LELP1

late cornified envelope like proline rich 1

Basic information

Region (hg38): 1:153203430-153205120

Links

ENSG00000203784 ∙ NCBI:149018 ∙ OMIM:611042 ∙ HGNC:32046 ∙ Uniprot:Q5T871 ∙ 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 LELP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LELP1 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			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	6	0	0

Variants in LELP1

This is a list of pathogenic ClinVar variants found in the LELP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153204715-G-C		not specified	Uncertain significance (Feb 06, 2023)
1-153204717-G-C		not specified	Uncertain significance (Dec 08, 2023)
1-153204765-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-153204811-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-153204846-T-C		not specified	Uncertain significance (Mar 24, 2023)
1-153204945-C-G		not specified	Uncertain significance (Jan 08, 2024)
1-153204973-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LELP1	protein_coding	protein_coding	ENST00000368747	1	1678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.428	0.470	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.290	60	54.0	1.11	0.00000281	643
Missense in Polyphen		10	7.8273	1.2776		75
Synonymous	-0.109	22	21.4	1.03	0.00000127	183
Loss of Function	1.06	0	1.30	0.00	5.64e-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

• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0794

Intolerance Scores

• loftool: 0.510
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.153
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000725

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lelp1

Gene ontology

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