Aliases for LCE3C Gene

Aliases for LCE3C Gene

  • Late Cornified Envelope 3C 2 3 5
  • LEP15 2 3 4
  • Small Proline-Rich-Like Epidermal Differentiation Complex Protein 3A 3 4
  • Small Proline Rich-Like (Epidermal Differentiation Complex) 3A 2 3
  • Late Cornified Envelope Protein 3C 3 4
  • Late Envelope Protein 15 3 4
  • SPRL3A 3 4
  • LCE3C 5

External Ids for LCE3C Gene

Previous HGNC Symbols for LCE3C Gene

  • SPRL3A

Previous GeneCards Identifiers for LCE3C Gene

  • GC01P149386
  • GC01P150839
  • GC01P152484
  • GC01P123946
  • GC01P152573
  • GC01P152513

Summaries for LCE3C Gene

GeneCards Summary for LCE3C Gene

LCE3C (Late Cornified Envelope 3C) is a Protein Coding gene. Diseases associated with LCE3C include Psoriasis 4 and Psoriasis 1. Among its related pathways are Keratinization and Developmental Biology. An important paralog of this gene is LCE3D.

UniProtKB/Swiss-Prot Summary for LCE3C 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 LCE3C Gene

Genomics for LCE3C Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LCE3C 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
GH01J152566 Enhancer 0.2 ENCODE 5.7 -33.3 -33304 0.1 HSALNG0007233 LCE3E LCE3C LCE3D lnc-LCE3D-1
GH01J152597 Enhancer 0.2 FANTOM5 0.7 -2.6 -2638 0.3 C1orf68 HRNR LCE3C LCE3D
GH01J152580 Promoter 0.3 EPDnew 0.4 -19.7 -19698 0.1 LCE3D lnc-LCE3D-1 LCE3C
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCE3C on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCE3C

Top Transcription factor binding sites by QIAGEN in the LCE3C gene promoter:
  • AML1a
  • AREB6
  • c-Myc
  • Max1
  • POU2F1
  • POU2F1a
  • PPAR-gamma1
  • PPAR-gamma2
  • TBP
  • Zic3

Genomic Locations for LCE3C Gene

Latest Assembly
chr1:152,600,234-152,601,086
(GRCh38/hg38)
Size:
853 bases
Orientation:
Plus strand

Previous Assembly
chr1:152,572,710-152,573,562
(GRCh37/hg19 by Entrez Gene)
Size:
853 bases
Orientation:
Plus strand

chr1:152,573,138-152,573,562
(GRCh37/hg19 by Ensembl)
Size:
425 bases
Orientation:
Plus strand

Genomic View for LCE3C Gene

Genes around LCE3C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCE3C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCE3C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCE3C Gene

Proteins for LCE3C Gene

  • Protein details for LCE3C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T5A8-LCE3C_HUMAN
    Recommended name:
    Late cornified envelope protein 3C
    Protein Accession:
    Q5T5A8
    Secondary Accessions:
    • A1L420

    Protein attributes for LCE3C Gene

    Size:
    94 amino acids
    Molecular mass:
    9729 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LCE3C Gene

Post-translational modifications for LCE3C Gene

No Post-translational modifications

Other Protein References for LCE3C Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LCE3C Gene

Domains & Families for LCE3C Gene

Gene Families for LCE3C Gene

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

Protein Domains for LCE3C Gene

InterPro:

Suggested Antigen Peptide Sequences for LCE3C Gene

GenScript: Design optimal peptide antigens:
  • Small proline-rich-like epidermal differentiation complex protein 3A (LCE3C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5T5A8

UniProtKB/Swiss-Prot:

LCE3C_HUMAN :
  • Belongs to the LCE family.
Family:
  • Belongs to the LCE family.
genes like me logo Genes that share domains with LCE3C: view

Function for LCE3C Gene

Molecular function for LCE3C 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).

Phenotypes From GWAS Catalog for LCE3C Gene

Gene Ontology (GO) - Molecular Function for LCE3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LCE3C: view
genes like me logo Genes that share phenotypes with LCE3C: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE3C

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCE3C Gene

Localization for LCE3C 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 LCE3C gene
Compartment Confidence
plasma membrane 2
extracellular 1
cytoskeleton 1
nucleus 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 LCE3C Gene

Pathways & Interactions for LCE3C Gene

PathCards logo

SuperPathways for LCE3C Gene

genes like me logo Genes that share pathways with LCE3C: view

Pathways by source for LCE3C Gene

Gene Ontology (GO) - Biological Process for LCE3C 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 LCE3C: view

No data available for SIGNOR curated interactions for LCE3C Gene

Drugs & Compounds for LCE3C Gene

No Compound Related Data Available

Transcripts for LCE3C Gene

mRNA/cDNA for LCE3C 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 LCE3C

Alternative Splicing Database (ASD) splice patterns (SP) for LCE3C Gene

No ASD Table

Relevant External Links for LCE3C Gene

GeneLoc Exon Structure for
LCE3C

Expression for LCE3C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCE3C Gene

mRNA differential expression in normal tissues according to GTEx for LCE3C Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x38.2).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCE3C

SOURCE GeneReport for Unigene cluster for LCE3C Gene:

Hs.490211

mRNA Expression by UniProt/SwissProt for LCE3C Gene:

Q5T5A8-LCE3C_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 LCE3C: 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 LCE3C Gene

Orthologs for LCE3C Gene

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

Orthologs for LCE3C Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LCE3C 30
  • 96 (a)
OneToOne
Species where no ortholog for LCE3C 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 LCE3C Gene

ENSEMBL:
Gene Tree for LCE3C (if available)
TreeFam:
Gene Tree for LCE3C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCE3C: view image
Alliance of Genome Resources:
Additional Orthologs for LCE3C

Paralogs for LCE3C Gene

genes like me logo Genes that share paralogs with LCE3C: view

Variants for LCE3C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCE3C Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs138652729 Benign: not provided 152,600,944(+) C/A
NM_178434.3(LCE3C):c.213C>A (p.Asn71Lys)
MISSENSE
rs148755167 Benign: not provided 152,600,988(+) G/A
NM_178434.3(LCE3C):c.257G>A (p.Arg86His)
MISSENSE
rs73019253 Benign: not provided 152,600,987(+) C/T
NM_178434.3(LCE3C):c.256C>T (p.Arg86Cys)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LCE3C 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 LCE3C Gene

Variant ID Type Subtype PubMed ID
dgv100e212 CNV loss 25503493
dgv201n106 CNV deletion 24896259
dgv21n16 CNV deletion 17901297
dgv23n111 CNV deletion 26073780
dgv2n31 CNV loss 19718026
dgv39n27 CNV loss 19166990
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
dgv424n100 CNV gain 25217958
dgv425n100 CNV gain 25217958
dgv426n100 CNV loss 25217958
dgv427n100 CNV gain 25217958
dgv428n100 CNV gain 25217958
dgv4n14 CNV loss 18776910
dgv4n50 CNV loss 21212237
dgv568n54 CNV loss 21841781
dgv570n54 CNV gain+loss 21841781
dgv571n54 CNV loss 21841781
dgv572n54 CNV gain 21841781
dgv573n54 CNV gain 21841781
dgv574n54 CNV gain 21841781
dgv5e213 CNV gain 24956385
dgv6e213 CNV loss 24956385
dgv71e199 CNV deletion 23128226
dgv76n67 CNV loss 20364138
dgv8n73 CNV deletion 24416366
esv2421966 CNV deletion 20811451
esv25112 CNV gain+loss 19812545
esv2615503 CNV loss 19546169
esv2718195 CNV deletion 23290073
esv2750810 CNV gain 17911159
esv2758970 CNV gain+loss 17122850
esv2762965 CNV loss 21179565
esv2764248 CNV gain+loss 21179565
esv2974901 CNV deletion 24192839
esv29957 CNV loss 18421352
esv33483 CNV gain+loss 17666407
esv3540812 CNV deletion 23714750
esv3587563 CNV loss 21293372
esv998954 CNV deletion 20482838
nsv1000122 CNV gain+loss 25217958
nsv1002425 CNV loss 25217958
nsv1078961 CNV deletion 25765185
nsv2888 CNV deletion 18451855
nsv437244 CNV loss 16327808
nsv437247 CNV loss 16327808
nsv438048 CNV loss 16468122
nsv441941 CNV loss 18776908
nsv469873 CNV loss 16826518
nsv471350 CNV loss 19718026
nsv498689 CNV loss 21111241
nsv510990 OTHER complex 20534489
nsv514007 CNV loss 21397061
nsv547862 CNV loss 21841781
nsv547891 CNV loss 21841781
nsv68 CNV deletion 15895083
nsv821155 CNV deletion 20802225
nsv8402 CNV gain+loss 18304495
nsv947446 CNV deletion 23825009

Variation tolerance for LCE3C Gene

Gene Damage Index Score: 2.86; 48.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCE3C Gene

Human Gene Mutation Database (HGMD)
LCE3C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCE3C
Leiden Open Variation Database (LOVD)
LCE3C

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCE3C Gene

Disorders for LCE3C Gene

MalaCards: The human disease database

(8) MalaCards diseases for LCE3C Gene - From: COP and GCD

Disorder Aliases PubMed IDs
psoriasis 4
  • psoriasis 4, susceptibility to
psoriasis 1
  • psoriasis 1, susceptibility to
psoriasis 10
  • psoriasis 10, susceptibility to
psoriasis 14, pustular
  • psors14
psoriatic arthritis
  • psoriatic arthritis, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search LCE3C in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LCE3C

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 LCE3C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCE3C Gene

Publications for LCE3C 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. Mutation analysis of the LCE3B/LCE3C genes in Psoriasis. (PMID: 20331852) Coto E … Alvarez V (BMC medical genetics 2010) 3 40
  3. Deletion of the late cornified envelope genes, LCE3C and LCE3B, is associated with rheumatoid arthritis. (PMID: 20213803) Docampo E … Estivill X (Arthritis and rheumatism 2010) 3 40
  4. Deletion of Late Cornified Envelope 3B and 3C genes is not associated with atopic dermatitis. (PMID: 20376060) Bergboer JG … Schalkwijk J (The Journal of investigative dermatology 2010) 3 40
  5. LCE3C_LCE3B-del genotype and psoriasis: a summative meta-analysis. (PMID: 20624365) Wiwanitkit V (Acta dermatovenerologica Croatica : ADC 2010) 3 40

Products for LCE3C Gene

Sources for LCE3C Gene