LENEP

lens epithelial protein

Basic information

Region (hg38): 1:154993586-154994315

Links

ENSG00000163352 ∙ NCBI:55891 ∙ OMIM:607377 ∙ HGNC:14429 ∙ Uniprot:Q9Y5L5 ∙ 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 LENEP gene.

Variants pathogenicity by type

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

Variants in LENEP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-154993669-G-C		not specified	Uncertain significance (Oct 03, 2022)
1-154993695-A-C		not specified	Uncertain significance (Jan 04, 2024)
1-154993746-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LENEP	protein_coding	protein_coding	ENST00000392487	1	730

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00339	0.400	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.400	29	35.7	0.812	0.00000206	376
Missense in Polyphen		1	3.4975	0.28592		36
Synonymous	-0.691	19	15.5	1.22	7.38e-7	139
Loss of Function	-0.636	3	2.02	1.48	1.54e-7	10

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: May play a role in lens epithelial cell differentiation.

Recessive Scores

• pRec: 0.0676

Intolerance Scores

• loftool: 0.481
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.170
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lenep

Gene ontology

• Biological process: multicellular organism development
• Molecular function: DNA binding