LCE1D

protein-coding

late cornified envelope 1D, the group of Late cornified envelope proteins

Gene summary

Enables identical protein binding activity. Involved in cognition. Acts upstream of or within cellular response to calcium ion. Located in cornified envelope and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_178352.3

Inheritance

—

ClinVar variants

U:18B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.31

Max pathogenic AF

—

Genomic locus

chr1:152,796,721-152,798,181

External References & Databases

Ensembl (ENSG00000172155)

Transcript & Mutation Effects

hg38 • Region Span ~1.5 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 LCE1D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178352.3. 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				1 clinvar		1
missense			18 clinvar	3 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	4	0	22

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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_178352.3	RefSeq	NP_848129.1	1	MANE Select
ENST00000326233.7	Ensembl	ENSP00000316737.6	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin D Receptor Pathway
Keratinization
Developmental Biology
Formation of the cornified envelope

Biological Process

peptide cross-linking
keratinocyte differentiation
keratinization
cognition
cellular response to calcium ion

Molecular Function

structural molecule activity
protein binding

Cellular Component

cornified envelope
cytoplasm
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326233
Coding exons: 1
Length: 1431
Individuals with no LoFs: 115551
Homozygous LoFs: 33
Heterozygous LoFs: 111
Defined: 115695
p: 0.000623

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0392	66	65.1	1.01	0.00000332	733
Missense (PolyPhen)
Synonymous	-1.19	35	27.1	1.29	0.00000150	222
Loss of Function	-0.437	3	2.29	1.31	9.72e-8	28

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0093	0.0074	notable
Latino/Admixed American	0.00060	0.00054	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.000090	rare
South Asian	0.000034	0.000034	rare
Other	0.00054	0.00036	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Precursors of the cornified envelope of the stratum corneum.;

Intolerance Scores

LoFtool: 0.587
RVIS EVS: 1.77
RVIS percentile EVS: 96.77

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.158

Gene Damage Prediction

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