LCE3A

protein-coding

late cornified envelope 3A, the group of Late cornified envelope proteins

Gene summary

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, Jul 2025]

MANE transcript

NM_178431.1

Inheritance

—

ClinVar variants

U:13B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr1:152,622,834-152,623,103

External References & Databases

Ensembl (ENSG00000185962)

Transcript & Mutation Effects

hg38 • Region Span ~0.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LCE3A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 13

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178431.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			13 clinvar		1 clinvar	14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	0	1	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178431.1	RefSeq	NP_848518.1	1	MANE Select
ENST00000335674.1	Ensembl	ENSP00000335006.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Keratinization
Developmental Biology
Formation of the cornified envelope

Biological Process

peptide cross-linking
keratinocyte differentiation
keratinization
killing of cells of other organism
defense response to Gram-negative bacterium

Molecular Function

structural molecule activity

Cellular Component

cornified envelope
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335674
Coding exons: 1
Length: 270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.257	57	51.8	1.10	0.00000321	588
Missense (PolyPhen)
Synonymous	0.364	19	21.1	0.899	0.00000127	171
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: 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). {ECO:0000269|PubMed:28634035, ECO:0000305|PubMed:28634035}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.353
RVIS EVS: 0.26
RVIS percentile EVS: 69.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0638

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium