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000411070
  ENSP00000411070.2
Reference Protein Sequences
RefSeq Acc Id: NP_001122072   ⟸   NM_001128600
- UniProtKB: A0A183 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016856816   ⟸   XM_017001327
- Peptide Label: isoform X1
- UniProtKB: A0A183 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000411070   ⟸   ENST00000431011
RefSeq Acc Id: XP_054192671   ⟸   XM_054336696
- Peptide Label: isoform X1
- UniProtKB: A0A183 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A183-F1-model_v2 AlphaFold A0A183 1-80 view protein structure

Promoters
RGD ID:6857148
Promoter ID:EPDNEW_H1739
Type:single initiation site
Name:LCE6A_1
Description:late cornified envelope 6A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,842,856 - 152,842,916EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31824 AgrOrtholog
COSMIC LCE6A COSMIC
Ensembl Genes ENSG00000235942 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000431011 ENTREZGENE
  ENST00000431011.3 UniProtKB/Swiss-Prot
GTEx ENSG00000235942 GTEx
HGNC ID HGNC:31824 ENTREZGENE
Human Proteome Map LCE6A Human Proteome Map
InterPro LCE6A UniProtKB/Swiss-Prot
KEGG Report hsa:448835 UniProtKB/Swiss-Prot
NCBI Gene 448835 ENTREZGENE
Pfam LCE6A UniProtKB/Swiss-Prot
PharmGKB PA162393834 PharmGKB
UniProt A0A183 ENTREZGENE, UniProtKB/Swiss-Prot