Aliases for LCE3A Gene

Aliases for LCE3A Gene

  • Late Cornified Envelope 3A 2 3 5
  • LEP13 2 3 4
  • Late Cornified Envelope Protein 3A 3 4
  • Late Envelope Protein 13 3 4
  • LCE3A 5

External Ids for LCE3A Gene

Previous GeneCards Identifiers for LCE3A Gene

  • GC01M149408
  • GC01M150861
  • GC01M123968

Summaries for LCE3A Gene

GeneCards Summary for LCE3A Gene

LCE3A (Late Cornified Envelope 3A) is a Protein Coding gene. Diseases associated with LCE3A include Psoriasis 10 and Psoriasis 4. Among its related pathways are Keratinization and Developmental Biology. An important paralog of this gene is LCE3C.

UniProtKB/Swiss-Prot Summary for LCE3A Gene

  • A structural component of the cornified envelope of the stratum corneum involved in innate cutaneous host defense (Probable). Possesses defensin-like antimicrobial activity against a broad spectrum of Gram-positive and Gram-negative bacteria, both aerobic and anaerobic species. Upon inflammation, may regulate skin barrier repair by shaping cutaneous microbiota composition and immune response to bacterial antigens (PubMed:28634035).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LCE3A Gene

Genomics for LCE3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LCE3A 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
GH01J152622 Enhancer 0.7 Ensembl ENCODE 250.7 -0.1 -110 2 GABPA CTCF SPI1 MYC POLR2A NRF1 TCF12 LCE3A LCE1D PGLYRP4 piR-43103-004 LCE2D
GH01J152480 Enhancer 0.6 Ensembl ENCODE 10 +142.5 142510 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 10.1 +103.2 103202 1.8 SPI1 POLR2A SREBF1 HSALNG0007230 HSALNG0007231 lnc-CRCT1-1 LCE3D LCE3A CRNN THEM5 CRCT1 LCE3E
GH01J152655 Promoter 0.3 EPDnew 10.7 -32.3 -32331 0.1 LCEP3 LINC00302 LCE2D LCE3A LCE3D HSALNG0007237
GH01J152143 Enhancer 0.6 FANTOM5 Ensembl 1.3 +479.4 479403 0.6 BATF ATF2 RUNX3 piR-48049-017 HRNR ENSG00000226716 TCHH PUDPP2 TCHHL1 S100A11 FLG ENSG00000229021 LCE3A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCE3A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCE3A

Top Transcription factor binding sites by QIAGEN in the LCE3A gene promoter:
  • AML1a
  • FOXI1
  • FOXO4
  • HFH-1
  • HFH-3
  • Ik-1
  • LyF-1
  • Tal-1beta
  • TBP
  • YY1

Genomic Locations for LCE3A Gene

Latest Assembly
chr1:152,622,834-152,623,103
(GRCh38/hg38)
Size:
270 bases
Orientation:
Minus strand

Previous Assembly
chr1:152,595,310-152,595,579
(GRCh37/hg19 by Entrez Gene)
Size:
270 bases
Orientation:
Minus strand

chr1:152,595,310-152,595,579
(GRCh37/hg19 by Ensembl)
Size:
270 bases
Orientation:
Minus strand

Genomic View for LCE3A Gene

Genes around LCE3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCE3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCE3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCE3A Gene

Proteins for LCE3A Gene

  • Protein details for LCE3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TA76-LCE3A_HUMAN
    Recommended name:
    Late cornified envelope protein 3A
    Protein Accession:
    Q5TA76

    Protein attributes for LCE3A Gene

    Size:
    89 amino acids
    Molecular mass:
    9146 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LCE3A Gene

Post-translational modifications for LCE3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LCE3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LCE3A Gene

Domains & Families for LCE3A Gene

Gene Families for LCE3A Gene

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

Protein Domains for LCE3A Gene

InterPro:

Suggested Antigen Peptide Sequences for LCE3A Gene

GenScript: Design optimal peptide antigens:
  • Late envelope protein 13 (LCE3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5TA76

UniProtKB/Swiss-Prot:

LCE3A_HUMAN :
  • Belongs to the LCE family.
Family:
  • Belongs to the LCE family.
genes like me logo Genes that share domains with LCE3A: view

Function for LCE3A Gene

Molecular function for LCE3A Gene

UniProtKB/Swiss-Prot Function:
A structural component of the cornified envelope of the stratum corneum involved in innate cutaneous host defense (Probable). Possesses defensin-like antimicrobial activity against a broad spectrum of Gram-positive and Gram-negative bacteria, both aerobic and anaerobic species. Upon inflammation, may regulate skin barrier repair by shaping cutaneous microbiota composition and immune response to bacterial antigens (PubMed:28634035).
UniProtKB/Swiss-Prot Induction:
Induced upon stimulation with inflammatory cytokines produced by T-helper 1 cells (IL1A, TNF, IFNG) and T-helper 17 cells (IL17A, IL22).

Phenotypes From GWAS Catalog for LCE3A Gene

Gene Ontology (GO) - Molecular Function for LCE3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with LCE3A: view
genes like me logo Genes that share phenotypes with LCE3A: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE3A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCE3A Gene

Localization for LCE3A 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 LCE3A gene
Compartment Confidence
extracellular 3
nucleus 2
plasma membrane 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for LCE3A Gene

Pathways & Interactions for LCE3A Gene

PathCards logo

SuperPathways for LCE3A Gene

genes like me logo Genes that share pathways with LCE3A: view

Pathways by source for LCE3A Gene

Gene Ontology (GO) - Biological Process for LCE3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008544 epidermis development IEA --
GO:0031424 keratinization IEA --
GO:0031640 killing of cells of other organism IDA 28634035
GO:0050829 defense response to Gram-negative bacterium IDA 28634035
GO:0050830 defense response to Gram-positive bacterium IDA 28634035
genes like me logo Genes that share ontologies with LCE3A: view

No data available for SIGNOR curated interactions for LCE3A Gene

Drugs & Compounds for LCE3A Gene

No Compound Related Data Available

Transcripts for LCE3A Gene

mRNA/cDNA for LCE3A Gene

1 REFSEQ mRNAs :
2 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 LCE3A

Alternative Splicing Database (ASD) splice patterns (SP) for LCE3A Gene

No ASD Table

Relevant External Links for LCE3A Gene

GeneLoc Exon Structure for
LCE3A

Expression for LCE3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCE3A Gene

mRNA differential expression in normal tissues according to GTEx for LCE3A Gene

This gene is overexpressed in Cervix - Ectocervix (x23.1), Vagina (x21.1), and Esophagus - Mucosa (x5.1).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCE3A

SOURCE GeneReport for Unigene cluster for LCE3A Gene:

Hs.553714

mRNA Expression by UniProt/SwissProt for LCE3A Gene:

Q5TA76-LCE3A_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.
genes like me logo Genes that share expression patterns with LCE3A: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCE3A Gene

Orthologs for LCE3A Gene

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

Orthologs for LCE3A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LCE3A 30
  • 96 (a)
OneToOne
Species where no ortholog for LCE3A 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 LCE3A Gene

ENSEMBL:
Gene Tree for LCE3A (if available)
TreeFam:
Gene Tree for LCE3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCE3A: view image
Alliance of Genome Resources:
Additional Orthologs for LCE3A

Paralogs for LCE3A Gene

genes like me logo Genes that share paralogs with LCE3A: view

Variants for LCE3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCE3A Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs190000383 Benign: not provided 152,623,089(-) C/G
NM_178431.1(LCE3A):c.15G>C (p.Gln5His)
MISSENSE
rs16834245 -- p.Arg59Cys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LCE3A 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 LCE3A Gene

Variant ID Type Subtype PubMed ID
dgv568n54 CNV loss 21841781
esv2750810 CNV gain 17911159
esv2758970 CNV gain+loss 17122850
esv2764248 CNV gain+loss 21179565
esv33483 CNV gain+loss 17666407
esv3587564 CNV gain 21293372
esv3890660 CNV gain 25118596
nsv2888 CNV deletion 18451855
nsv469873 CNV loss 16826518
nsv510990 OTHER complex 20534489
nsv547891 CNV loss 21841781
nsv68 CNV deletion 15895083

Variation tolerance for LCE3A Gene

Residual Variation Intolerance Score: 59.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.20; 24.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCE3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCE3A
Leiden Open Variation Database (LOVD)
LCE3A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCE3A Gene

Disorders for LCE3A Gene

MalaCards: The human disease database

(3) MalaCards diseases for LCE3A Gene - From: COP

Disorder Aliases PubMed IDs
psoriasis 10
  • psoriasis 10, susceptibility to
psoriasis 4
  • psoriasis 4, susceptibility to
psoriasis 1
  • psoriasis 1, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search LCE3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LCE3A

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 LCE3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCE3A Gene

Publications for LCE3A Gene

  1. Psoriasis-Associated Late Cornified Envelope (LCE) Proteins Have Antibacterial Activity. (PMID: 28634035) Niehues H … Schalkwijk J (The Journal of investigative dermatology 2017) 3 4
  2. 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
  3. Variation in genes of the epidermal differentiation complex in German atopic dermatitis patients. (PMID: 19601998) Stemmler S … Hoffjan S (International journal of immunogenetics 2009) 3 40
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  5. 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

Products for LCE3A Gene

Sources for LCE3A Gene