LCE1D

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

Basic information

Region (hg38): 1:152796720-152798181

Links

ENSG00000172155 ∙ NCBI:353134 ∙ OMIM:612606 ∙ HGNC:29465 ∙ Uniprot:Q5T752 ∙ 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 LCE1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE1D 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	2		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	7	2	0

Variants in LCE1D

This is a list of pathogenic ClinVar variants found in the LCE1D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152797855-A-C		not specified	Likely benign (Aug 16, 2022)
1-152797871-C-T		not specified	Uncertain significance (Nov 29, 2023)
1-152797916-G-A		not specified	Uncertain significance (Dec 13, 2021)
1-152797978-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-152797988-G-A		not specified	Uncertain significance (Jul 05, 2022)
1-152797993-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-152797997-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-152798041-C-T		not specified	Likely benign (Dec 21, 2023)
1-152798101-G-A		not specified	Uncertain significance (Apr 08, 2024)
1-152798114-G-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE1D	protein_coding	protein_coding	ENST00000326233	1	1431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00406	0.434	115551	33	111	115695	0.000623

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0392	66	65.1	1.01	0.00000332	733
Missense in Polyphen
Synonymous	-1.19	35	27.1	1.29	0.00000150	222
Loss of Function	-0.437	3	2.29	1.31	9.72e-8	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00995	0.00803
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000131	0.0000900
Middle Eastern	0.00	0.00
South Asian	0.0000339	0.0000339
Other	0.000537	0.000356

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.587
• rvis_EVS: 1.77
• rvis_percentile_EVS: 96.77

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

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;cognition;cellular response to calcium ion
• Cellular component: cornified envelope;cytoplasm;perinuclear region of cytoplasm
• Molecular function: structural molecule activity;protein binding