LCE1A

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

Basic information

Region (hg38): 1:152827473-152828097

Links

ENSG00000186844 ∙ NCBI:353131 ∙ OMIM:612603 ∙ HGNC:29459 ∙ Uniprot:Q5T7P2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCE1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE1A 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in LCE1A

This is a list of pathogenic ClinVar variants found in the LCE1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-152827483-A-G		not specified	Uncertain significance (May 06, 2022)
1-152827566-A-G		not specified	Uncertain significance (Nov 18, 2022)
1-152827627-G-T		not specified	Uncertain significance (Nov 17, 2023)
1-152827660-G-A		not specified	Uncertain significance (May 15, 2024)
1-152827756-C-A		not specified	Uncertain significance (Jan 30, 2024)
1-152827775-C-G		not specified	Uncertain significance (Oct 30, 2023)
1-152827779-G-A		not specified	Likely benign (Nov 28, 2023)
1-152827780-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-152827797-T-G		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE1A	protein_coding	protein_coding	ENST00000335123	1	625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00437	0.449	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.525	75	63.3	1.19	0.00000329	711
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Precursors of the cornified envelope of the stratum corneum.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.636
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.146
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

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;cornification
• Cellular component: cornified envelope;cytoplasm;cytosol
• Molecular function: structural molecule activity