LCE3A
Basic information
Region (hg38): 1:152622834-152623103
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE3A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 1 |
Variants in LCE3A
This is a list of pathogenic ClinVar variants found in the LCE3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-152622847-G-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 1-152622859-C-A | not specified | Uncertain significance (Dec 14, 2023) | ||
| 1-152622886-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
| 1-152622974-C-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 1-152622976-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 1-152623015-G-A | not specified | Uncertain significance (Jun 03, 2022) | ||
| 1-152623067-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-152623082-G-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 1-152623089-C-G | Benign (Mar 29, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LCE3A | protein_coding | protein_coding | ENST00000335674 | 1 | 270 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.257 | 57 | 51.8 | 1.10 | 0.00000321 | 588 |
| Missense in Polyphen | ||||||
| Synonymous | 0.364 | 19 | 21.1 | 0.899 | 0.00000127 | 171 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- 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}.;
- Pathway
- Keratinization;Developmental Biology;Formation of the cornified envelope
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.353
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 69.83
Haploinsufficiency Scores
- pHI
- 0.0962
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0638
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- peptide cross-linking;keratinocyte differentiation;keratinization;killing of cells of other organism;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
- Cellular component
- cornified envelope;cytoplasm
- Molecular function
- structural molecule activity