EVPL

envoplakin, the group of Plakins

Basic information

Region (hg38): 17:76004502-76027306

Links

ENSG00000167880 ∙ NCBI:2125 ∙ OMIM:601590 ∙ HGNC:3503 ∙ Uniprot:Q92817 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EVPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVPL 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				5		5
missense			212	15	1	228
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	212	20	1

Variants in EVPL

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

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

Position	Type	Phenotype	Significance	ClinVar
17-76005298-C-G		not specified	Uncertain significance (Feb 27, 2024)
17-76005350-C-A		not specified	Uncertain significance (Nov 25, 2024)
17-76005410-G-A		not specified	Uncertain significance (Apr 17, 2024)
17-76007108-G-A		not specified	Uncertain significance (Jul 26, 2022)
17-76007119-G-T		not specified	Uncertain significance (Feb 14, 2023)
17-76007123-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-76007128-G-T		not specified	Uncertain significance (Dec 22, 2023)
17-76007129-G-A		not specified	Uncertain significance (Dec 10, 2024)
17-76007141-G-A		not specified	Uncertain significance (May 11, 2022)
17-76007186-C-T		not specified	Uncertain significance (Jan 17, 2024)
17-76007187-G-T		not specified	Uncertain significance (Apr 22, 2024)
17-76007196-G-T		not specified	Uncertain significance (Jul 05, 2024)
17-76007209-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-76007222-C-T		not specified	Uncertain significance (Jun 07, 2023)
17-76007236-C-T		not specified	Uncertain significance (Jun 07, 2023)
17-76007237-G-A		not specified	Uncertain significance (Jun 22, 2021)
17-76007321-C-T		not specified	Uncertain significance (Nov 27, 2024)
17-76007359-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-76007381-C-T		not specified	Uncertain significance (May 31, 2023)
17-76007403-G-T		not specified	Uncertain significance (Apr 27, 2024)
17-76007414-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-76007420-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-76007423-G-A		not specified	Uncertain significance (Oct 27, 2022)
17-76007444-C-T		not specified	Likely benign (Dec 19, 2023)
17-76007469-C-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVPL	protein_coding	protein_coding	ENST00000301607	22	22951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.70e-25	1.00	125463	1	284	125748	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.307	1302	1.27e+3	1.02	0.0000924	13012
Missense in Polyphen		347	357.22	0.97139		3803
Synonymous	-0.340	574	564	1.02	0.0000402	4154
Loss of Function	3.55	54	90.4	0.597	0.00000460	974

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00337	0.00272
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.00134	0.00131
Finnish	0.000407	0.000370
European (Non-Finnish)	0.00128	0.00122
Middle Eastern	0.00134	0.00131
South Asian	0.00163	0.00160
Other	0.00165	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cornified envelope of keratinocytes. May link the cornified envelope to desmosomes and intermediate filaments.
• Pathway: Keratinization;Developmental Biology;Validated transcriptional targets of TAp63 isoforms;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.859
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.9

Haploinsufficiency Scores

• pHI: 0.458
• hipred: Y
• hipred_score: 0.530
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evpl
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: epidermis development;peptide cross-linking;keratinocyte differentiation;wound healing;intermediate filament cytoskeleton organization;cornification
• Cellular component: cornified envelope;cytoplasm;cytosol;intermediate filament;membrane;desmosome;intermediate filament cytoskeleton;extracellular exosome
• Molecular function: structural molecule activity;intermediate filament binding;protein binding, bridging;cadherin binding