Aliases for LCE2D Gene

Aliases for LCE2D Gene

  • Late Cornified Envelope 2D 2 3 5
  • Small Proline-Rich-Like Epidermal Differentiation Complex Protein 1A 3 4
  • Small Proline Rich-Like (Epidermal Differentiation Complex) 1A 2 3
  • Late Cornified Envelope Protein 2D 3 4
  • Late Envelope Protein 12 3 4
  • SPRL1A 3 4
  • LEP12 3 4

External Ids for LCE2D Gene

Previous HGNC Symbols for LCE2D Gene

  • SPRL1A

Previous GeneCards Identifiers for LCE2D Gene

  • GC01P149449
  • GC01P150903
  • GC01P152635
  • GC01P124009

Summaries for LCE2D Gene

GeneCards Summary for LCE2D Gene

LCE2D (Late Cornified Envelope 2D) is a Protein Coding gene. Among its related pathways are Keratinization and Developmental Biology. An important paralog of this gene is LCE2C.

UniProtKB/Swiss-Prot Summary for LCE2D Gene

Additional gene information for LCE2D Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LCE2D Gene

Genomics for LCE2D Gene

GeneHancer (GH) Regulatory Elements for LCE2D Gene

Promoters and enhancers for LCE2D 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
GH01J152663 Promoter 0.4 EPDnew 500.7 0.0 -19 0.1 BHLHE40 LCE2D ENSG00000285753 LCEP3
GH01J152655 Promoter 0.3 EPDnew 500.4 -7.9 -7946 0.1 ENSG00000285753 LCEP3 LINC00302 LCE2D LCE3A LCE3D
GH01J152639 Enhancer 0.2 ENCODE 11.7 -22.9 -22906 1.2 RF00994-056 LCE2D LCE2C LCE2B LCE3D piR-43103-004
GH01J152675 Promoter 0.3 EPDnew 0.4 +11.9 11880 0.1 LCE2C LCE2D
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCE2D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCE2D

Top Transcription factor binding sites by QIAGEN in the LCE2D gene promoter:
  • AML1a
  • ATF6
  • NRSF form 1
  • NRSF form 2

Genomic Locations for LCE2D Gene

Genomic Locations for LCE2D Gene
chr1:152,663,380-152,664,659
(GRCh38/hg38)
Size:
1,280 bases
Orientation:
Plus strand
chr1:152,635,872-152,637,135
(GRCh37/hg19)
Size:
1,264 bases
Orientation:
Plus strand

Genomic View for LCE2D Gene

Genes around LCE2D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCE2D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCE2D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCE2D Gene

Proteins for LCE2D Gene

  • Protein details for LCE2D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TA82-LCE2D_HUMAN
    Recommended name:
    Late cornified envelope protein 2D
    Protein Accession:
    Q5TA82
    Secondary Accessions:
    • A1L4M8

    Protein attributes for LCE2D Gene

    Size:
    110 amino acids
    Molecular mass:
    11180 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Belongs to the LCE cluster present on 1q21.

neXtProt entry for LCE2D Gene

Post-translational modifications for LCE2D Gene

No Post-translational modifications

Other Protein References for LCE2D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LCE2D Gene

Domains & Families for LCE2D Gene

Gene Families for LCE2D Gene

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

Protein Domains for LCE2D Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LCE2D Gene

GenScript: Design optimal peptide antigens:
  • Small proline-rich-like epidermal differentiation complex protein 1A (LCE2D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5TA82

UniProtKB/Swiss-Prot:

LCE2D_HUMAN :
  • Belongs to the LCE family.
Family:
  • Belongs to the LCE family.
genes like me logo Genes that share domains with LCE2D: view

Function for LCE2D Gene

Molecular function for LCE2D Gene

UniProtKB/Swiss-Prot Function:
Precursors of the cornified envelope of the stratum corneum.
UniProtKB/Swiss-Prot Induction:
By calcium and UVB.

Phenotypes From GWAS Catalog for LCE2D Gene

Gene Ontology (GO) - Molecular Function for LCE2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LCE2D: view

Phenotypes for LCE2D Gene

genes like me logo Genes that share phenotypes with LCE2D: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE2D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCE2D Gene

Localization for LCE2D 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 LCE2D gene
Compartment Confidence
nucleus 2
plasma membrane 1
extracellular 1
cytosol 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 LCE2D Gene

Pathways & Interactions for LCE2D Gene

PathCards logo

SuperPathways for LCE2D Gene

genes like me logo Genes that share pathways with LCE2D: view

Pathways by source for LCE2D Gene

Gene Ontology (GO) - Biological Process for LCE2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008544 epidermis development IEA --
GO:0031424 keratinization IEA --
genes like me logo Genes that share ontologies with LCE2D: view

No data available for SIGNOR curated interactions for LCE2D Gene

Drugs & Compounds for LCE2D Gene

(1) Drugs for LCE2D Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with LCE2D: view

Transcripts for LCE2D Gene

mRNA/cDNA for LCE2D Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCE2D

Alternative Splicing Database (ASD) splice patterns (SP) for LCE2D Gene

No ASD Table

Relevant External Links for LCE2D Gene

GeneLoc Exon Structure for
LCE2D

Expression for LCE2D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCE2D Gene

mRNA differential expression in normal tissues according to GTEx for LCE2D Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x32.0) and Skin - Not Sun Exposed (Suprapubic) (x20.4).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCE2D

SOURCE GeneReport for Unigene cluster for LCE2D Gene:

Hs.490225

mRNA Expression by UniProt/SwissProt for LCE2D Gene:

Q5TA82-LCE2D_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 LCE2D Gene

  • Skin(2.3)
genes like me logo Genes that share expression patterns with LCE2D: view

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCE2D Gene

Orthologs for LCE2D Gene

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

Orthologs for LCE2D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LCE2D 31
  • 96 (a)
OneToOne
Species where no ortholog for LCE2D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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 LCE2D Gene

ENSEMBL:
Gene Tree for LCE2D (if available)
TreeFam:
Gene Tree for LCE2D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCE2D: view image

Paralogs for LCE2D Gene

genes like me logo Genes that share paralogs with LCE2D: view

Variants for LCE2D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCE2D Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs11205064 - p.Cys92Tyr

Additional dbSNP identifiers (rs#s) for LCE2D Gene

Structural Variations from Database of Genomic Variants (DGV) for LCE2D Gene

Variant ID Type Subtype PubMed ID
esv2750810 CNV gain 17911159
esv2758970 CNV gain+loss 17122850
esv33483 CNV gain+loss 17666407
esv3587564 CNV gain 21293372
nsv1005047 CNV loss 25217958
nsv469873 CNV loss 16826518
nsv547891 CNV loss 21841781

Variation tolerance for LCE2D Gene

Residual Variation Intolerance Score: 71.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.32; 26.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCE2D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCE2D

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCE2D Gene

Disorders for LCE2D Gene

Additional Disease Information for LCE2D

No disorders were found for LCE2D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LCE2D Gene

Publications for LCE2D Gene

  1. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  2. 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 54
  3. 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 54
  4. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3 54
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 54

Products for LCE2D Gene

Sources for LCE2D Gene