LCE1A

protein-coding

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

Gene summary

LCE1A belongs to the late cornified envelope (LCE) gene cluster within the epidermal differentiation complex (EDC) on chromosome 1. The LCE cluster contains multiple conserved genes that encode stratum corneum proteins, and these genes are expressed relatively late during fetal assembly of the skin cornified envelope (Jackson et al., 2005 [PubMed 15854049]). For further information on the LCE gene cluster, see GENE FAMILY below.[supplied by OMIM, Feb 2009]

MANE transcript

NM_178348.2

Inheritance

—

ClinVar variants

U:22B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr1:152,827,473-152,828,097

External References & Databases

Ensembl (ENSG00000186844)

Transcript & Mutation Effects

hg38 • Region Span ~0.6 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 LCE1A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178348.2. 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			22 clinvar	4 clinvar		26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	4	0	26

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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_178348.2	RefSeq	NP_848125.1	1	MANE Select
ENST00000335123.4	Ensembl	ENSP00000334869.2	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
cornification

Molecular Function

structural molecule activity

Cellular Component

cornified envelope
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335123
Coding exons: 1
Length: 625
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.525	75	63.3	1.19	0.00000329	711
Missense (PolyPhen)
Synonymous	-1.59	36	25.8	1.40	0.00000142	216
Loss of Function	-0.360	3	2.40	1.25	1.02e-7	29

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

Intolerance Scores

LoFtool: 0.636
RVIS EVS: 0.04
RVIS percentile EVS: 56.64

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.179

Gene Damage Prediction

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