LCE3C

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

Basic information

Region (hg38): 1:152600234-152601086

Previous symbols: [ "SPRL3A" ]

Links

ENSG00000244057 ∙ NCBI:353144 ∙ OMIM:612615 ∙ HGNC:16612 ∙ Uniprot:Q5T5A8 ∙ 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 LCE3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE3C 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			4		3	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	4	0	3

Variants in LCE3C

This is a list of pathogenic ClinVar variants found in the LCE3C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152600868-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-152600927-C-T		not specified	Uncertain significance (May 03, 2023)
1-152600928-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-152600944-C-A			Benign (May 24, 2018)
1-152600975-G-A		not specified	Uncertain significance (Apr 04, 2024)
1-152600987-C-T			Benign (Jan 30, 2018)
1-152600988-G-A			Benign (Jun 21, 2018)
1-152600994-A-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE3C	protein_coding	protein_coding	ENST00000333881	1	425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.475	0.447	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.942	33	52.1	0.633	0.00000276	610
Missense in Polyphen
Synonymous	1.70	11	20.9	0.526	0.00000107	187
Loss of Function	1.21	0	1.72	0.00	7.36e-8	19

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: A structural component of the cornified envelope of the stratum corneum involved in innate cutaneous host defense (Probable). Possesses defensin-like antimicrobial activity against a broad spectrum of Gram-positive and Gram-negative bacteria, both aerobic and anaerobic species. Upon inflammation, may regulate skin barrier repair by shaping cutaneous microbiota composition and immune response to bacterial antigens (PubMed:28634035). {ECO:0000269|PubMed:28634035, ECO:0000305|PubMed:28634035}.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0820

Intolerance Scores

• loftool: 0.614
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.63

Haploinsufficiency Scores

• pHI: 0.0697
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00215

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;killing of cells of other organism;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: cornified envelope;cytoplasm
• Molecular function: structural molecule activity;protein binding