PRICKLE3

prickle planar cell polarity protein 3, the group of Prickle planar cell polarity proteins|LIM domain containing

Basic information

Region (hg38): X:49174801-49186528

Previous symbols: [ "LMO6" ]

Links

ENSG00000012211 ∙ NCBI:4007 ∙ OMIM:300111 ∙ HGNC:6645 ∙ Uniprot:O43900 ∙ 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 PRICKLE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRICKLE3 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				2		2
missense			38	1		39
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	3	0

Variants in PRICKLE3

This is a list of pathogenic ClinVar variants found in the PRICKLE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-49175699-G-C		not specified	Uncertain significance (Mar 22, 2023)
X-49175707-C-G		not specified	Uncertain significance (Dec 27, 2023)
X-49175708-G-C		not specified	Uncertain significance (Jan 26, 2023)
X-49175738-G-A		not specified	Uncertain significance (Sep 27, 2021)
X-49175812-A-T		not specified	Uncertain significance (Jun 17, 2024)
X-49175932-C-T		not specified	Uncertain significance (Nov 29, 2023)
X-49176118-C-A		not specified	Uncertain significance (Mar 13, 2023)
X-49176127-G-A			Likely benign (Dec 01, 2022)
X-49176163-G-A		not specified	Uncertain significance (Jan 08, 2024)
X-49176257-G-A		not specified	Uncertain significance (Dec 19, 2022)
X-49176923-G-A		not specified	Uncertain significance (Dec 08, 2023)
X-49176947-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-49176948-C-T		not specified	Uncertain significance (Jul 20, 2021)
X-49176971-G-A		not specified	Uncertain significance (Jan 02, 2024)
X-49177005-C-T		not specified	Uncertain significance (Nov 06, 2023)
X-49177020-G-A		not specified	Uncertain significance (Nov 22, 2023)
X-49177023-G-A		not specified	Uncertain significance (Aug 14, 2023)
X-49177028-G-A		not specified	Conflicting classifications of pathogenicity (Jun 05, 2023)
X-49177055-A-G		not specified	Uncertain significance (Aug 08, 2023)
X-49177067-C-T		not specified	Uncertain significance (May 27, 2022)
X-49177092-G-A		not specified	Uncertain significance (Mar 29, 2022)
X-49177095-G-A		not specified	Uncertain significance (Aug 08, 2022)
X-49177106-C-T		not specified	Uncertain significance (Oct 14, 2023)
X-49177149-G-A		not specified	Uncertain significance (Aug 02, 2021)
X-49178039-G-A			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRICKLE3	protein_coding	protein_coding	ENST00000376317	9	11695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.632	0.368	125733	5	4	125742	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	232	289	0.803	0.0000275	3948
Missense in Polyphen		48	77.652	0.61815		1171
Synonymous	0.885	98	110	0.893	0.0000101	1238
Loss of Function	3.04	3	16.2	0.185	0.00000121	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000377	0.0000377
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000730	0.0000544
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.0000744	0.0000527
Middle Eastern	0.0000730	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the planar cell polarity (PCP) pathway that is essential for the polarization of epithelial cells during morphogenetic processes, including gastrulation and neurulation (By similarity). PCP is maintained by two molecular modules, the global and the core modules, PRICKLE3 being part of the core module (By similarity). Distinct complexes of the core module segregate to opposite sides of the cell, where they interact with the opposite complex in the neighboring cell at or near the adherents junctions (By similarity). Involved in the organization of the basal body (By similarity). Involved in cilia growth and positioning (By similarity). {ECO:0000250|UniProtKB:A8WH69}.
• Pathway: Wnt signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.210
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.242
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.693

Mouse Genome Informatics

• Gene name: Prickle3

Gene ontology

• Biological process: multicellular organism development;biological_process;cell projection organization
• Cellular component: cellular_component;nucleus;cytoplasm;centrosome;plasma membrane
• Molecular function: protein binding;zinc ion binding