LCE3D late cornified envelope 3D [Homo sapiens (human)] - Gene

Summary

Official Symbol: LCE3Dprovided by HGNC
Official Full Name: late cornified envelope 3Dprovided by HGNC
Primary source: HGNC:HGNC:16615
See related: Ensembl:ENSG00000163202 MIM:612616; AllianceGenome:HGNC:16615
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LEP16; SPRL6A; SPRL6B
Summary: Predicted to be involved in keratinization. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
Expression: Biased expression in skin (RPKM 6.3) and esophagus (RPKM 3.1) See more
Orthologs: all
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Genomic context

Location:: 1q21.3

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (152579381..152580516, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (151715934..151717069, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (152551857..152552992, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

genetic polymorphism is associated with psoriasis vulgaris among Mongolians from Inner Mongolia
Title: Association between LCE gene polymorphisms and psoriasis vulgaris among Mongolians from Inner Mongolia.
We identified significant combined effects between MHC and LCE, MHC and IL12B on the risk of psoriasis in Chinese population.
Title: Variants in MHC, LCE and IL12B have epistatic effects on psoriasis risk in Chinese population.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21.
paper describing nomenclature changes and expression in range of tissues and in response to UV
Title: Late cornified envelope family in differentiating epithelia--response to calcium and ultraviolet irradiation.
LEP16 is one of a cluster of 16-20 related genes at 1q21 which includes XP5. Proteins incorporate into the cornified envelope of stratified, terminally differentiating epithelia. LEP16 transcripts detected in heart, skin and esophagus.
Title: Differentially expressed late constituents of the epidermal cornified envelope.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:483458

NoName (e-PCR)
- UniSTS:480714

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in epidermis development	IEA Inferred from Electronic Annotation more info
involved_in keratinization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: late cornified envelope protein 3D

Names: late envelope protein 16; small proline rich-like (epidermal differentiation complex) 6A; small proline rich-like (epidermal differentiation complex) 6B; small proline-rich-like epidermal differentiation complex protein 6A; small proline-rich-like epidermal differentiation complex protein 6B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.