Aliases for LCE3D Gene

Aliases for LCE3D Gene

  • Late Cornified Envelope 3D 2 3 5
  • LEP16 2 3 4
  • Small Proline-Rich-Like Epidermal Differentiation Complex Protein 6A 3 4
  • Small Proline-Rich-Like Epidermal Differentiation Complex Protein 6B 3 4
  • Small Proline Rich-Like (Epidermal Differentiation Complex) 6B 2 3
  • Late Cornified Envelope Protein 3D 3 4
  • Late Envelope Protein 16 3 4
  • SPRL6A 3 4
  • SPRL6B 3 4
  • Small Proline Rich-Like (Epidermal Differentiation Complex) 6A 3
  • LCE3D 5

External Ids for LCE3D Gene

Previous HGNC Symbols for LCE3D Gene

  • SPRL6B
  • SPRL6A

Previous GeneCards Identifiers for LCE3D Gene

  • GC01M149364
  • GC01M150818
  • GC01M152551
  • GC01M123925

Summaries for LCE3D Gene

GeneCards Summary for LCE3D Gene

LCE3D (Late Cornified Envelope 3D) is a Protein Coding gene. Diseases associated with LCE3D include Psoriasis 1 and Psoriasis 10. Among its related pathways are Keratinization and Developmental Biology. An important paralog of this gene is LCE3E.

UniProtKB/Swiss-Prot Summary for LCE3D Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LCE3D Gene

Genomics for LCE3D Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LCE3D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J152580 Promoter 0.3 EPDnew 250.7 0.0 -20 0.1 LCE3D lnc-LCE3D-1 LCE3C
GH01J152480 Enhancer 0.6 Ensembl ENCODE 9.9 +99.9 99923 0.8 CTCF GABPB1 MAFK ZNF143 SMARCA5 LCE5A CRCT1 LCE3A LCE3D HRNR CRNN S100A11 FLG-AS1 MN296878 lnc-LCE5A-5
GH01J152519 Enhancer 0.4 Ensembl 10.2 +60.6 60615 1.8 SPI1 POLR2A SREBF1 HSALNG0007230 HSALNG0007231 lnc-CRCT1-1 LCE3D LCE3A CRNN THEM5 CRCT1 LCE3E
GH01J152517 Enhancer 0.4 Ensembl 9.1 +63.0 63015 1 EGR2 ESRRA MAFK ZFHX2 HSALNG0007230 LCE3D CRNN CRCT1 LCE3E
GH01J152655 Promoter 0.3 EPDnew 9.4 -74.9 -74918 0.1 LCEP3 LINC00302 LCE2D LCE3A LCE3D HSALNG0007237
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCE3D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCE3D

Top Transcription factor binding sites by QIAGEN in the LCE3D gene promoter:
  • c-Myc
  • C/EBPbeta
  • GR
  • GR-alpha
  • GR-beta
  • Max1
  • Spz1
  • TBP

Genomic Locations for LCE3D Gene

Latest Assembly
chr1:152,579,381-152,580,516
(GRCh38/hg38)
Size:
1,136 bases
Orientation:
Minus strand

Previous Assembly
chr1:152,551,857-152,552,992
(GRCh37/hg19 by Entrez Gene)
Size:
1,136 bases
Orientation:
Minus strand

chr1:152,551,857-152,552,980
(GRCh37/hg19 by Ensembl)
Size:
1,124 bases
Orientation:
Minus strand

Genomic View for LCE3D Gene

Genes around LCE3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCE3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCE3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCE3D Gene

Proteins for LCE3D Gene

  • Protein details for LCE3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BYE3-LCE3D_HUMAN
    Recommended name:
    Late cornified envelope protein 3D
    Protein Accession:
    Q9BYE3
    Secondary Accessions:
    • Q3MIL1

    Protein attributes for LCE3D Gene

    Size:
    92 amino acids
    Molecular mass:
    9444 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Belongs to the LCE cluster present on 1q21.

neXtProt entry for LCE3D Gene

Post-translational modifications for LCE3D Gene

No Post-translational modifications

Other Protein References for LCE3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LCE3D Gene

Domains & Families for LCE3D Gene

Gene Families for LCE3D Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LCE3D Gene

InterPro:

Suggested Antigen Peptide Sequences for LCE3D Gene

GenScript: Design optimal peptide antigens:
  • Small proline-rich-like epidermal differentiation complex protein 6B (LCE3D_HUMAN)
  • LCE3D protein (Q0IJ72_HUMAN)
  • Late cornified envelope 3D (Q0VAS7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BYE3

UniProtKB/Swiss-Prot:

LCE3D_HUMAN :
  • Belongs to the LCE family.
Family:
  • Belongs to the LCE family.
genes like me logo Genes that share domains with LCE3D: view

Function for LCE3D Gene

Molecular function for LCE3D Gene

UniProtKB/Swiss-Prot Function:
Precursors of the cornified envelope of the stratum corneum.

Phenotypes From GWAS Catalog for LCE3D Gene

Gene Ontology (GO) - Molecular Function for LCE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with LCE3D: view
genes like me logo Genes that share phenotypes with LCE3D: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE3D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCE3D Gene

Localization for LCE3D Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCE3D gene
Compartment Confidence
cytosol 4
extracellular 3
plasma membrane 2
nucleus 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for LCE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with LCE3D: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for LCE3D Gene

Pathways & Interactions for LCE3D Gene

PathCards logo

SuperPathways for LCE3D Gene

genes like me logo Genes that share pathways with LCE3D: view

Pathways by source for LCE3D Gene

Gene Ontology (GO) - Biological Process for LCE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008544 epidermis development IEA --
GO:0031424 keratinization IEA --
GO:0070268 cornification TAS --
genes like me logo Genes that share ontologies with LCE3D: view

No data available for SIGNOR curated interactions for LCE3D Gene

Drugs & Compounds for LCE3D Gene

No Compound Related Data Available

Transcripts for LCE3D Gene

mRNA/cDNA for LCE3D Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE3D

Alternative Splicing Database (ASD) splice patterns (SP) for LCE3D Gene

No ASD Table

Relevant External Links for LCE3D Gene

GeneLoc Exon Structure for
LCE3D

Expression for LCE3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCE3D Gene

mRNA differential expression in normal tissues according to GTEx for LCE3D Gene

This gene is overexpressed in Cervix - Ectocervix (x23.0), Vagina (x17.6), and Skin - Sun Exposed (Lower leg) (x5.6).

Protein differential expression in normal tissues from HIPED for LCE3D Gene

This gene is overexpressed in Pancreatic juice (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LCE3D Gene



Protein tissue co-expression partners for LCE3D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCE3D

SOURCE GeneReport for Unigene cluster for LCE3D Gene:

Hs.244349

mRNA Expression by UniProt/SwissProt for LCE3D Gene:

Q9BYE3-LCE3D_HUMAN
Tissue specificity: Skin-specific. Expression was readily detected in adult trunk skin, adult arm skin, fetal skin, penal skin, vulva, esophagus and tongue. Not expressed in the cervix, rectum, lung, colon, or placenta.

Evidence on tissue expression from TISSUES for LCE3D Gene

  • Skin(4.5)
  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with LCE3D: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCE3D Gene

Orthologs for LCE3D Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for LCE3D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LCE3D 30
  • 98 (a)
OneToOne
Species where no ortholog for LCE3D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for LCE3D Gene

ENSEMBL:
Gene Tree for LCE3D (if available)
TreeFam:
Gene Tree for LCE3D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCE3D: view image
Alliance of Genome Resources:
Additional Orthologs for LCE3D

Paralogs for LCE3D Gene

genes like me logo Genes that share paralogs with LCE3D: view

Variants for LCE3D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCE3D Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs512208 -- p.Gly43Val
rs57201979 -- p.Gly81Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LCE3D Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LCE3D Gene

Variant ID Type Subtype PubMed ID
dgv100e212 CNV loss 25503493
dgv23n111 CNV deletion 26073780
dgv2n31 CNV loss 19718026
dgv37n27 CNV loss 19166990
dgv38n27 CNV loss 19166990
dgv39n27 CNV loss 19166990
dgv416n100 CNV loss 25217958
dgv417n100 CNV gain 25217958
dgv418n100 CNV loss 25217958
dgv419n100 CNV loss 25217958
dgv420n100 CNV gain+loss 25217958
dgv421n100 CNV loss 25217958
dgv422n100 CNV gain+loss 25217958
dgv423n100 CNV gain 25217958
dgv565n54 CNV loss 21841781
dgv566n54 CNV loss 21841781
dgv567n54 CNV loss 21841781
dgv568n54 CNV loss 21841781
dgv569n54 CNV loss 21841781
dgv5e213 CNV gain 24956385
dgv6e213 CNV loss 24956385
esv2750810 CNV gain 17911159
esv2758970 CNV gain+loss 17122850
esv2762965 CNV loss 21179565
esv33483 CNV gain+loss 17666407
esv3587561 CNV loss 21293372
esv3587562 CNV gain 21293372
nsv1002425 CNV loss 25217958
nsv2888 CNV deletion 18451855
nsv437244 CNV loss 16327808
nsv470739 CNV loss 18288195
nsv516961 CNV loss 19592680
nsv547862 CNV loss 21841781
nsv68 CNV deletion 15895083
nsv997268 CNV loss 25217958

Variation tolerance for LCE3D Gene

Residual Variation Intolerance Score: 91.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.10; 61.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCE3D Gene

Human Gene Mutation Database (HGMD)
LCE3D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCE3D
Leiden Open Variation Database (LOVD)
LCE3D

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCE3D Gene

Disorders for LCE3D Gene

MalaCards: The human disease database

(2) MalaCards diseases for LCE3D Gene - From: COP

Disorder Aliases PubMed IDs
psoriasis 1
  • psoriasis 1, susceptibility to
psoriasis 10
  • psoriasis 10, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search LCE3D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LCE3D

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LCE3D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCE3D Gene

Publications for LCE3D Gene

  1. Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. (PMID: 19169255) Zhang XJ … Liu JJ (Nature genetics 2009) 3 40
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  3. Late cornified envelope family in differentiating epithelia--response to calcium and ultraviolet irradiation. (PMID: 15854049) Jackson B … Byrne C (The Journal of investigative dermatology 2005) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Differentially expressed late constituents of the epidermal cornified envelope. (PMID: 11698679) Marshall D … Byrne C (Proceedings of the National Academy of Sciences of the United States of America 2001) 2 3

Products for LCE3D Gene

Sources for LCE3D Gene