LCE2A

late cornified envelope 2A, the group of Late cornified envelope proteins

Basic information

Region (hg38): 1:152698345-152699442

Links

ENSG00000187173 ∙ NCBI:353139 ∙ OMIM:612609 ∙ HGNC:29469 ∙ Uniprot:Q5TA79 ∙ 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 LCE2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE2A 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in LCE2A

This is a list of pathogenic ClinVar variants found in the LCE2A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152698982-G-T		not specified	Uncertain significance (Apr 07, 2022)
1-152698999-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-152699040-A-T		not specified	Uncertain significance (Jun 21, 2022)
1-152699049-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-152699061-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-152699124-C-T		not specified	Uncertain significance (Sep 22, 2022)
1-152699136-C-T		not specified	Uncertain significance (Feb 09, 2022)
1-152699137-G-A		not specified	Uncertain significance (May 14, 2024)
1-152699143-G-T		not specified	Uncertain significance (Jan 03, 2024)
1-152699160-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-152699160-T-G		not specified	Uncertain significance (Oct 03, 2022)
1-152699209-G-C		not specified	Uncertain significance (Aug 17, 2022)
1-152699212-A-G		not specified	Likely benign (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE2A	protein_coding	protein_coding	ENST00000368779	1	1079

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00717	0.550	125680	0	66	125746	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.03	85	62.2	1.37	0.00000360	690
Missense in Polyphen
Synonymous	-2.15	38	24.5	1.55	0.00000134	212
Loss of Function	0.0905	3	3.17	0.945	2.23e-7	26

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000237	0.000237
Middle Eastern	0.0000545	0.0000544
South Asian	0.00111	0.00111
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0914

Intolerance Scores

• loftool: 0.754
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• pHI: 0.0634
• hipred: N
• hipred_score: 0.123
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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
• Cellular component: cornified envelope;cytoplasm
• Molecular function: structural molecule activity;protein binding