PKP3

plakophilin 3, the group of Armadillo repeat containing|Plakophilins

Basic information

Region (hg38): 11:392614-404908

Links

ENSG00000184363 ∙ NCBI:11187 ∙ OMIM:605561 ∙ HGNC:9025 ∙ Uniprot:Q9Y446 ∙ 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 PKP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKP3 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				4	1	5
missense			87	4	2	93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	8	3

Variants in PKP3

This is a list of pathogenic ClinVar variants found in the PKP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-392702-G-A			Likely benign (May 01, 2022)
11-394299-G-A		not specified	Uncertain significance (Aug 09, 2021)
11-394321-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-394354-C-T		not specified	Uncertain significance (Jan 29, 2024)
11-394387-G-A		not specified	Uncertain significance (Aug 20, 2024)
11-394389-G-A		not specified	Uncertain significance (Jul 12, 2023)
11-394410-C-T		Neutropenia;Lymphopenia	Uncertain significance (-)
11-394417-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-394423-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-394446-G-A		not specified	Uncertain significance (Dec 16, 2023)
11-394477-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-394485-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-394491-G-A		not specified	Uncertain significance (Nov 08, 2024)
11-394523-A-C		not specified	Uncertain significance (Jan 03, 2022)
11-396671-G-C		not specified	Uncertain significance (Mar 25, 2024)
11-396674-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-396686-C-T		not specified	Uncertain significance (Dec 19, 2023)
11-396821-G-A		not specified	Uncertain significance (May 03, 2023)
11-396823-C-G		not specified	Uncertain significance (May 23, 2023)
11-396865-C-T			Benign (Feb 09, 2018)
11-396866-G-A		not specified	Uncertain significance (Apr 25, 2022)
11-396871-G-T		not specified	Uncertain significance (Feb 23, 2023)
11-396874-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-396892-C-T		not specified	Uncertain significance (May 11, 2022)
11-396893-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKP3	protein_coding	protein_coding	ENST00000331563	13	12295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000628	0.999	125103	1	28	125132	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.734	523	478	1.09	0.0000339	4982
Missense in Polyphen		203	192.96	1.052		1897
Synonymous	-1.98	258	221	1.17	0.0000162	1736
Loss of Function	2.88	12	28.6	0.420	0.00000162	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.000106	0.0000997
East Asian	0.000117	0.000109
Finnish	0.000261	0.000185
European (Non-Finnish)	0.000121	0.000115
Middle Eastern	0.000117	0.000109
South Asian	0.000138	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in junctional plaques.
• Pathway: Keratinization;Developmental Biology;EGFR1;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.507
• hipred: Y
• hipred_score: 0.670
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.407

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkp3
• Phenotype: immune system phenotype; normal phenotype; cellular 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); growth/size/body region phenotype

Gene ontology

• Biological process: desmosome assembly;regulation of translation;cell-cell junction assembly;positive regulation of gene expression;keratinization;cornification;protein localization to plasma membrane;cell-cell adhesion;negative regulation of mRNA catabolic process
• Cellular component: cornified envelope;nucleus;nucleoplasm;cytoplasm;plasma membrane;cell-cell junction;cell-cell adherens junction;cell junction;desmosome;messenger ribonucleoprotein complex
• Molecular function: RNA binding;protein binding;enzyme binding;translation regulator activity;alpha-catenin binding;cadherin binding;cell adhesion molecule binding;cadherin binding involved in cell-cell adhesion