LCE2B

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

Basic information

Region (hg38): 1:152686123-152687397

Previous symbols: [ "SPRL1B" ]

Links

ENSG00000159455 ∙ NCBI:26239 ∙ OMIM:612610 ∙ HGNC:16610 ∙ Uniprot:O14633 ∙ 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 LCE2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCE2B 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in LCE2B

This is a list of pathogenic ClinVar variants found in the LCE2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152686902-G-T		not specified	Uncertain significance (Aug 09, 2021)
1-152686907-C-G		not specified	Uncertain significance (Aug 12, 2021)
1-152686917-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-152686928-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-152686949-T-C		not specified	Uncertain significance (Mar 29, 2022)
1-152686964-T-G		not specified	Uncertain significance (Nov 07, 2022)
1-152686965-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-152687052-G-T		not specified	Uncertain significance (Oct 13, 2023)
1-152687090-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-152687139-G-C		not specified	Uncertain significance (Mar 21, 2024)
1-152687169-G-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCE2B	protein_coding	protein_coding	ENST00000368780	1	12107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0979	0.595	125703	0	1	125704	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.84	104	62.9	1.65	0.00000344	707
Missense in Polyphen
Synonymous	-2.23	37	23.3	1.59	0.00000111	221
Loss of Function	0.116	1	1.13	0.883	4.93e-8	9

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)	0.00000879	0.00000879
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: Vitamin D Receptor Pathway;Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0912

Intolerance Scores

• loftool: 0.541
• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.96

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: epidermis development;peptide cross-linking;keratinocyte differentiation;keratinization
• Cellular component: cornified envelope;cellular_component;cytoplasm
• Molecular function: molecular_function;structural molecule activity