LCE1C

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

Basic information

Region (hg38): 1:152804831-152806651

Links

ENSG00000197084 ∙ NCBI:353133 ∙ OMIM:612605 ∙ HGNC:29464 ∙ Uniprot:Q5T751 ∙ 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 LCE1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE1C 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			3	1	2	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	2

Variants in LCE1C

This is a list of pathogenic ClinVar variants found in the LCE1C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152805162-C-T			Benign (Aug 16, 2018)
1-152805174-C-A		not specified	Uncertain significance (Mar 01, 2023)
1-152805220-A-G		not specified	Likely benign (Feb 16, 2023)
1-152805279-C-A			Benign (Apr 04, 2018)
1-152805292-T-C		not specified	Uncertain significance (May 02, 2024)
1-152805366-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-152805372-T-C		not specified	Uncertain significance (Apr 09, 2024)
1-152805445-G-T		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE1C	protein_coding	protein_coding	ENST00000368768	1	1797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0280	0.596	125720	0	19	125739	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.574	80	66.8	1.20	0.00000348	759
Missense in Polyphen
Synonymous	-3.89	53	27.2	1.95	0.00000141	234
Loss of Function	0.119	2	2.19	0.913	9.38e-8	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
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)

Intolerance Scores

• loftool: 0.528
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• pHI: 0.0515
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

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