PPL

periplakin, the group of Plakins

Basic information

Region (hg38): 16:4882506-4960741

Links

ENSG00000118898 ∙ NCBI:5493 ∙ OMIM:602871 ∙ HGNC:9273 ∙ Uniprot:O60437 ∙ 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 PPL gene.

• Inborn genetic diseases (128 variants)
• not provided (50 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPL 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				11	11	22
missense			125	16	10	151
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	125	27	23

Variants in PPL

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

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

Position	Type	Phenotype	Significance	ClinVar
16-4883401-C-G		not specified	Uncertain significance (Dec 21, 2023)
16-4883408-C-G			Likely benign (Jul 01, 2022)
16-4883416-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-4883477-C-G		not specified	Uncertain significance (Jul 13, 2022)
16-4883544-T-A		not specified	Uncertain significance (Feb 27, 2023)
16-4883544-T-C		not specified	Uncertain significance (Nov 13, 2023)
16-4883573-G-T		not specified	Uncertain significance (Jun 22, 2021)
16-4883616-A-G		not specified	Uncertain significance (Jan 25, 2023)
16-4883651-C-T			Likely benign (Jul 01, 2022)
16-4883680-C-G		not specified	Uncertain significance (Nov 21, 2023)
16-4883685-G-C		not specified	Uncertain significance (May 04, 2022)
16-4883715-C-G		not specified	Uncertain significance (Aug 04, 2023)
16-4883728-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-4883752-C-T		not specified	Uncertain significance (May 11, 2022)
16-4883758-T-C		not specified	Uncertain significance (Feb 15, 2023)
16-4883761-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-4883839-T-A		not specified	Uncertain significance (Jul 20, 2022)
16-4883860-T-C		not specified	Uncertain significance (Jun 18, 2021)
16-4883865-C-T		not specified	Uncertain significance (Jan 02, 2024)
16-4883874-C-T		not specified	Conflicting classifications of pathogenicity (Feb 01, 2024)
16-4883883-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-4883893-T-C		not specified	Uncertain significance (Sep 26, 2022)
16-4883916-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-4883925-A-G		not specified	Uncertain significance (Jun 14, 2022)
16-4884006-T-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPL	protein_coding	protein_coding	ENST00000345988	22	78235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-42	0.000143	125495	1	252	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.66	1408	1.07e+3	1.31	0.0000744	11425
Missense in Polyphen		414	305.05	1.3572		3382
Synonymous	-4.86	603	469	1.29	0.0000322	3418
Loss of Function	1.33	72	85.2	0.845	0.00000443	948

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00205	0.00204
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00120	0.00120
Finnish	0.000981	0.000924
European (Non-Finnish)	0.000796	0.000783
Middle Eastern	0.00120	0.00120
South Asian	0.00193	0.00190
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cornified envelope of keratinocytes. May link the cornified envelope to desmosomes and intermediate filaments. May act as a localization signal in PKB/AKT-mediated signaling. {ECO:0000269|PubMed:9412476}.
• Pathway: miR-targeted genes in epithelium - TarBase;Keratinization;Developmental Biology;Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.300

Intolerance Scores

• loftool: 0.597
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.55

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.564
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.894

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ppl
• Phenotype: normal phenotype

Gene ontology

• Biological process: response to mechanical stimulus;wound healing;intermediate filament cytoskeleton organization;cornification
• Cellular component: cornified envelope;nucleus;cytoplasm;mitochondrion;cytosol;cytoskeleton;intermediate filament;membrane;desmosome;extracellular exosome
• Molecular function: structural molecule activity;structural constituent of cytoskeleton;protein binding;cadherin binding