LCE3A Gene

HGNC Family	Late cornified envelope proteins (LCE)
Name	late cornified envelope 3A
Description	Involved in defense response to Gram-negative bacterium; defense response to Gram-positive bacterium; and killing of cells of another organism. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n LCE3A is one of several genes encoding late cornified envelope proteins that are expressed in terminally differentiated keratinocytes and that play roles in skin barrier function and innate host defense. In psoriasis, genetic variants near LCE3A have been implicated in disease susceptibility, particularly in the presence of the HLA‐Cw6 allele. Studies have demonstrated that in psoriatic skin, LCE3A expression is significantly upregulated, especially in patients with the risk genotype, sometimes as a consequence of a deletion of adjacent LCE3B and LCE3C genes – a genetic change that appears to trigger compensatory LCE3A overexpression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " Moreover, regulatory investigations identified an enhancer region upstream of LCE3A harboring a functional SNP that disrupts STAT3 binding; in the presence of IL‑6 and the HLA‐Cw6 allele, phosphorylated STAT3 translocates to the nucleus to activate LCE3A transcription in keratinocytes of psoriatic lesions."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " Further analyses in diverse populations have confirmed that polymorphisms within the LCE gene cluster – including those influencing LCE3A – are associated with psoriasis susceptibility."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Functional studies have also demonstrated that LCE3A, along with its LCE3 counterparts, exhibits defensin-like antimicrobial activity, suggesting that beyond its structural role in the cornified envelope, LCE3A contributes to the modulation of the skin microbiota and to cutaneous innate immunity"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": ";."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Aditi Chandra, Anirudhya Lahiri, Swapan Senapati, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Increased Risk of Psoriasis due to combined effect of HLA-Cw6 and LCE3 risk alleles in Indian population."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/srep24059"}], "href": "https://doi.org/10.1038/srep24059"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27048876"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27048876"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Aditi Chandra, Shantanab Das, Sayani Mazumder, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Functional Mapping of Genetic Interactions between HLA-Cw6 and LCE3A in Psoriasis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Invest Dermatol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jid.2021.04.020"}], "href": "https://doi.org/10.1016/j.jid.2021.04.020"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34029573"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34029573"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Li Sun, Yuting Cao, Nagonbilig He, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Association between LCE gene polymorphisms and psoriasis vulgaris among Mongolians from Inner Mongolia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Arch Dermatol Res (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00403-018-1813-0"}], "href": "https://doi.org/10.1007/s00403-018-1813-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29397434"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29397434"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Nathan K Archer, Migena N Dilolli, Lloyd S Miller "}, {"type": "b", "children": [{"type": "t", "text": "Pushing the Envelope in Psoriasis: Late Cornified Envelope Proteins Possess Antimicrobial Activity."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Invest Dermatol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jid.2017.08.026"}], "href": "https://doi.org/10.1016/j.jid.2017.08.026"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29055413"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29055413"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Hanna Niehues, Danique A van der Krieken, Thomas H A Ederveen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Antimicrobial Late Cornified Envelope Proteins: The Psoriasis Risk Factor Deletion of LCE3B/C Genes Affects Microbiota Composition."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Invest Dermatol (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jid.2021.11.036"}], "href": "https://doi.org/10.1016/j.jid.2021.11.036"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34942199"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34942199"}]}]}]}
Synonyms	LEP13
Proteins	LCE3A_HUMAN
NCBI Gene ID	353142
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

LCE3A has 1,147 functional associations with biological entities spanning 9 categories (molecular profile, organism, functional term, phrase or reference, disease, phenotype or trait, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 55 datasets.

Click the + buttons to view associations for LCE3A from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

LCE3A Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of LCE3A gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of LCE3A gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of LCE3A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of LCE3A gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of LCE3A gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of LCE3A gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of LCE3A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of LCE3A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of LCE3A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with LCE3A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with LCE3A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of LCE3A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with LCE3A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by LCE3A gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with LCE3A gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with LCE3A gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with LCE3A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with LCE3A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with LCE3A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at LCE3A gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of LCE3A gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of LCE3A gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	GAD Gene-Disease Associations	diseases associated with LCE3A gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with LCE3A gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	gene perturbations changing expression of LCE3A gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	kinase perturbations changing expression of LCE3A gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of LCE3A gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	transcription factor perturbations changing expression of LCE3A gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Viral Infections	virus perturbations changing expression of LCE3A gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset.
	GO Biological Process Annotations 2015	biological processes involving LCE3A gene from the curated GO Biological Process Annotations 2015 dataset.
	GO Biological Process Annotations 2023	biological processes involving LCE3A gene from the curated GO Biological Process Annotations 2023 dataset.
	GO Biological Process Annotations 2025	biological processes involving LCE3A gene from the curated GO Biological Process Annotations2025 dataset.
	GTEx eQTL 2025	SNPs regulating expression of LCE3A gene from the GTEx eQTL 2025 dataset.
	GTEx Tissue Gene Expression Profiles	tissues with high or low expression of LCE3A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
	GTEx Tissue Gene Expression Profiles 2023	tissues with high or low expression of LCE3A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
	GWAS Catalog SNP-Phenotype Associations 2025	phenotypes associated with LCE3A gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	cell lines with high or low expression of LCE3A gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset.
	HuBMAP Azimuth Cell Type Annotations	cell types associated with LCE3A gene from the HuBMAP Azimuth Cell Type Annotations dataset.
	HuGE Navigator Gene-Phenotype Associations	phenotypes associated with LCE3A gene by text-mining GWAS publications from the HuGE Navigator Gene-Phenotype Associations dataset.
	InterPro Predicted Protein Domain Annotations	protein domains predicted for LCE3A protein from the InterPro Predicted Protein Domain Annotations dataset.
	JASPAR Predicted Human Transcription Factor Targets 2025	transcription factors regulating expression of LCE3A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
	JASPAR Predicted Transcription Factor Targets	transcription factors regulating expression of LCE3A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
	KEGG Pathways 2026	pathways involving LCE3A protein from the KEGG Pathways 2026 dataset.
	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	cell lines with high or low copy number of LCE3A gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
	LOCATE Predicted Protein Localization Annotations	cellular components predicted to contain LCE3A protein from the LOCATE Predicted Protein Localization Annotations dataset.
	MotifMap Predicted Transcription Factor Targets	transcription factors regulating expression of LCE3A gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset.
	Pathway Commons Protein-Protein Interactions	interacting proteins for LCE3A from the Pathway Commons Protein-Protein Interactions dataset.
	Reactome Pathways 2024	pathways involving LCE3A protein from the Reactome Pathways 2024 dataset.
	Roadmap Epigenomics Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at LCE3A gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
	Rummagene Transcription Factor Associations 2026	transcription factors regulating expression of LCE3A gene from the Rummagene Transcription Factor Associations 2026 dataset.
	RummaGEO Drug Perturbation Signatures	drug perturbations changing expression of LCE3A gene from the RummaGEO Drug Perturbation Signatures dataset.
	RummaGEO Gene Perturbation Signatures	gene perturbations changing expression of LCE3A gene from the RummaGEO Gene Perturbation Signatures dataset.
	TCGA Signatures of Differentially Expressed Genes for Tumors	tissue samples with high or low expression of LCE3A gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.
	TISSUES Text-mining Tissue Protein Expression Evidence Scores	tissues co-occuring with LCE3A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset.
	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	tissues co-occuring with LCE3A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.