LCE2D
protein-codinglate cornified envelope 2D, the group of Late cornified envelope proteins
Gene summary
Predicted to be involved in keratinization. [provided by Alliance of Genome Resources, Jul 2025]
- SPRL1A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.3 kbGenCC 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 LCE2D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_178430.4. 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 | 1 | ||||
| missense | 21 | 1 | 22 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 2 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_848517.1 | 1 | MANE Select | |
| Ensembl | ENSP00000357773.1 | 1 | MANE Select | |
| Ensembl | ENSP00000787125.1 | 1 | Standard | |
| Ensembl | ENSP00000787126.1 | 1 | Standard |
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
Molecular Function
- structural molecule activity
- protein binding
Cellular Component
- cornified envelope
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368784
- Coding exons
- 1
- Length
- 1264
- Individuals with no LoFs
- 125575
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125576
- p
- 0.00000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.659 | 81 | 65.9 | 1.23 | 0.00000362 | 719 |
| Missense (PolyPhen) | ||||||
| Synonymous | -0.607 | 27 | 23.3 | 1.16 | 0.00000109 | 218 |
| Loss of Function | -0.135 | 1 | 0.865 | 1.16 | 3.79e-8 | 6 |
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) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Precursors of the cornified envelope of the stratum corneum.;
Intolerance Scores
- LoFtool
- 0.489
- RVIS EVS
- 0.77
- RVIS percentile EVS
- 86.95
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.147
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |