LCE2D

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

Basic information

Region (hg38): 1:152663380-152664659

Previous symbols: [ "SPRL1A" ]

Links

ENSG00000187223 ∙ NCBI:353141 ∙ OMIM:612612 ∙ HGNC:16518 ∙ Uniprot:Q5TA82 ∙ 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 LCE2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE2D 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in LCE2D

This is a list of pathogenic ClinVar variants found in the LCE2D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152664164-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-152664200-G-T		not specified	Uncertain significance (May 11, 2022)
1-152664208-C-G		not specified	Uncertain significance (Mar 26, 2024)
1-152664235-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-152664320-G-C		not specified	Uncertain significance (Jun 24, 2022)
1-152664369-C-A		not specified	Uncertain significance (Dec 06, 2021)
1-152664389-A-T		not specified	Uncertain significance (Dec 19, 2023)
1-152664401-C-G		not specified	Likely benign (Oct 03, 2022)
1-152664427-G-A		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE2D	protein_coding	protein_coding	ENST00000368784	1	1264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0852	0.573	125575	0	1	125576	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.659	81	65.9	1.23	0.00000362	719
Missense in Polyphen
Synonymous	-0.607	27	23.3	1.16	0.00000109	218
Loss of Function	-0.135	1	0.865	1.16	3.79e-8	6

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)	0.00000881	0.00000881
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: 0.489
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.95

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

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