PKP4

plakophilin 4, the group of p120 catenin family|Armadillo repeat containing

Basic information

Region (hg38): 2:158456951-158682879

Links

ENSG00000144283 ∙ NCBI:8502 ∙ OMIM:604276 ∙ HGNC:9026 ∙ Uniprot:Q99569 ∙ 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 PKP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKP4 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				169	1	170
missense			246	6		252
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				2		2
non coding				1	31	32
Total	0	0	246	176	33

Variants in PKP4

This is a list of pathogenic ClinVar variants found in the PKP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-158532879-C-T			Benign (Jun 19, 2021)
2-158533189-C-T		not specified	Uncertain significance (Jun 22, 2024)
2-158533204-C-A		not specified	Uncertain significance (Oct 02, 2023)
2-158533208-A-G		not specified	Likely benign (May 11, 2023)
2-158533209-T-C		not specified	Likely benign (Oct 18, 2019)
2-158533221-G-A		not specified	Uncertain significance (Oct 20, 2023)
2-158533237-G-T		not specified	Uncertain significance (Feb 14, 2022)
2-158533240-A-G		not specified	Uncertain significance (May 03, 2023)
2-158533250-C-G		not specified	Likely benign (Jun 29, 2019)
2-158533250-C-T			Benign (May 05, 2021)
2-158533255-C-G		not specified	Uncertain significance (May 21, 2023)
2-158533266-A-C		not specified	Uncertain significance (May 11, 2023)
2-158533274-C-T		not specified	Likely benign (May 27, 2021)
2-158533275-G-A		not specified	Uncertain significance (Oct 25, 2023)
2-158533277-G-C		not specified	Uncertain significance (Jul 25, 2022)
2-158533314-C-A		not specified	Uncertain significance (Nov 14, 2021)
2-158577156-A-G			Benign (May 14, 2021)
2-158577274-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-158577295-C-G		not specified	Uncertain significance (Jun 02, 2024)
2-158577296-G-A		not specified	Uncertain significance (May 09, 2022)
2-158577315-G-A		not specified	Likely benign (Mar 07, 2023)
2-158577336-A-G		not specified	Likely benign (Jul 21, 2020)
2-158577340-A-G		not specified	Uncertain significance (Oct 27, 2022)
2-158577342-A-G		not specified	Likely benign (Jul 16, 2023)
2-158577345-T-C		not specified	Likely benign (Jan 29, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKP4	protein_coding	protein_coding	ENST00000389759	21	225916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-13	1.00	124318	34	1396	125748	0.00570

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.973	613	685	0.895	0.0000391	7633
Missense in Polyphen		167	217.26	0.76865		2581
Synonymous	0.382	267	275	0.971	0.0000164	2459
Loss of Function	3.97	32	67.1	0.477	0.00000401	719

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0405	0.0405
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.000163	0.000163
South Asian	0.000755	0.000719
Other	0.00408	0.00408

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a regulator of Rho activity during cytokinesis. May play a role in junctional plaques. {ECO:0000269|PubMed:17115030}.
• Pathway: Keratinization;Developmental Biology;TCR;Fibroblast growth factor-1;EGFR1;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.319
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.32

Haploinsufficiency Scores

• pHI: 0.753
• hipred: Y
• hipred_score: 0.698
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkp4
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cell-cell junction assembly;cell-cell signaling;regulation of cell adhesion;keratinization;positive regulation of cytokinesis;positive regulation of GTPase activity;cornification;cell-cell adhesion
• Cellular component: spindle pole;cornified envelope;nucleus;cytoplasm;cytoskeleton;plasma membrane;cell-cell junction;cell-cell adherens junction;cytoplasmic side of plasma membrane;postsynaptic density;cell junction;desmosome;midbody;cell-cell contact zone;perinuclear region of cytoplasm;spindle midzone;mitotic spindle
• Molecular function: protein binding;cadherin binding