LCE3D

late cornified envelope 3D, the group of Late cornified envelope proteins

Basic information

Region (hg38): 1:152579381-152580516

Previous symbols: [ "SPRL6B", "SPRL6A" ]

Links

ENSG00000163202 ∙ NCBI:84648 ∙ OMIM:612616 ∙ HGNC:16615 ∙ Uniprot:Q9BYE3 ∙ 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 LCE3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE3D 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 LCE3D

This is a list of pathogenic ClinVar variants found in the LCE3D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152579696-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-152579699-C-T		not specified	Uncertain significance (Sep 28, 2021)
1-152579746-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-152579752-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-152579761-C-T		not specified	Likely benign (Jun 29, 2023)
1-152579762-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-152579786-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-152579804-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-152579812-C-T		not specified	Uncertain significance (May 17, 2023)
1-152579830-C-A		not specified	Uncertain significance (Dec 21, 2023)
1-152579885-A-G		not specified	Uncertain significance (Dec 02, 2021)
1-152579905-T-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE3D	protein_coding	protein_coding	ENST00000368787	1	1124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0206	0.534	125663	0	5	125668	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.767	70	54.1	1.29	0.00000339	594
Missense in Polyphen
Synonymous	-1.75	33	22.4	1.47	0.00000133	189
Loss of Function	-0.237	2	1.67	1.20	7.20e-8	18

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
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)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.837
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.0589
• hipred: N
• hipred_score: 0.112
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

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